%%bash
echo "TODAY'S DATE:"
date
echo "------------"
echo ""
#Display operating system info
lsb_release -a
echo ""
echo "------------"
echo "HOSTNAME: "; hostname
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh
TODAY'S DATE:
Wed Nov 28 12:01:27 PST 2018
------------
Distributor ID: Ubuntu
Description: Ubuntu 16.04.5 LTS
Release: 16.04
Codename: xenial
------------
HOSTNAME:
swoose
------------
Computer Specs:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 24
On-line CPU(s) list: 0-23
Thread(s) per core: 2
Core(s) per socket: 6
Socket(s): 2
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 44
Model name: Intel(R) Xeon(R) CPU X5670 @ 2.93GHz
Stepping: 2
CPU MHz: 2925.866
BogoMIPS: 5851.93
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 12288K
NUMA node0 CPU(s): 0-23
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
------------
Memory Specs
total used free shared buff/cache available
Mem: 70G 3.0G 65G 112M 2.5G 67G
Swap: 4.7G 0B 4.7G
No LSB modules are available.
%%bash
mkdir /home/sam/data/geoduck
mkdir /home/sam/data/geoduck/transcriptomes
mkdir /home/sam/data/geoduck/transcriptomes/transdecoder_fasta_splits
%%bash
cd /home/sam/data/geoduck/transcriptomes
# Uncomment following line to retrieve file using wget
# wget http://gannet.fish.washington.edu/Atumefaciens/20181121_geo_transdecoder/20180827_trinity_geoduck.fasta.transdecoder.cds
rsync gannet:/volume1/web/Atumefaciens/20181121_geo_transdecoder/20180827_trinity_geoduck.fasta.transdecoder.cds
ls -lh
-rw-r--r-- 283,967,118 2018/11/23 15:42:16 20180827_trinity_geoduck.fasta.transdecoder.cds total 4.0K drwxrwxr-x 2 sam sam 4.0K Nov 28 12:04 transdecoder_fasta_splits
%%bash
cd /home/sam/data/geoduck/transcriptomes/
# Count sequences in FastA
echo "-------------------"
echo "NUMBER OF SEQUENCES IN ORIGINAL FASTA"
grep -c ">" 20180827_trinity_geoduck.fasta.transdecoder.cds
echo "-------------------"
echo ""
echo ""
cd /home/sam/data/geoduck/transcriptomes/transdecoder_fasta_splits/
# Split FastA
time \
/home/sam/software/bin/pyfaidx-0.5.5.2 \
--split-files \
../20180827_trinity_geoduck.fasta.transdecoder.cds
# Count number of individual FastA files
echo "-------------------"
echo "NUMBER OF INDIVIDUAL FASTA FILES"
ls -1 | wc -l
echo "-------------------"
------------------- NUMBER OF SEQUENCES IN ORIGINAL FASTA ------------------- ------------------- NUMBER OF INDIVIDUAL FASTA FILES 0 -------------------
grep: 20180827_trinity_geoduck.fasta.transdecoder.cds: No such file or directory
Traceback (most recent call last):
File "/home/sam/software/bin/pyfaidx-0.5.5.2", line 9, in <module>
load_entry_point('pyfaidx==0.5.5.2', 'console_scripts', 'faidx')()
File "build/bdist.linux-x86_64/egg/pyfaidx/cli.py", line 197, in main
File "build/bdist.linux-x86_64/egg/pyfaidx/cli.py", line 21, in write_sequence
File "build/bdist.linux-x86_64/egg/pyfaidx/__init__.py", line 996, in __init__
File "build/bdist.linux-x86_64/egg/pyfaidx/__init__.py", line 368, in __init__
pyfaidx.FastaNotFoundError: Cannot read FASTA file ../20180827_trinity_geoduck.fasta.transdecoder.cds
real 0m0.150s
user 0m0.104s
sys 0m0.020s
Whoops! Ran rsync command incorrectly. Duh!
%%bash
cd /home/sam/data/geoduck/transcriptomes
rsync \
--archive \
gannet:/volume1/web/Atumefaciens/20181121_geo_transdecoder/20180827_trinity_geoduck.fasta.transdecoder.cds .
echo "-------------------"
ls -lh
------------------- total 271M -rw-r--r-- 1 sam users 271M Nov 23 15:42 20180827_trinity_geoduck.fasta.transdecoder.cds drwxrwxr-x 2 sam sam 4.0K Nov 28 12:04 transdecoder_fasta_splits
%%bash
cd /home/sam/data/geoduck/transcriptomes/
# Count sequences in FastA
echo "-------------------"
echo "NUMBER OF SEQUENCES IN ORIGINAL FASTA"
grep -c ">" 20180827_trinity_geoduck.fasta.transdecoder.cds
echo "-------------------"
echo ""
echo ""
cd /home/sam/data/geoduck/transcriptomes/transdecoder_fasta_splits/
# Split FastA
time \
/home/sam/software/bin/pyfaidx-0.5.5.2 \
--split-files \
../20180827_trinity_geoduck.fasta.transdecoder.cds
# Count number of individual FastA files
echo "-------------------"
echo "NUMBER OF INDIVIDUAL FASTA FILES"
ls -1 | wc -l
echo "-------------------"
------------------- NUMBER OF SEQUENCES IN ORIGINAL FASTA 210586 ------------------- ------------------- NUMBER OF INDIVIDUAL FASTA FILES 210586 -------------------
real 0m43.789s user 0m36.340s sys 0m6.656s
uses grep to search for vitellogenin terms and the word "complete"
translates commas to spaces to aid in parsing/formatting for sort command
sorts in reverse order, using the "version" flag to help sort strings that contain numbers and sorts on column 7 (i.e. the "score" column
awk prints a header line to provide column descriptions and then prints out desired columns
column -t formats output into nicely spaced columns
tee prints output to file and to screen
%%bash
cd /home/sam/data/geoduck/transcriptomes/
grep --ignore-case "Vitellogenin" 20180827_trinity_geoduck.fasta.transdecoder.cds \
| grep "complete" \
| tr "," " " \
| sort -Vr -k7 \
| awk 'BEGIN{print "transcript_ID", "transcript_type", "transcript_length", "strand", "score", "annotation"}; \
{print $1, $4, $5, $6, $7 , $8}' \
| column -t \
| tee 20181127_geoduck_Vitellogenin_cds_matches.txt
transcript_ID transcript_type transcript_length strand score annotation >TRINITY_DN51983_c0_g1_i8.p1 type:complete len:4828 (-) score=1005.69 sp|Q9U943|APLP_LOCMI|27.089|3.28e-109 >TRINITY_DN51983_c0_g1_i4.p1 type:complete len:4680 (-) score=971.32 sp|Q9U943|APLP_LOCMI|27.089|2.82e-109 >TRINITY_DN3302_c0_g1_i4.p1 type:complete len:4277 (+) score=941.33 sp|Q9U943|APLP_LOCMI|29.133|9.20e-117 >TRINITY_DN3302_c0_g1_i8.p1 type:complete len:4277 (+) score=941.04 sp|Q9U943|APLP_LOCMI|29.133|1.08e-116 >TRINITY_DN3302_c0_g1_i1.p1 type:complete len:4277 (+) score=941.04 sp|Q9U943|APLP_LOCMI|29.133|1.08e-116 >TRINITY_DN1469_c0_g4_i1.p1 type:complete len:6053 (-) score=859.49 sp|Q2PZL6|FAT4_MOUSE|38.356|1.43e-08 >TRINITY_DN1469_c0_g3_i1.p1 type:complete len:6053 (+) score=859.49 sp|Q2PZL6|FAT4_MOUSE|38.356|1.43e-08 >TRINITY_DN20178_c0_g1_i3.p1 type:complete len:2501 (-) score=554.86 sp|P18948|VIT6_CAEEL|21.949|2.79e-40 >TRINITY_DN20178_c0_g1_i1.p1 type:complete len:2501 (-) score=554.86 sp|P18948|VIT6_CAEEL|21.949|2.79e-40 >TRINITY_DN15643_c1_g1_i3.p1 type:complete len:2487 (-) score=475.86 sp|E9Q414|APOB_MOUSE|20.790|2.08e-25 >TRINITY_DN15643_c1_g1_i4.p1 type:complete len:2487 (-) score=475.26 sp|E9Q414|APOB_MOUSE|20.790|2.08e-25 >TRINITY_DN15643_c1_g1_i2.p1 type:complete len:2487 (-) score=475.08 sp|E9Q414|APOB_MOUSE|20.790|2.02e-25 >TRINITY_DN108893_c0_g1_i2.p1 type:complete len:1576 (-) score=272.48 Vitellogenin_N|PF01347.21|4.2e-08 >TRINITY_DN108893_c0_g1_i7.p1 type:complete len:1576 (-) score=271.82 Vitellogenin_N|PF01347.21|4e-08 >TRINITY_DN6438_c0_g1_i13.p1 type:complete len:887 (-) score=178.80 sp|Q865F1|MTP_PIG|28.196|4.04e-112 >TRINITY_DN6438_c0_g1_i10.p1 type:complete len:887 (-) score=178.80 sp|Q865F1|MTP_PIG|28.196|4.04e-112 >TRINITY_DN6438_c0_g1_i9.p1 type:complete len:887 (-) score=178.80 sp|Q865F1|MTP_PIG|28.196|4.04e-112 >TRINITY_DN6438_c0_g1_i8.p1 type:complete len:887 (-) score=178.80 sp|Q865F1|MTP_PIG|28.196|4.04e-112 >TRINITY_DN6438_c0_g1_i5.p1 type:complete len:887 (-) score=178.80 sp|Q865F1|MTP_PIG|28.196|4.04e-112 >TRINITY_DN6438_c0_g1_i4.p1 type:complete len:887 (-) score=178.80 sp|Q865F1|MTP_PIG|28.196|4.04e-112 >TRINITY_DN108893_c0_g1_i10.p2 type:complete len:541 (-) score=83.27 Vitellogenin_N|PF01347.21|2e-07 >TRINITY_DN108893_c0_g1_i4.p2 type:complete len:541 (-) score=82.43 Vitellogenin_N|PF01347.21|2.3e-07 >TRINITY_DN461352_c0_g1_i1.p1 type:complete len:169 (+) score=36.69 sp|O94390|ATP7_SCHPO|26.923|3.10e-07
%%bash
cd /home/sam/data/geoduck/transcriptomes/
grep --ignore-case "Vtg" 20180827_trinity_geoduck.fasta.transdecoder.cds \
| grep "complete" \
| tr "," " " \
| sort -Vr -k7 \
| awk 'BEGIN{print "transcript_ID", "transcript_type", "transcript_length", "strand", "score", "annotation"}; \
{print $1, $4, $5, $6, $7 , $8}' \
| column -t \
| tee 20181127_geoduck_Vtg_cds_matches.txt
transcript_ID transcript_type transcript_length strand score annotation
%%bash
cd /home/sam/data/geoduck/transcriptomes/
grep --ignore-case "Vg" 20180827_trinity_geoduck.fasta.transdecoder.cds \
| grep "complete" \
| tr "," " " \
| sort -Vr -k7 \
| awk 'BEGIN{print "transcript_ID", "transcript_type", "transcript_length", "strand", "score", "annotation"}; \
{print $1, $4, $5, $6, $7 , $8}' \
| column -t \
| tee 20181127_geoduck_Vg_cds_matches.txt
transcript_ID transcript_type transcript_length strand score annotation >TRINITY_DN306895_c2_g2_i2.p1 type:complete len:106 (-) score=-21.67 zf-LITAF-like|PF10601.8|2.4e+03 >TRINITY_DN306895_c2_g2_i1.p1 type:complete len:106 (-) score=-21.67 zf-LITAF-like|PF10601.8|2.4e+03 >TRINITY_DN48461_c1_g1_i1.p1 type:complete len:119 (-) score=-4.86 VGCC_alpha2|PF08473.10|0.02 >TRINITY_DN42237_c0_g1_i8.p3 type:complete len:153 (+) score=-3.34 VGCC_beta4Aa_N|PF12052.7|1 >TRINITY_DN100845_c0_g2_i1.p1 type:complete len:180 (+) score=-3.08 sp|Q6VGS5|DAPLE_MOUSE|27.350|5.18e-09 >TRINITY_DN29517_c1_g1_i2.p1 type:complete len:2177 (-) score=515.83 sp|Q0VGT4|ZGRF1_MOUSE|46.659|0.0 >TRINITY_DN29517_c1_g1_i5.p1 type:complete len:2188 (-) score=515.51 sp|Q0VGT4|ZGRF1_MOUSE|46.659|0.0 >TRINITY_DN29517_c1_g1_i8.p1 type:complete len:2187 (-) score=514.52 sp|Q0VGT4|ZGRF1_MOUSE|46.476|0.0 >TRINITY_DN27045_c0_g1_i6.p1 type:complete len:1760 (+) score=449.51 sp|Q4VGL6|RC3H1_MOUSE|70.386|0.0 >TRINITY_DN27045_c0_g1_i5.p2 type:complete len:1740 (+) score=442.48 sp|Q4VGL6|RC3H1_MOUSE|70.386|0.0 >TRINITY_DN27045_c0_g1_i2.p1 type:complete len:1740 (+) score=442.48 sp|Q4VGL6|RC3H1_MOUSE|70.386|0.0 >TRINITY_DN27045_c0_g1_i6.p2 type:complete len:1741 (-) score=439.59 sp|Q4VGL6|RC3H1_MOUSE|70.386|0.0 >TRINITY_DN27045_c0_g1_i5.p1 type:complete len:1741 (-) score=439.59 sp|Q4VGL6|RC3H1_MOUSE|70.386|0.0 >TRINITY_DN27045_c0_g1_i2.p2 type:complete len:1721 (-) score=432.56 sp|Q4VGL6|RC3H1_MOUSE|70.386|0.0 >TRINITY_DN29517_c1_g1_i9.p1 type:complete len:1782 (-) score=414.11 sp|Q0VGT4|ZGRF1_MOUSE|46.659|0.0 >TRINITY_DN10176_c6_g1_i5.p1 type:complete len:1894 (-) score=385.96 sp|Q9VGG5|CAD87_DROME|29.038|1.08e-141 >TRINITY_DN10176_c6_g1_i4.p1 type:complete len:1890 (-) score=382.65 sp|Q9VGG5|CAD87_DROME|29.106|3.43e-142 >TRINITY_DN28397_c0_g1_i16.p1 type:complete len:1204 (-) score=343.96 sp|Q9BVG8|KIFC3_HUMAN|49.348|2.39e-169 >TRINITY_DN28397_c0_g1_i12.p1 type:complete len:1204 (-) score=343.96 sp|Q9BVG8|KIFC3_HUMAN|49.348|2.39e-169 >TRINITY_DN28397_c0_g1_i8.p1 type:complete len:1197 (-) score=341.08 sp|Q9BVG8|KIFC3_HUMAN|47.943|8.46e-170 >TRINITY_DN28397_c0_g1_i3.p1 type:complete len:1197 (-) score=341.08 sp|Q9BVG8|KIFC3_HUMAN|47.943|8.46e-170 >TRINITY_DN28397_c0_g1_i19.p1 type:complete len:1149 (-) score=322.22 sp|Q9BVG8|KIFC3_HUMAN|50.398|8.22e-167 >TRINITY_DN28397_c0_g1_i6.p1 type:complete len:1149 (-) score=322.22 sp|Q9BVG8|KIFC3_HUMAN|50.398|8.22e-167 >TRINITY_DN21793_c0_g1_i13.p1 type:complete len:1456 (-) score=265.28 sp|P35969|VGFR1_MOUSE|32.039|3.86e-164 >TRINITY_DN21793_c0_g1_i12.p1 type:complete len:1456 (-) score=265.28 sp|P35969|VGFR1_MOUSE|32.039|3.86e-164 >TRINITY_DN29517_c1_g1_i3.p1 type:complete len:925 (-) score=222.35 sp|Q0VGT4|ZGRF1_MOUSE|47.563|0.0 >TRINITY_DN29517_c1_g1_i10.p1 type:complete len:925 (-) score=220.07 sp|Q0VGT4|ZGRF1_MOUSE|47.563|0.0 >TRINITY_DN2197_c0_g1_i9.p1 type:complete len:736 (-) score=204.95 sp|F1R4Y7|CEP83_DANRE|36.143|6.98e-122 >TRINITY_DN2197_c0_g1_i6.p1 type:complete len:738 (-) score=204.33 sp|F1R4Y7|CEP83_DANRE|36.286|7.50e-123 >TRINITY_DN2197_c0_g1_i4.p1 type:complete len:738 (-) score=204.33 sp|F1R4Y7|CEP83_DANRE|36.286|7.50e-123 >TRINITY_DN2197_c0_g1_i1.p1 type:complete len:738 (-) score=204.33 sp|F1R4Y7|CEP83_DANRE|36.286|7.50e-123 >TRINITY_DN21793_c0_g1_i10.p1 type:complete len:1155 (-) score=200.21 sp|P17948|VGFR1_HUMAN|34.033|2.20e-151 >TRINITY_DN21793_c0_g1_i5.p1 type:complete len:1155 (-) score=200.21 sp|P17948|VGFR1_HUMAN|34.033|2.20e-151 >TRINITY_DN64188_c0_g1_i2.p1 type:complete len:1644 (-) score=194.69 sp|Q8C5K5|CX038_MOUSE|25.514|2.59e-10 >TRINITY_DN64188_c0_g1_i4.p1 type:complete len:1644 (-) score=194.04 sp|Q8C5K5|CX038_MOUSE|25.514|2.55e-10 >TRINITY_DN16250_c0_g1_i7.p1 type:complete len:849 (-) score=186.97 sp|Q3UVG3|F91A1_MOUSE|55.454|0.0 >TRINITY_DN36889_c0_g1_i2.p1 type:complete len:1380 (+) score=182.20 sp|Q8IVG5|SAM9L_HUMAN|22.931|1.51e-09 >TRINITY_DN2363_c3_g1_i10.p1 type:complete len:820 (+) score=178.17 sp|Q0VGE8|ZN816_HUMAN|28.452|1.83e-14 >TRINITY_DN2363_c3_g1_i8.p1 type:complete len:820 (+) score=178.17 sp|Q0VGE8|ZN816_HUMAN|28.452|1.83e-14 >TRINITY_DN16250_c0_g1_i11.p1 type:complete len:774 (-) score=166.94 sp|Q3UVG3|F91A1_MOUSE|54.271|0.0 >TRINITY_DN8048_c1_g1_i10.p1 type:complete len:946 (+) score=160.87 sp|Q5JVG2|ZN484_HUMAN|34.375|2.49e-35 >TRINITY_DN8048_c1_g1_i7.p1 type:complete len:946 (+) score=160.87 sp|Q5JVG2|ZN484_HUMAN|34.375|2.49e-35 >TRINITY_DN8048_c1_g1_i5.p1 type:complete len:946 (+) score=160.87 sp|Q5JVG2|ZN484_HUMAN|34.375|2.49e-35 >TRINITY_DN8048_c1_g1_i4.p1 type:complete len:946 (+) score=158.93 sp|Q5JVG2|ZN484_HUMAN|33.984|3.50e-34 >TRINITY_DN4220_c1_g1_i4.p1 type:complete len:1377 (-) score=156.18 sp|Q8IVG5|SAM9L_HUMAN|26.226|2.38e-19 >TRINITY_DN4220_c1_g1_i2.p1 type:complete len:1377 (-) score=156.18 sp|Q8IVG5|SAM9L_HUMAN|26.226|2.38e-19 >TRINITY_DN24751_c0_g1_i4.p1 type:complete len:1313 (+) score=154.36 sp|Q8IVG5|SAM9L_HUMAN|24.645|2.24e-15 >TRINITY_DN24751_c0_g1_i9.p1 type:complete len:1313 (+) score=153.65 sp|Q8IVG5|SAM9L_HUMAN|24.645|2.46e-15 >TRINITY_DN24751_c0_g1_i8.p1 type:complete len:1313 (+) score=153.65 sp|Q8IVG5|SAM9L_HUMAN|24.645|2.46e-15 >TRINITY_DN24751_c0_g1_i2.p1 type:complete len:1313 (+) score=153.65 sp|Q8IVG5|SAM9L_HUMAN|24.645|2.46e-15 >TRINITY_DN16582_c0_g1_i5.p1 type:complete len:1249 (-) score=146.06 sp|Q8IVG5|SAM9L_HUMAN|24.525|7.25e-10 >TRINITY_DN16582_c0_g1_i3.p1 type:complete len:1249 (-) score=146.06 sp|Q8IVG5|SAM9L_HUMAN|24.525|7.25e-10 >TRINITY_DN16582_c0_g1_i2.p1 type:complete len:1249 (-) score=143.25 sp|Q8IVG5|SAM9L_HUMAN|24.525|8.09e-10 >TRINITY_DN16582_c0_g1_i4.p1 type:complete len:1249 (-) score=140.58 sp|Q8IVG5|SAM9L_HUMAN|24.178|7.75e-10 >TRINITY_DN27885_c0_g1_i1.p1 type:complete len:446 (+) score=138.91 sp|Q86VG3|CK074_HUMAN|35.652|1.19e-07 >TRINITY_DN17404_c0_g1_i7.p1 type:complete len:917 (-) score=134.65 sp|Q0VGW6|S12A9_XENLA|47.552|0.0 >TRINITY_DN17404_c0_g1_i6.p1 type:complete len:917 (-) score=134.65 sp|Q0VGW6|S12A9_XENLA|47.552|0.0 >TRINITY_DN3518_c0_g1_i10.p1 type:complete len:662 (+) score=127.58 sp|Q6PHS9|CA2D2_MOUSE|29.799|2.84e-76 >TRINITY_DN3518_c0_g1_i5.p1 type:complete len:630 (+) score=125.39 sp|Q6PHS9|CA2D2_MOUSE|30.618|6.96e-80 >TRINITY_DN14465_c0_g2_i2.p1 type:complete len:630 (-) score=125.24 sp|Q0VGK3|GLCTK_RAT|42.054|1.43e-125 >TRINITY_DN14465_c0_g2_i1.p1 type:complete len:630 (-) score=125.24 sp|Q0VGK3|GLCTK_RAT|42.054|1.43e-125 >TRINITY_DN3588_c1_g1_i3.p1 type:complete len:611 (+) score=123.14 sp|Q9HGN1|GCN2_SCHPO|31.720|7.99e-40 >TRINITY_DN3588_c1_g1_i6.p1 type:complete len:611 (+) score=122.20 sp|Q9HGN1|GCN2_SCHPO|31.720|7.49e-40 >TRINITY_DN3588_c1_g1_i7.p1 type:complete len:611 (+) score=122.11 sp|Q9HGN1|GCN2_SCHPO|31.720|7.49e-40 >TRINITY_DN3588_c1_g1_i2.p1 type:complete len:594 (+) score=117.20 sp|Q9HGN1|GCN2_SCHPO|31.720|4.68e-40 >TRINITY_DN5529_c0_g1_i9.p1 type:complete len:482 (-) score=117.11 sp|Q80V24|VGLL4_MOUSE|31.841|2.07e-11 >TRINITY_DN5529_c0_g1_i4.p1 type:complete len:482 (-) score=117.11 sp|Q80V24|VGLL4_MOUSE|31.841|2.07e-11 >TRINITY_DN3588_c1_g1_i8.p1 type:complete len:594 (+) score=116.25 sp|Q9HGN1|GCN2_SCHPO|31.720|5.47e-40 >TRINITY_DN3588_c1_g1_i4.p1 type:complete len:594 (+) score=116.17 sp|Q9HGN1|GCN2_SCHPO|31.720|5.47e-40 >TRINITY_DN17404_c0_g1_i1.p1 type:complete len:820 (-) score=115.98 sp|Q0VGW6|S12A9_XENLA|48.010|0.0 >TRINITY_DN29773_c0_g1_i6.p1 type:complete len:533 (+) score=115.30 sp|Q9VGZ5|CWO_DROME|39.336|1.74e-29 >TRINITY_DN5529_c0_g1_i8.p1 type:complete len:418 (-) score=111.04 sp|Q80V24|VGLL4_MOUSE|32.124|9.29e-12 >TRINITY_DN5529_c0_g1_i6.p1 type:complete len:418 (-) score=111.04 sp|Q80V24|VGLL4_MOUSE|32.124|9.29e-12 >TRINITY_DN47836_c0_g1_i18.p1 type:complete len:573 (-) score=106.21 sp|Q9MZL5|CACB2_BOVIN|64.516|2.92e-177 >TRINITY_DN47836_c0_g1_i17.p1 type:complete len:573 (-) score=106.21 sp|Q9MZL5|CACB2_BOVIN|64.516|2.92e-177 >TRINITY_DN47836_c0_g1_i9.p1 type:complete len:573 (-) score=106.21 sp|Q9MZL5|CACB2_BOVIN|64.516|2.92e-177 >TRINITY_DN47836_c0_g1_i4.p1 type:complete len:573 (-) score=106.21 sp|Q9MZL5|CACB2_BOVIN|64.516|2.92e-177 >TRINITY_DN47836_c0_g1_i3.p1 type:complete len:573 (-) score=106.21 sp|Q9MZL5|CACB2_BOVIN|64.516|2.92e-177 >TRINITY_DN47836_c0_g1_i1.p1 type:complete len:573 (-) score=106.21 sp|Q9MZL5|CACB2_BOVIN|64.516|2.92e-177 >TRINITY_DN47836_c0_g1_i20.p1 type:complete len:575 (-) score=101.92 sp|P54288|CACB2_RABIT|60.811|4.45e-180 >TRINITY_DN47836_c0_g1_i13.p1 type:complete len:575 (-) score=101.92 sp|P54288|CACB2_RABIT|60.811|4.45e-180 >TRINITY_DN47836_c0_g1_i10.p1 type:complete len:575 (-) score=101.92 sp|P54288|CACB2_RABIT|60.811|4.45e-180 >TRINITY_DN47836_c0_g1_i19.p1 type:complete len:550 (-) score=95.91 sp|P54288|CACB2_RABIT|63.221|4.48e-179 >TRINITY_DN47836_c0_g1_i11.p1 type:complete len:550 (-) score=95.91 sp|P54288|CACB2_RABIT|63.221|4.48e-179 >TRINITY_DN47836_c0_g1_i6.p1 type:complete len:550 (-) score=95.91 sp|P54288|CACB2_RABIT|63.221|4.48e-179 >TRINITY_DN2363_c3_g1_i9.p1 type:complete len:524 (+) score=93.90 sp|Q0VGE8|ZN816_HUMAN|28.452|8.96e-15 >TRINITY_DN997_c0_g1_i8.p1 type:complete len:573 (+) score=87.07 sp|A2AVA0|SVEP1_MOUSE|23.906|2.67e-08 >TRINITY_DN138924_c0_g3_i5.p1 type:complete len:503 (+) score=85.59 sp|Q9JI12|VGLU2_RAT|42.085|2.89e-139 >TRINITY_DN2443_c0_g1_i2.p1 type:complete len:452 (+) score=85.33 MIEAP|PF16026.4|1.4e-22 >TRINITY_DN135629_c0_g1_i5.p1 type:complete len:619 (+) score=76.12 sp|Q1L8X9|VGLU3_DANRE|33.948|1.25e-107 >TRINITY_DN135629_c0_g1_i3.p1 type:complete len:619 (+) score=76.12 sp|Q1L8X9|VGLU3_DANRE|33.948|1.25e-107 >TRINITY_DN111_c0_g1_i13.p1 type:complete len:373 (+) score=74.54 sp|Q9WVG9|MS3L1_MOUSE|42.574|1.03e-14 >TRINITY_DN111_c0_g1_i10.p1 type:complete len:373 (+) score=74.54 sp|Q9WVG9|MS3L1_MOUSE|42.574|1.03e-14 >TRINITY_DN3518_c0_g1_i3.p1 type:complete len:375 (+) score=74.03 sp|Q6PHS9|CA2D2_MOUSE|30.914|3.29e-42 >TRINITY_DN2014_c3_g1_i9.p2 type:complete len:316 (+) score=68.65 sp|P27980|POL_SIVVG|28.125|1.36e-09 >TRINITY_DN294228_c0_g1_i4.p2 type:complete len:184 (+) score=68.13 EPTP|PF03736.16|1.2e+02 >TRINITY_DN36853_c0_g1_i13.p1 type:complete len:384 (-) score=66.64 sp|Q6X0I2|VGR_SOLIN|32.168|4.25e-14 >TRINITY_DN36853_c0_g1_i12.p1 type:complete len:384 (-) score=66.64 sp|Q6X0I2|VGR_SOLIN|32.168|4.25e-14 >TRINITY_DN36853_c0_g1_i5.p1 type:complete len:384 (-) score=66.64 sp|Q6X0I2|VGR_SOLIN|32.168|4.25e-14 >TRINITY_DN6486_c1_g1_i1.p1 type:complete len:762 (+) score=66.21 sp|P52583|VGFR2_COTJA|30.556|1.49e-08 >TRINITY_DN6486_c1_g1_i2.p1 type:complete len:762 (+) score=65.92 sp|P52583|VGFR2_COTJA|30.556|1.49e-08 >TRINITY_DN75615_c0_g1_i17.p1 type:complete len:457 (+) score=65.36 sp|Q8CFG5|CA2D3_RAT|25.225|2.56e-28 >TRINITY_DN36853_c0_g1_i3.p1 type:complete len:384 (-) score=64.58 sp|Q6X0I2|VGR_SOLIN|32.168|4.25e-14 >TRINITY_DN75615_c0_g1_i18.p1 type:complete len:433 (+) score=62.01 sp|Q8CFG5|CA2D3_RAT|25.765|4.15e-26 >TRINITY_DN75615_c0_g1_i14.p1 type:complete len:433 (+) score=62.01 sp|Q8CFG5|CA2D3_RAT|25.765|4.15e-26 >TRINITY_DN75615_c0_g1_i10.p1 type:complete len:433 (+) score=62.01 sp|Q8CFG5|CA2D3_RAT|25.765|4.15e-26 >TRINITY_DN75615_c0_g1_i3.p1 type:complete len:433 (+) score=62.01 sp|Q8CFG5|CA2D3_RAT|25.765|4.15e-26 >TRINITY_DN75615_c0_g1_i1.p1 type:complete len:433 (+) score=62.01 sp|Q8CFG5|CA2D3_RAT|25.765|4.15e-26 >TRINITY_DN11016_c1_g3_i3.p1 type:complete len:327 (+) score=61.77 sp|Q5FVG6|PRR5_RAT|42.781|1.08e-43 >TRINITY_DN143974_c2_g1_i1.p1 type:complete len:531 (+) score=60.92 sp|A4FV52|VGLU1_BOVIN|34.524|2.27e-92 >TRINITY_DN14092_c0_g1_i23.p2 type:complete len:156 (-) score=46.70 LZ_Tnp_IS66|PF13007.6|0.024 >TRINITY_DN14092_c0_g1_i12.p2 type:complete len:156 (-) score=46.70 LZ_Tnp_IS66|PF13007.6|0.024 >TRINITY_DN14092_c0_g1_i6.p2 type:complete len:156 (-) score=46.70 LZ_Tnp_IS66|PF13007.6|0.024 >TRINITY_DN138924_c0_g2_i1.p1 type:complete len:293 (-) score=46.58 sp|Q9JI12|VGLU2_RAT|42.667|2.30e-78 >TRINITY_DN209_c1_g1_i1.p1 type:complete len:293 (+) score=44.73 sp|Q9BXJ4|C1QT3_HUMAN|30.405|2.78e-12 >TRINITY_DN41639_c0_g2_i6.p1 type:complete len:742 (-) score=44.50 sp|Q9UT27|PVG1_SCHPO|35.535|4.17e-38 >TRINITY_DN23922_c0_g1_i13.p2 type:complete len:638 (-) score=40.62 sp|Q0VGY8|TANC1_MOUSE|24.176|1.18e-09 >TRINITY_DN23922_c0_g1_i12.p2 type:complete len:638 (-) score=40.62 sp|Q0VGY8|TANC1_MOUSE|24.176|1.18e-09 >TRINITY_DN23922_c0_g1_i8.p2 type:complete len:638 (-) score=40.62 sp|Q0VGY8|TANC1_MOUSE|24.176|1.18e-09 >TRINITY_DN23922_c0_g1_i6.p2 type:complete len:638 (-) score=40.62 sp|Q0VGY8|TANC1_MOUSE|24.176|1.18e-09 >TRINITY_DN23922_c0_g1_i5.p2 type:complete len:638 (-) score=40.62 sp|Q0VGY8|TANC1_MOUSE|24.176|1.18e-09 >TRINITY_DN23922_c0_g1_i2.p2 type:complete len:638 (-) score=40.62 sp|Q0VGY8|TANC1_MOUSE|24.176|1.18e-09 >TRINITY_DN138924_c0_g3_i1.p1 type:complete len:221 (+) score=36.00 sp|A6QLI1|VGLU2_BOVIN|47.087|9.73e-63 >TRINITY_DN41639_c0_g2_i1.p1 type:complete len:744 (-) score=34.17 sp|Q9UT27|PVG1_SCHPO|32.416|3.02e-33 >TRINITY_DN27205_c0_g1_i1.p1 type:complete len:135 (+) score=33.57 sp|P35917|VGFR3_MOUSE|100.000|3.46e-20 >TRINITY_DN120833_c0_g1_i2.p1 type:complete len:296 (-) score=31.98 sp|Q8BGW8|VGLL2_MOUSE|46.739|8.45e-17 >TRINITY_DN41639_c0_g2_i4.p1 type:complete len:744 (-) score=29.44 sp|Q9UT27|PVG1_SCHPO|32.416|1.35e-33 >TRINITY_DN120833_c0_g1_i1.p1 type:complete len:272 (-) score=28.17 sp|Q8BGW8|VGLL2_MOUSE|46.739|5.13e-17 >TRINITY_DN232640_c0_g1_i3.p2 type:complete len:136 (-) score=27.74 sp|Q9NVG8|TBC13_HUMAN|60.150|2.22e-50 >TRINITY_DN5529_c0_g1_i2.p1 type:complete len:108 (-) score=27.66 sp|Q80V24|VGLL4_MOUSE|50.877|4.78e-09 >TRINITY_DN5529_c0_g1_i1.p1 type:complete len:108 (-) score=27.66 sp|Q80V24|VGLL4_MOUSE|50.877|4.78e-09 >TRINITY_DN42213_c0_g1_i3.p1 type:complete len:228 (+) score=26.44 DivIC|PF04977.14|0.00019 >TRINITY_DN138924_c0_g3_i1.p2 type:complete len:125 (+) score=21.32 sp|Q9JI12|VGLU2_RAT|44.800|9.00e-27 >TRINITY_DN41639_c0_g2_i5.p1 type:complete len:429 (-) score=18.80 sp|Q9UT27|PVG1_SCHPO|32.416|2.12e-34 >TRINITY_DN41639_c0_g2_i3.p1 type:complete len:429 (-) score=18.80 sp|Q9UT27|PVG1_SCHPO|32.416|2.12e-34 >TRINITY_DN120833_c0_g1_i3.p1 type:complete len:184 (-) score=17.34 sp|Q8BGW8|VGLL2_MOUSE|50.000|4.61e-10 >TRINITY_DN5608_c0_g2_i7.p1 type:complete len:249 (-) score=16.95 sp|Q9SVG0|AVT3C_ARATH|27.143|2.88e-17 >TRINITY_DN374945_c0_g1_i2.p1 type:complete len:200 (-) score=16.68 sp|A4FV52|VGLU1_BOVIN|60.479|1.69e-67 >TRINITY_DN374945_c0_g1_i5.p1 type:complete len:274 (-) score=15.76 sp|Q05B21|VGLU1_XENTR|55.187|2.20e-89 >TRINITY_DN100416_c0_g1_i8.p1 type:complete len:120 (-) score=13.59 sp|Q1L8X9|VGLU3_DANRE|34.426|9.89e-16 >TRINITY_DN100416_c0_g1_i6.p1 type:complete len:120 (-) score=13.59 sp|Q1L8X9|VGLU3_DANRE|34.426|9.89e-16 >TRINITY_DN100416_c0_g1_i5.p1 type:complete len:120 (-) score=13.59 sp|Q1L8X9|VGLU3_DANRE|34.426|9.89e-16 >TRINITY_DN100416_c0_g1_i3.p1 type:complete len:120 (-) score=13.59 sp|Q1L8X9|VGLU3_DANRE|34.426|9.89e-16 >TRINITY_DN5608_c0_g2_i1.p1 type:complete len:135 (-) score=13.37 sp|Q9SVG0|AVT3C_ARATH|30.097|9.81e-08 >TRINITY_DN356433_c0_g1_i1.p1 type:complete len:122 (+) score=11.24 sp|Q6INC8|VGLU1_XENLA|54.701|7.48e-38 >TRINITY_DN133015_c0_g1_i11.p1 type:complete len:171 (+) score=9.55 sp|Q00130|VG50_ICHVA|35.714|1.49e-07 >TRINITY_DN30354_c0_g2_i1.p1 type:complete len:125 (+) score=7.76 SpoVG|PF04026.11|10 >TRINITY_DN133015_c0_g1_i10.p1 type:complete len:111 (+) score=4.68 sp|Q00130|VG50_ICHVA|36.170|3.85e-06 >TRINITY_DN374945_c0_g1_i1.p1 type:complete len:170 (-) score=0.22 sp|Q5W8I8|VGL2A_DANRE|53.691|6.74e-49
Looks like the only search that produced viable results is the "vitellogenin". Will use the top scoring (i.e. best e-value) match for primer design.
%%bash
mkdir /home/sam/analyses
mkdir /home/sam/analyses/20181129_geoduck_vtg_primers
SEQUENCE_ID=${seq_id}
SEQUENCE_TEMPLATE=${sequence}
PRIMER_TASK=generic
PRIMER_PICK_LEFT_PRIMER=3
PRIMER_PICK_RIGHT_PRIMER=3
PRIMER_OPT_SIZE=18
PRIMER_MIN_SIZE=15
PRIMER_MAX_SIZE=21
PRIMER_MAX_NS_ACCEPTED=1
PRIMER_PRODUCT_SIZE_RANGE=75-150
P3_FILE_FLAG=1
PRIMER_EXPLAIN_FLAG=1
=
Values after the "=" on each line can be changed to whatever values the user decides. The ${sequence} must be a nucletoide sequence on a single line, with no line breaks.
The code below uses a heredoc to write this information to a file. Everything between the following two lines gets printed (via cat) as shown and then redirected to the indicated file (20181129_primer3_params.txt):
cat << EOF > /home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_params.txt
EOF
--format_output to make a nice, human-readable output format.%%bash
cd /home/sam/analyses/20181129_geoduck_vtg_primers
# Store sequence only from desired FastA.
# Print all lines after the first line and then delete newlines
# Creates a sequence that exists on a single line, which is necessary for Primer3
sequence=$(tail -n +2 /home/sam/data/geoduck/transcriptomes/transdecoder_fasta_splits/TRINITY_DN51983_c0_g1_i8.p1.cds | tr -d '\n')
# Store file name of targeted FastA file.
seq_id=$(echo "$(head -n 1 /home/sam/data/geoduck/transcriptomes/transdecoder_fasta_splits/TRINITY_DN51983_c0_g1_i8.p1.cds | tr -d '>').cds")
# Use heredoc to create Primer3 parameters file
cat << EOF > /home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_params.txt
SEQUENCE_ID=${seq_id}
SEQUENCE_TEMPLATE=${sequence}
PRIMER_TASK=generic
PRIMER_PICK_LEFT_PRIMER=3
PRIMER_PICK_RIGHT_PRIMER=3
PRIMER_OPT_SIZE=18
PRIMER_MIN_SIZE=15
PRIMER_MAX_SIZE=21
PRIMER_MAX_NS_ACCEPTED=1
PRIMER_PRODUCT_SIZE_RANGE=75-150
P3_FILE_FLAG=1
PRIMER_EXPLAIN_FLAG=1
=
EOF
# Run Primer3
/home/sam/software/primer3-2.4.0/src/primer3_core \
--format_output \
--output=/home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_primers.txt \
/home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_params.txt
%%bash
cat /home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_primers.txt
PRIMER_ERROR=thermodynamic approach chosen, but path to thermodynamic parameters not specified =
%%bash
cd /home/sam/analyses/20181129_geoduck_vtg_primers
# Store sequence only from desired FastA.
# Print all lines after the first line and then delete newlines
sequence=$(tail -n +2 /home/sam/data/geoduck/transcriptomes/transdecoder_fasta_splits/TRINITY_DN51983_c0_g1_i8.p1.cds | tr -d '\n')
#
seq_id=$(echo "$(head -n 1 /home/sam/data/geoduck/transcriptomes/transdecoder_fasta_splits/TRINITY_DN51983_c0_g1_i8.p1.cds | tr -d '>').cds")
# Use heredoc to create Primer3 parameters file
cat << EOF > /home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_params.txt
SEQUENCE_ID=${seq_id}
SEQUENCE_TEMPLATE=${sequence}
PRIMER_TASK=generic
PRIMER_PICK_LEFT_PRIMER=3
PRIMER_PICK_RIGHT_PRIMER=3
PRIMER_OPT_SIZE=18
PRIMER_MIN_SIZE=15
PRIMER_MAX_SIZE=21
PRIMER_MAX_NS_ACCEPTED=1
PRIMER_PRODUCT_SIZE_RANGE=75-150
P3_FILE_FLAG=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/home/sam/software/primer3-2.4.0/src/primer3_config/
=
EOF
# Run Primer3
/home/sam/software/primer3-2.4.0/src/primer3_core \
--format_output \
--output=/home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_primers.txt \
/home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_params.txt
%%bash
cat /home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_primers.txt
PRIMER PICKING RESULTS FOR TRINITY_DN51983_c0_g1_i8.p1.cds
No mispriming library specified
Using 0-based sequence positions
OLIGO start len tm gc% any_th 3'_th hairpin seq
LEFT PRIMER 1347 18 59.89 55.56 9.11 0.13 42.06 TTACGCCACGGCAACTGT
RIGHT PRIMER 1471 18 60.05 61.11 10.11 0.00 0.00 CGCAGTGCCAACAAGCTG
SEQUENCE SIZE: 14484
INCLUDED REGION SIZE: 14484
PRODUCT SIZE: 125, PAIR ANY_TH COMPL: 10.66, PAIR 3'_TH COMPL: 0.00
0 ATGGAGCGATTGGTTTTAGCGCTAATCGTTTTGGCGGTCTGTGTCCACGCAGGTCCGATA
60 CAGAAAATCTCAGTTGATACCTGTGCAAGAACTTGTACAGGCAACAGCAAGTTTAATTAT
120 GTTGCTGGTAAGACTTACCAGTACAAGTATGATGCCGACATCAAGACTGGGGTCCAGGGA
180 GCATCAGAAGATAATGCGAAAATACACATGTCGGCAACAGTCGAGATGGAGGTCATATCA
240 AAGTGTGACCTTGTCATGCGGCTGAATGATGTCACATTGACAGAATATGACCCCATTGAC
300 TTGATAATGAAGGAAACGTCATCTGAATTCCGCAGTGGTCTTGAGAAGGCTCCCATCCGA
360 ATCTCTTTCCAAGATGGAAACATAGAGGAACTTTGTCTGAAACGAGAGGAGCCAAATTGG
420 GTGCTGAATGCCAAACGTGGAATCCTGTCAATGTTCCAGAACAACATGGACGATTTCTCA
480 ACCAATAAAACAGTGTCTGAGACTGATGTGTCTGGTGTGTGTGATACAGAGTACCACGTG
540 AGTAAATCTGGCTGGTACAAGACCACAGTCAGCAAGTCTAAGAATCTCCTAGGTTGTACT
600 GACAGGACCGGGTACAACACTGCCGTCCAGGGAGTGCCATATACCGCAGCTTCTGGCATC
660 CAGTCACTGCCAGTTGTGAAGAGCAACCATAACTGTGAACATGAGATTGACATTAAGTCG
720 CACATTCTCCATTCGGCAACTTGTAATGAACAGCACATGTTCCTGCCATTCTCACGCTCA
780 GACAGTGGAGCTGTAACATACAACACTCAGACTCTCAAGTTCGTGAAAGTAACAACTGGA
840 ATCAAGTCACCATTTGATACCAGTACTCGCAAATCAATGAAATTCGATCACATCAATGAT
900 GCAGGCAGAGAAGCAAAATCGAGGAAAGATATTACACGTAAGCTTATTGAAATCTGTGAG
960 AAGACGAAGTCTGGTGTTCGCCCTGAAACCCCACGTCTGTTCACAGACCTCGTGTTTATG
1020 ATGAAGACTGTTGATTCTGACACTCTAGCAGACACGTACAAACTGCTCCAAGAAGGTGCC
1080 ATCTGCACTGACAATAAAGAAAGAACCAGGAAGTTTTTCCTTGATGCCTTACCGATTGCT
1140 GGTTCCAGTTCCTCACTGCACTTGATGACCCAACTCTTGACCACAAAGGCTGTGACTGGA
1200 ATTGAGGCAGACATGTGGCTGTCGGCCATCTCTTTTCTCAAGAACCCAACTAAAGACATG
1260 CTGAAGGAAGTCAAGCCTTTGATCAACATGAAGGACACAACTGACAAGGCCCTGCTTTCT
1320 GTCGGTACCCTGATCCACAGTTATTGTTTACGCCACGGCAACTGTGAACGTGATGACATG
>>>>>>>>>>>>>>>>>>
1380 GTGAAGGCTGTCATCTCCGCAATGCAGAACAAGATCGCTAAAGGATGCAAGATCAAGCCA
1440 GACAACTTCAAAACCAGCTTGTTGGCACTGCGAGGCATCGGCAATGCCGGATATGCCGTA
<<<<<<<<<<<<<<<<<<
1500 TCAGCAATCCCCACCCTGGAGATTTGTGTGAAGATCACCTCGAACCCCATCGAAATTCGT
1560 CTGTCCGCTATTGAGGCTTTCAGGAGGATGCCATGTGATGCAAGCAGAAAAGCTTTGGTA
1620 AAGACATTCTTACAGAAGGAGGAAGATTCCGAAGTGAGGATCGCAGCATACAGGGTCTTG
1680 ATGGAATGTCCATCACCTCAGTTCCTCAGCCTAGTCCGCTCCACGTTAGAGAGTGAGGAA
1740 ATCAATCAAGTTGGGTCTTACATCTGGTCGCATCTTACAAACCTGATGGAGACATCTGAC
1800 AGACATAAGCAGGACATCAGAGCAATCCTTGAGGATGAAACATTTAAGAAGGAATTTGAC
1860 CTTGACAAAAGGAAGTTCTCACGTAACTACGAAGGTTCCATGTTTATTGAGAAACTCAAT
1920 GCCGGCGCGAAAGTTGAAGGTGATCTTGTCTGGTCATCAAGATCTTTTGTTCCAAGATCG
1980 GCCATGATGAATTTCACTGTTGATCTTTTTGGACATTCTATAAATCTTCTGGAATTCGGT
2040 GGTCGAGCTGAAGGAATAGAATACTTCTTGGAATCATTCTTTGGACCCAATGGCTACTTC
2100 AGTGGACAGGACACAAAGGGTGGAAATGATATGTTGGCCAATGGAATCAAACAGGAGAAA
2160 ATGAAGAAGATTGATAACAGGTACGGCAGCAAGATGGACGAGCTCCGTGGCTCTATGTAC
2220 ATGAGGGTGTTTGGCAATGAATTGCGTTACAAGAGCTTCCAGGGAGTGGAGGATCTGATG
2280 TCTGGTCCTAACTTCAACCTGTTCGATATGCTGATACAGCTGGCCAAGGACAACGATTAT
2340 ACTTTCAGCCATTCTACTATGTTCCTGGACACCAGCATCATTATCCCAACTGGAGCAGGT
2400 TTCCCAATGAATCTAACAGTCAACGGAACTGCAACAATTGATCTGAGAATGAAGGGAAAG
2460 ATGGATCTTAGGTCCCCGCCAGCTGTCAACATAGCAGGACTTGTACAACCAAGTGCGGCT
2520 ATCGACATATCATCAATGATGAGCGTGGATGCATTTGTAACCAAGTCCGGAATTAAGATG
2580 GTGTCCACCCTACACTCCAGTACAGCTGTCCAGGGCAAGTTCCAGGTGAACGAGGCTGGT
2640 GTGATAAGCGCAGAATACGAGATGCCACAACCCAAGATGGAGATCATTGATGTCAAGTCA
2700 TCATTCTTCACTGTTCATCGAGACATGGAGAAGGAACAAAAAATGATTGCTGATAACATT
2760 CATACAAAGAAATTCTGCTCCCCAGAGAAACTTGTCACCATCACAGGACTTGAACTATGC
2820 GCAGAGGTTACATACCCGAATGCATCTCTGAAATCAGATGCCCCATACTTCCCCCTTACA
2880 GGCCCAGTCACTGCTGGTGTCTATCTCTACAACAGAGATACCCACAAGAAATACAAGATG
2940 GAGGCCAGATCCACACATAACAAGGCAAGCAACATCCTGCATTTTACCTTTGACACACCA
3000 GAATCTCGCATCGACAGACATATTGTCCTAGATCTCAACCTCAACAAACGAGCAACAACC
3060 ATTGATATGACTTTGAACTCTCCATGGAAGAAGGCAAATCTGCAAGGTGCTATTACAAAT
3120 GACAAAGGTATCATGGGTATTAACAGCAAGATGTCGGTGGATGGCAAATCTGGTTTCTCG
3180 GTCAACTCCAAGTTTGTGAAATCCCGTGTCGGTAACAGCATCAAGTATGTTCCTTCTCTG
3240 GAAATCAGTATACCGCAGATGAAGCCCGTGAGCATCCGAGGCATGTTGATGCATAATGGT
3300 TACCGGCAGCTGGATTTGGAATATGACATGTCCGGACTGACTGCCGCACCAGTCTCCGCT
3360 CAGTTGACCATTAACAACAAACCGGCCCTAAAAGGCGTACGAGGAAGTTTGTCTTTGCAA
3420 AAGGACAAGGCCTACTCATTTGACACAAGGGTCATGATTTCATCTGACAACAACAAGATT
3480 GGATATAAGCCATTTGTCTCCCTCCGTTCTCCAACAGGGGAGGTCCTTGCATTTGGCGGA
3540 TCTGCTAATATTATCTTCAACAAGAAGGTTGTTGTAGACCTTGTCCTTGATAAGGCTTTT
3600 GCCAAAGCAGTAACACTCAAAGGTTTCGTAACCAAGACAACGAAGAACCGAGGTCGTGTT
3660 ATATACAACACTAAGATGACTTATACATCCAGTCCAGTGGATCTTCTGCTGAAAGCCAAG
3720 ATAGACAACAGAAACTCTCGTGCAGTTGCGACAGTTGTAGACTTCACCTACGTCATTCGC
3780 AAAATTGCCCGTAACAACATCAAACTTGTGTCAAAGGTCACGAACCTCAGCAGTAAATAC
3840 CTTACCAAGGCCAAAGCTTCAGCGAATGTACTAGTAAAAAGGAATCCTGAGTTGAACTTG
3900 AAATTTATGGGTAATCTAGAGCACAACAAGAAACACTCCGAGTTTGACGTCGATGTTCGC
3960 TATGGTCGTGACTTCAAAGATGAAAGCAAACATATCGACATGAGTTTTGAGATGAATAGA
4020 AAGTTCAAGGACATTACGGCAGCATCTGCCAATCTCCAGACAAGATTAACATTCCCTGGA
4080 CAGGGTCTTAATATAATCGTAAAGGGTAATCACAAACACAGCAGTAAGGAACTTGATTCC
4140 AACATCTTCCTGCGTCTTGGTAAAGGACAACCTATTGAGAGCAGTTTGCTCATACAGGAC
4200 AAAACAGAACAATTGGTGAAGGTCGTCAGTGAATACAAGCTTAGTTATCCAGGCAGGGAA
4260 GTCATCTTCAATCATACATTAGCACAGACAGATAAAACCACTTTTGTTAGTTCCTTCAAA
4320 TCTCAACTGGAGAAAAATGGAAAGAATACCATTATTACAACACTGAAAACTTACCCTGAC
4380 AAGGAAAGGGTTTCCATCTCATCAGATTTGAAACTAAGCAAACAAACACCAGTCCATTTG
4440 CAAGGAGACTTTGATTTCAATCCAGCAGACTTTATCACCAGTATGTCATATGAGAAAGAT
4500 TTAAAAAAATATTCTGGATCATTGACATCTCTGACCAAGGGAACTGAGTCATCAAGCTTA
4560 ACAATTGATTTGCAACACCCAGAAAGACGCATTGTCATGGACCTTAGTGGCAAGAGCATG
4620 ATGAAGAAATACCAGGTTGAGGCAGATTTAAAGTGGAATGCAGGCAGAAATGATTCTGAA
4680 AATGTGCATATATCATCTTGGATTGAGCCACCGACAGAAGAAAAATTGAATGGCTCCATA
4740 ACCATCACTTATCCGACAAGAACACTCACTTTGAACGCCCATCAATTACTATCAGACAAA
4800 TATAACATGCATGCTGATTTTACATGGGAAACTGACAAGAAAGTTACTATGGATACAATC
4860 GTCTTATACAAAAACAACATGATGATAAACACCTTAAAGTTGACCTCTCCATTTAGTAAG
4920 ATGCGTAGACTTGACCTAGCTGTAAACCATAAAGATGACCACGAAGAATATGCAACTAAC
4980 GTTGAGGTCAAGTGGAACAAAGGTGAATCTGTAACTTCTGAGCTCATACTTAAAAAGCCC
5040 GCCAGTCTTAAAACCGTTGTTGGTAGTGTCTTCATGAAAACAAGCTTCAAGGTTCTGAAG
5100 AAGATAAGATTAGACGTAAATCATAAATTAAGTGACTCCCTGGCTTCGTCTGTGAAATTT
5160 GCATGGAACAGGCAACTCATTAATGTAGATGTAAACCTGAAAAACACAACCAAAGGTAAG
5220 AAGATGGGATTTAATGGAAATGTTGATGTTAAGACCTCCTTTGCCTACTTGAAGAAGGGA
5280 CAACTTAAAATCTCCCATGATAACAATGGTAAGACATTCAACACTTTGACGACTTTGATG
5340 AAGAACAAGAAAACATACAAAATCGACAGTAAGATAACTCACATCCCCACAGCTAATAAA
5400 TATGAAAACACTGGAGCTATTTCTATTTCTGCACCTACTGGAAAGTCTGATATAGTATGG
5460 AGTCATATGCACACTTCAGAAAAAGTCACGTCCATGTTCGCTTCATCACAGGGAAAGAAG
5520 GGTGATAAGAATATAACAGTGAGACTAAATGGAGAATTTAAAGACCTATATGCTGCCAGT
5580 CTTAGCATTCAAACACCATATAAGTCTGCTCGTGATGCCTTGCTGGAGGTTAGTATGAAG
5640 CATGATGGGTATGTTATGGTTGACAGCAAGGCTAACGTAAATGTAAATGGTGCGAAAGTT
5700 GCTGCTGCTACCATTAGCTACAACTTGCGGAGCCCTGCTACCATTACTACACTTAATATT
5760 CCTGCCCTTGATATCAACTGCAGGATTCAAGGTAATGCAACATCAGAGAAAAACTCAGAA
5820 ACTGTTATAATGGAGGTTGTTCTTACACCAGAAATTAGTATGGCCCTCTCAGCATCACAG
5880 AAATTTTTTGATGTCACTGGTAACCCTGATGCTTTTGCCCAGTCTCTCATTTCATGGAAA
5940 TCTTCCTTCCCAGGATATGAGCATGCCAAATTCGTTTACGAAATTAGTGATAACAAAGAC
6000 GAGTCCAGTGTTACAACACATACAAAACTTGAGTATAGCCAGGGTAAAGTCATAGAAGTT
6060 AAATCTGAATTAGATAAAAACAGTTACTATTCATCACTGGCTACACCTTATGAATCGTTG
6120 CCATTTATGGAAGGAAAAATCAGTTTCGTTGGCAAACCAGAATCTTTCAGAAGCTCTGCA
6180 TTTATCAAGATACTACCTGTATTGGAGAAAACGTCTGCATCTGTATCATGGAGCACCCTT
6240 GATGGATTGAAAACTGAACTGAGAGTGGATACACCATCTACCCAGTATCCTTATATTCAG
6300 GTTAACTTGGAGGCAAAGAAAACGGAAAACGGAAAAACAACCGGTGATCTTGTAGTTGAA
6360 TATCTTCCCAGAGAAACTGTCCGAGTGGAGGTGATGAGCGATATTAGTGATATTGTCAAC
6420 CTCTCTGCAAAGGTGACATCACCATTTGTAATGATTGATCTATACCACAGTGGAAACCTA
6480 CAATCATTTAAATCCAGTGCAGAGATTGAGGGGACACCTGGCAAGAAATATGGTCTCATT
6540 GTAGGCTATACAAATGGTACAACGATTGAAGGCTATGCAACTATATCTGTGCCAGGAAGA
6600 AGAGACATAAATGCAGTCTTCTCACACCAAGGATCTGCAATGAACTTTATCACTCATGCA
6660 GAAATAACACACAACAGAATGAACCAATTCACCTCTGACTTTAAATTTGCAGCAGGCAAC
6720 TCAATAACTGTGTCTGCATCCACTTCACTTAGGTCTTTGCTCCTCATATCAGAAGACAAA
6780 TATAGAGCAGCTTTTACTACGAAGGTCATCCCATTGAAAAAGATGTCTGCTCATGGAGAA
6840 TTTGTGACAACAACCATAGGAAAGTCTGAAGCAGATGTGTCTTTTGACCTGACTAAAGAT
6900 ATTGAGGGTAGTCTTACTGTTAAATCACCTTTGATTAAAAACATTGAAGCTTCTTTTAAT
6960 CATCATCAGAGTGAAAAATATATAAACAGTAGAGCAGAAATCGTCCATGACGGTAAAAAA
7020 AATATTGATGTGCAGGCCTCTCTAAATGTTGATGAAGATTCTGTTGTTGGTGAAATAGGT
7080 ATCAAATCCCCATTGTCTGATGATATCCAGGTCCTGTCTAGGTTTGATGGTGGTAAAGAC
7140 AACTTTGTTGTTCATTTTGAAGGCTCTGTCGGTGTTAACAAATCTGAAATTGATTTATCC
7200 CACAAATGGGTTGAGAGAAACAGCCAGCAGACGATAAGTGTGAGATCGACAGGGATGAAG
7260 GACGTGACAGCAGAGATAAGTAACACCGGTGATTACTATAACTTAAGATCATATGCTGAG
7320 TTAAATCATGGACTTGAAAAACATAGAATTGATTCTACATTTAAACATCTGATAGGCAAC
7380 ACTGAAGGAAGTATTTCCATATCTTCTCCCCTGGGTGATCCACTATCCACAAACTTCTTT
7440 GTAAAGGTCACTGAGGCAAATTTAGAGTCAAATGTTGAACTGAACATAGGCTCAGACAAG
7500 AGTGAAGTTCATGTTTCTGTTGGTTCAAAACCAAATCTGGAAGGAAGCATTCGTGTCAAT
7560 TCACCTTACGTCACTGATGTCTCAGCTGGATTTGATCACACTGGAGAGTTTCCAAATATT
7620 GTTTCTCACGCACAAGTGAACATAGCCAATAAAGACATTGTTGATGTTAAGTTGATGTCA
7680 CAATCCACAGAGAGGGGAATAGCTGGATCATTTGCACTGCAGACACCATTGAAAAACTAT
7740 TCAAGTATTGAGACATCTTTCTTCCACCAAGGCATGTCTAACAATTTCAGAAGTCATGGA
7800 GATTTTGCCATTAATTCTGATAAGTCTGAAATTAATCTTTTCTACAGTTCAATGTACAAG
7860 TATGAGGGTATGGTCTCCATCAAATCTCATCTCATTGATGACCTTAAGATTGGCTTTGAA
7920 CATGATGGAACAAAAACTAACTTTGACTCTCATGGGGAAATCAGTGTTGGATTTGAGAAA
7980 TATGAACTCGATGTTAATGCAAATGTAGATTCAGATGTCATATTGAGCATGATTGTAAAA
8040 TCTCCCAGAAATGAAGATATCATTGCTAGGTTTTCACACTCGGGTAATTTCTCAGATTTT
8100 AGATGCCATGCAGAACTAATGCATGATAAAGACAGCAAATGGGAGGGAGATGTCAGTTTT
8160 TCTGCTGGTGATGAAATAAGAGGAGAGATTGTTTTCAAACCATGTCATCATCTTCACAAA
8220 GTTTTCATTTTCGATTCTAATATCAAGTTTGAATTCAGTAAATACCATGCTGAAATAAAT
8280 GGAGATTTACCATTTTTAGGAGAAGTACTTCTGAATTTCAAACGCACAGGAGAACTAAAT
8340 GACTTTAACATACATGCAGATGCTAGTTTCAGAAATAAGAAATCAGATGCAGATGTCACT
8400 TTCCAGCTTGCAAAGAAATTACTCTCTTCATCTGTAAACCTTAGATTTCCACATATGGAA
8460 GATGTGTCTTTTAGTTTCAATCACAATGGAGGTTTGAAAAACTTCAACACAAAAACTGAA
8520 ATGACAATTGGACAGAATAGAACCCAAGGAGCTGTAAGGGTGAGAATCACTGGTTCATCC
8580 ATTTATTCAAACTTAGCAATTCAATCCCATTACATGGACAGGATAAATGTTAACTTCAAC
8640 CACAATGGACAATTTGGAGATTTCACCACCAGTGGAGATGTCACTATTGGCAACATGAAA
8700 AATGAAGCAGACATGGCATTCCACCTTTCTGGCAAAGTTATGTCATCATCAGCCAGTGTC
8760 AAATCGCCTTTAATGGATAGTGTCAGCATAGACTTTAACCACAATGGAGCACCAACAGAC
8820 TTTACTACCAAAGCTTCTGTGACCATAGGTGATAAAAAAAATGAAGGAGACATTACATTC
8880 CAGATTACAGAAAAGGCTGTCATCTCTTCACTTAATATCAAATCACCATACATGGACAAC
8940 ATCAATGCTAATTTCAATCACGAAGGATTTGCTACGAAATTCACTACCAAGGCTGATGTA
9000 ACAATTGGTGTTGAAAAAAGTGAAGGTGATGTTTCATTCCAGTGGTCCAACACTTCTACG
9060 ACAATCTCTGGGAACCTGAAATCGCCATCAATGGAAGATATTACTTTTAACCAGTACACC
9120 TTATCTATGCCAACAAAGTATACGTATCATCAGGATTACTCGGTTGGTGATGCAAAAACT
9180 GAAACTGATATGATGCTGGACTACACCAACCTGAAGGCCACCTTTGCTTTGACTTCGCCA
9240 AAAACTTCCCTAAATTTTGACCACTCTGGTGATATTAAGAATTTCATCTCCGCATTGGAC
9300 CTAACAACTGAAATGGGAAGATATTCTTCTGAAGCAAAATTCACACTGAATGATAATGTA
9360 GAAGCAAGCTTCAAACTCACTTCCCCTGTTGAAGGAATGGAGTCAATTTCAGCACTTTAT
9420 ACCCACAATGGCAAACCATCCAACTTCAGATGCCATGGGGAGTTATCTCTTCCAAATAAA
9480 GCTAATGTTGCTGATTTAATTATCAATGTTGAGCAACTAACAAATATGAAAGGAAGTCTT
9540 CAAATTAAATCTGAAATCATTCCAGACTTCACAGCGAAATTCTCCAACATACTCACAGAA
9600 ACATCTCTGCAGTCAATGTCTGAGATCAGTGTTGATGATGAAGTACTCTATGGTATAGCT
9660 GTCTCTTTCACCAACAATTCATTCCTTAAAGCTGAACTGGAAGTGAAAACACCAGTAACA
9720 GAATATCGTGTTATTAGGCTGTCAGGAATTAATCAAATGGACAAAGACCAGGTAAAAGCA
9780 TCTGCAGAGCTTCTTATTGGAAGTGATAGCAGTGTAATGGAACTTTCATTTTCTTCTAAA
9840 CCAAATGTTGCGGGCGTTTTCGAACTCAGATCTGTATACCTACCTCATCTTAAGGCTACC
9900 CTAGATGCTACTGGAACACCAACTAATTTTAGAGGAAACTCAGAACTTATTTTTGATGGT
9960 GAAAAGAAAGGAAGTGTTGATGCTTCTTTCAATATGGAAGGTATATTAGATGCAAATCTC
10020 AAGATGGAACTGCCCCTGGAAAATTACACAAGGATAAATGGAGACATCTCAATTAGGAGC
10080 AGTAGTGACTTACTTGACATAAAATCTGCACTGAGTATTGAAGATAGAGAGTTAGTTGAC
10140 GGCAGTGTTCGAATTACAAACCAAAATCAGCTCTCAGGAGAAATATCTCTGAAATCTATT
10200 TACATTAACCCTTTGACTGTGAGCTTTGATTTATCTGGGGATCTTAAAGACTTCAGTACA
10260 ACAGCCGACATAAGCTACAATAATGAGAAACTGGCTGCAAGTAGTATGAAATTCAATTTC
10320 AACCCAACTCCTTTGAAAACATCTGGGTTTGCATCGTTCAACAAGATGTCTTTTGCATAC
10380 AGCTTAGATAATGCCCCAAAAGATTTTAAATCCCATGCAGAGGTAAAAGTAGAAGAAAAG
10440 ATGTGGTCTCTTGATGCAACCTGCACTAGAAAGCAAGACATTGATGCTTCATTTAAGGTC
10500 ATTATTCCAGAGATTGATCCAATTTCTGGAAAATTGTCTCATAGCCAGAGACAGTTCAGA
10560 TGTGCATCTCATGTCGAGCTTAAAACAGATTCCTCAACAAAATACCAGTATGACATGCTT
10620 CTCAAGTGGAGACGTGCCTTGGAAGGAACTTTCAGTGTCAAAACACCCATCAAAGGAATG
10680 GAAATTACAAAAGTTGTCCTCAATCATGATGGCACTTTCCCAAACATCAAATCTTCAGCT
10740 GAAGTCAATTTCAACAAGACAGACATTTCAGCCGCTGTCAGTCTGATGCATGGTGATTTA
10800 ACCAAAGGAGATGTTTCCATTAAAACTCCATTTGAAGGATTGGAAGATGTCAGTGTAACA
10860 TTCTATTCTGAAGGTGATATTGAAAAATTCCAAGCAGGTGGAAAGGTTTTGTATGCTCCA
10920 GGAAAAGATATTGAGGCAGGAGTGGAACATAGTTTGTCTGACAATAAGCTGCAGTCCCGC
10980 ATCCATTTTATGTCACCCTTCACCGATGAAATCGTTGTCAGTGCTAACCATACTGGGGTT
11040 CCTATGAATTTTGTGTCAAGTTATGAATTAGCCATGGGTTCAGATAATAGAATCAAATCT
11100 GAGACATCTTTGAAAACTGGATTCCAGTATGTTCAATTCAAATCTTCTGTCACTACAACA
11160 ATGAGTGGGGAAACATTTGTACAAAAGGTTGAGCTAAAGCATGATGGCGCTATAGAGAAG
11220 TTCAAAACAGAGGCAATGGTACAAGCAATGGAGAAATTAGTAAGAGTTGATACATCCTTC
11280 CAGCTTGAACCAGTCATTGAAGGATCAGCCTCAATCATTACACCATTCTTTGAAAAGTCA
11340 GAGGAAATAAAGGTAATCTTTTCACATAGTGGTAGTACTAGTGGATTCCTCTCAACTGGA
11400 GAGTTACAGTATTCTCCAAAGAAAAAGATAAGTGGAAAAATTGATTTCCTCAATAATGGT
11460 TGGAGGAGGAGAGTTGCAACTGTCGAAGTAAGAACGCCATTTAAGGGCATGGAGGTGAAC
11520 AAGGTTACCTACCAGCATACAGGCAACTCGGACAGCTTTGATTGTGATGCAGATATTTTT
11580 GTTGCTTCCCAGCCACTCAGCGCTACTTTCAAAGGATCTAAAGCACCTTTAAGCATGGAT
11640 CTGAACATCAAAACACCATTTGAAGGATATGAGAGTTTTGGACTTAACGGGAACTTCCTA
11700 AACAACACAATGGGCAGATATAGCGGCAGAATGGAAGCCTCATGGCACCCAAATCAGGCA
11760 GTCATTTTTGAAAGTTCATTTGCTGCATTGAGAAATAAAATTGAAGGAAGTGCCTCACTA
11820 ACAACTCCATTTGTCATGCTCCAACGGTCCTCAATTGAATTCTCACACCAGGAGCTCTCT
11880 CAAAAATTCATTGAAAATCTAAAAGCAACTTTCAATGGAAGTAGAATTGTGGATGTTGAG
11940 GTTGATCACAGCCTGATGAATGAACGCAAACATGCCATTATTACAATGCGTGCTCCACGC
12000 TCCATGAAATTTGACATGAGTGGTGATTTCACTCTGGAAAGTTCAGCAGTTGATGCATCT
12060 GCCAACTGGAACACTGAAGATAGTAAAAGTAATCTGAAACTTGAGGGAGTTTATGACATA
12120 AGAACAGACAAGAGAATGAACTTCAAACTGACCCGACCTGGACAGGTGATTTCCTATTCC
12180 GGATTATTGGACAGAAGACACAGTAAATCTGACCTTGTCTGGGGTATAGGATCAACACAA
12240 AAAGCAGGCTATGAAGTCGCAATCAATGATTATGACTCCAGACTGAAACTTATACTTCCA
12300 ACACGAAGCCTAGAGCTAACCGGGTCCCATCGATCAAAGGTCACAGAAGGGTCATTTCTA
12360 TGGGATGCTGATGTGGATGAAACAAAGAAGGTTGGCTTCCGTTCTGTGATAGTGCCATCA
12420 GATGATGCTATTAAGGCCGATGTTACATTCCAGCTTCCAAGCTTAGGAAAGAGAGTACAA
12480 GTCGGTTCAGAGGTTGTGGTCAATAGAGGACGTGTAATTTTCGACGGCAAGACAGAGTTC
12540 TCTTACTCTCCTGATGAGAGAAAGAAGATTGTGTTTTCATCAAGGCTTGAGGATAAGTCC
12600 CTTGGAGCCACGAAAAACTACAGCTTCAGCATGGGTCTAAGTCATCCATACACGACTGTT
12660 GATATCAAACTGGCATCACATGTTGGCAAATCCAAGAACAGATATTCCGCTGGTATGGGG
12720 CTTGAGTACCTTAACACACACAGACAGACCAAGACCTTCCAAGTCAATGGACAGATTAAC
12780 AAACTCAGGAAAACCATCAGCTTCGAGCTGCAGAGTCCAGTCAAATCTATCAGTATTTCG
12840 GGCAGTGCTCAGACTGAAGACAAGTTCCGTGTGTCTATCCTCAACATCTATGACCAGAAG
12900 ATGCCACTGACGACTGTTTTCACCGTCGACCCTGCCACCAGATCACTTGACTTTTACATT
12960 AATTATGACCTTGAGAACCCAAGTAGTGAGTTCCACATAAATGCCAAGTATGTGAACAGT
13020 TCTGCATTGGCTGCCGAGGTGTTCCATATCGTCAACCGTGAACGAGTGACTGACATTCTG
13080 GTTACTGCCAGACTCAACAACTCTCACCTCCTTCACACAAGAGTTCACTGGAGACCGGAA
13140 ATGATCAAGGAATACGAGACTGTTCGAGAGAGGAAACTTGAGGACTACAAGAGACGCCTG
13200 GAAATTTCAGCAGTTAAAGTAGAGGCTGCTGTAATTGAGGAAACTGTTGAGAAGTTTAAG
13260 ATGATCTGGGAAGCTGTTGTAGAGGAGATTGGCCAAGACAATGCTCTAGCTATAGAGGCT
13320 GCTGTTATCCCCATGTTTGAAGATGGACTGAGGACATATGCACAAGTGCAGGGACATGTG
13380 CAGGCAAACTTCCTTCCATTTGCCTTGGATTTGGCCAACATAACACAGTACAAGTACAAC
13440 AGATTTGTACAAACATACAGAGAGTTTTCACAGGCAGTAAAGCTTCCAGAAACAATGAAG
13500 GATCTTGACTTCCTGTCGTCTGCCAGACAACCATTGGAGAAGCCCTTTAATTATGCACTG
13560 GATCTGATCAAGATCCCTGCGAAGCACCTTCCAACCCAGGTGACCGGAGCACTGAAATAC
13620 CCGGCCAAATATATGTTTTCTAATATGGATACTGCTATGTTGGAGCAGCTTAACAAGAAC
13680 TGGGAACTTGAACACCATCTAGAATCTGTCATTGAAACCATTCTTCTTGCAATTGAGGAG
13740 GAAGCTGAGGAAGGCATACTTAAATTGAAGAGTATCATTCTCAACTCGGCACAATCCCCA
13800 ATCACTGTGTACGACCCAACCCACGGGGAGATCCAGGCAGAATTTCACTCACCCATACCA
13860 CTGAAGTCTCTGGATGAGCTACCTGTTATCAATATTGAAAGATATATTAACATGGTTATG
13920 AAAACTCGCAGTAGAAAGACAGAAAATGTTCCCAGCAAGACATCAGAATGGTTGCCACCA
13980 TTTACTGGTGTTGCCAGTATTACCAGCGGTCATAAAATCACAACTTTCGACGGGTATATC
14040 TATGACCTTGATGCTGACTGCACGTTTGTGCTTGTCCGTGATTTCAGGAATGGCAACTTC
14100 AGTATTATTCTGAACAACAATGATGGGACAACTCTGTCAATCCTTTCACATGGAAAACCA
14160 ATAGAAATCAAGCAGAGCGGAGAGATCTCTGTTGCCATGGAGCCTGTCACTCTCCCATAC
14220 AAAGAAAACAACATCACAATTACATCATCAGATGACGGAATCATCAGCATTGATGGGGCT
14280 AACCACTTCAAGGTAGATTATGACCTCTCAGTCGATCACATCGATGTAGAGATCAATGGA
14340 TGGTATTACGGCAAAACTGCAGGACTTCTTGGTACCTTTGACAACGAGCCCTCAAATGAC
14400 CTTATGACCTCCTTTGGAAAAATCATCAATAATCCTAAACGTTTCGCCAGAACTTGGGAT
14460 GTTGGAAACACAAATTGCCGTTAA
KEYS (in order of precedence):
>>>>>> left primer
<<<<<< right primer
ADDITIONAL OLIGOS
start len tm gc% any_th 3'_th hairpin seq
1 LEFT PRIMER 3266 18 59.89 61.11 7.91 0.00 31.82 CGTGAGCATCCGAGGCAT
RIGHT PRIMER 3362 18 60.13 66.67 0.00 0.00 0.00 CTGAGCGGAGACTGGTGC
PRODUCT SIZE: 97, PAIR ANY_TH COMPL: 0.78, PAIR 3'_TH COMPL: 0.78
2 LEFT PRIMER 3253 18 60.13 61.11 0.00 0.00 0.00 CGCAGATGAAGCCCGTGA
RIGHT PRIMER 3362 18 60.13 66.67 0.00 0.00 0.00 CTGAGCGGAGACTGGTGC
PRODUCT SIZE: 110, PAIR ANY_TH COMPL: 0.00, PAIR 3'_TH COMPL: 0.00
3 LEFT PRIMER 1922 18 59.83 61.11 12.10 0.00 0.00 CGGCGCGAAAGTTGAAGG
RIGHT PRIMER 2053 18 60.13 66.67 0.00 0.00 40.25 CCTTCAGCTCGACCACCG
PRODUCT SIZE: 132, PAIR ANY_TH COMPL: 11.23, PAIR 3'_TH COMPL: 14.04
4 LEFT PRIMER 1921 18 59.83 61.11 12.10 0.00 0.00 CCGGCGCGAAAGTTGAAG
RIGHT PRIMER 2053 18 60.13 66.67 0.00 0.00 40.25 CCTTCAGCTCGACCACCG
PRODUCT SIZE: 133, PAIR ANY_TH COMPL: 5.41, PAIR 3'_TH COMPL: 9.34
Statistics
con too in in not no tm tm high high high high
sid many tar excl ok bad GC too too any_th 3'_th hair- poly end
ered Ns get reg reg GC% clamp low high compl compl pin X stab ok
libprimer3 release 2.4.0
%%bash
cd /home/sam/analyses/
rsync \
--archive \
--relative \
./20181129_geoduck_vtg_primers/ gannet:/volume1/web/Atumefaciens
%%bash
cd /home/sam/analyses/20181129_geoduck_vtg_primers
# Store sequence only from desired FastA.
# Print all lines after the first line and then delete newlines
sequence=$(tail -n +2 /home/sam/data/geoduck/transcriptomes/transdecoder_fasta_splits/TRINITY_DN51983_c0_g1_i8.p1.cds | tr -d '\n')
#
seq_id=$(echo "$(head -n 1 /home/sam/data/geoduck/transcriptomes/transdecoder_fasta_splits/TRINITY_DN51983_c0_g1_i8.p1.cds | tr -d '>').cds")
# Use heredoc to create Primer3 parameters file
cat << EOF > /home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_params.txt
SEQUENCE_ID=${seq_id}
SEQUENCE_TEMPLATE=${sequence}
PRIMER_TASK=generic
PRIMER_PICK_LEFT_PRIMER=3
PRIMER_PICK_RIGHT_PRIMER=3
PRIMER_OPT_SIZE=18
PRIMER_MIN_SIZE=15
PRIMER_MAX_SIZE=21
PRIMER_MAX_NS_ACCEPTED=1
PRIMER_PRODUCT_SIZE_RANGE=75-150
P3_FILE_FLAG=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/home/sam/software/primer3-2.4.0/src/primer3_config/
=
EOF
# Run Primer3
/home/sam/software/primer3-2.4.0/src/primer3_core \
--output=/home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_primers_default_format.txt \
/home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_params.txt
cat /home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_primers_default_format.txt
SEQUENCE_ID=TRINITY_DN51983_c0_g1_i8.p1.cds SEQUENCE_TEMPLATE=ATGGAGCGATTGGTTTTAGCGCTAATCGTTTTGGCGGTCTGTGTCCACGCAGGTCCGATACAGAAAATCTCAGTTGATACCTGTGCAAGAACTTGTACAGGCAACAGCAAGTTTAATTATGTTGCTGGTAAGACTTACCAGTACAAGTATGATGCCGACATCAAGACTGGGGTCCAGGGAGCATCAGAAGATAATGCGAAAATACACATGTCGGCAACAGTCGAGATGGAGGTCATATCAAAGTGTGACCTTGTCATGCGGCTGAATGATGTCACATTGACAGAATATGACCCCATTGACTTGATAATGAAGGAAACGTCATCTGAATTCCGCAGTGGTCTTGAGAAGGCTCCCATCCGAATCTCTTTCCAAGATGGAAACATAGAGGAACTTTGTCTGAAACGAGAGGAGCCAAATTGGGTGCTGAATGCCAAACGTGGAATCCTGTCAATGTTCCAGAACAACATGGACGATTTCTCAACCAATAAAACAGTGTCTGAGACTGATGTGTCTGGTGTGTGTGATACAGAGTACCACGTGAGTAAATCTGGCTGGTACAAGACCACAGTCAGCAAGTCTAAGAATCTCCTAGGTTGTACTGACAGGACCGGGTACAACACTGCCGTCCAGGGAGTGCCATATACCGCAGCTTCTGGCATCCAGTCACTGCCAGTTGTGAAGAGCAACCATAACTGTGAACATGAGATTGACATTAAGTCGCACATTCTCCATTCGGCAACTTGTAATGAACAGCACATGTTCCTGCCATTCTCACGCTCAGACAGTGGAGCTGTAACATACAACACTCAGACTCTCAAGTTCGTGAAAGTAACAACTGGAATCAAGTCACCATTTGATACCAGTACTCGCAAATCAATGAAATTCGATCACATCAATGATGCAGGCAGAGAAGCAAAATCGAGGAAAGATATTACACGTAAGCTTATTGAAATCTGTGAGAAGACGAAGTCTGGTGTTCGCCCTGAAACCCCACGTCTGTTCACAGACCTCGTGTTTATGATGAAGACTGTTGATTCTGACACTCTAGCAGACACGTACAAACTGCTCCAAGAAGGTGCCATCTGCACTGACAATAAAGAAAGAACCAGGAAGTTTTTCCTTGATGCCTTACCGATTGCTGGTTCCAGTTCCTCACTGCACTTGATGACCCAACTCTTGACCACAAAGGCTGTGACTGGAATTGAGGCAGACATGTGGCTGTCGGCCATCTCTTTTCTCAAGAACCCAACTAAAGACATGCTGAAGGAAGTCAAGCCTTTGATCAACATGAAGGACACAACTGACAAGGCCCTGCTTTCTGTCGGTACCCTGATCCACAGTTATTGTTTACGCCACGGCAACTGTGAACGTGATGACATGGTGAAGGCTGTCATCTCCGCAATGCAGAACAAGATCGCTAAAGGATGCAAGATCAAGCCAGACAACTTCAAAACCAGCTTGTTGGCACTGCGAGGCATCGGCAATGCCGGATATGCCGTATCAGCAATCCCCACCCTGGAGATTTGTGTGAAGATCACCTCGAACCCCATCGAAATTCGTCTGTCCGCTATTGAGGCTTTCAGGAGGATGCCATGTGATGCAAGCAGAAAAGCTTTGGTAAAGACATTCTTACAGAAGGAGGAAGATTCCGAAGTGAGGATCGCAGCATACAGGGTCTTGATGGAATGTCCATCACCTCAGTTCCTCAGCCTAGTCCGCTCCACGTTAGAGAGTGAGGAAATCAATCAAGTTGGGTCTTACATCTGGTCGCATCTTACAAACCTGATGGAGACATCTGACAGACATAAGCAGGACATCAGAGCAATCCTTGAGGATGAAACATTTAAGAAGGAATTTGACCTTGACAAAAGGAAGTTCTCACGTAACTACGAAGGTTCCATGTTTATTGAGAAACTCAATGCCGGCGCGAAAGTTGAAGGTGATCTTGTCTGGTCATCAAGATCTTTTGTTCCAAGATCGGCCATGATGAATTTCACTGTTGATCTTTTTGGACATTCTATAAATCTTCTGGAATTCGGTGGTCGAGCTGAAGGAATAGAATACTTCTTGGAATCATTCTTTGGACCCAATGGCTACTTCAGTGGACAGGACACAAAGGGTGGAAATGATATGTTGGCCAATGGAATCAAACAGGAGAAAATGAAGAAGATTGATAACAGGTACGGCAGCAAGATGGACGAGCTCCGTGGCTCTATGTACATGAGGGTGTTTGGCAATGAATTGCGTTACAAGAGCTTCCAGGGAGTGGAGGATCTGATGTCTGGTCCTAACTTCAACCTGTTCGATATGCTGATACAGCTGGCCAAGGACAACGATTATACTTTCAGCCATTCTACTATGTTCCTGGACACCAGCATCATTATCCCAACTGGAGCAGGTTTCCCAATGAATCTAACAGTCAACGGAACTGCAACAATTGATCTGAGAATGAAGGGAAAGATGGATCTTAGGTCCCCGCCAGCTGTCAACATAGCAGGACTTGTACAACCAAGTGCGGCTATCGACATATCATCAATGATGAGCGTGGATGCATTTGTAACCAAGTCCGGAATTAAGATGGTGTCCACCCTACACTCCAGTACAGCTGTCCAGGGCAAGTTCCAGGTGAACGAGGCTGGTGTGATAAGCGCAGAATACGAGATGCCACAACCCAAGATGGAGATCATTGATGTCAAGTCATCATTCTTCACTGTTCATCGAGACATGGAGAAGGAACAAAAAATGATTGCTGATAACATTCATACAAAGAAATTCTGCTCCCCAGAGAAACTTGTCACCATCACAGGACTTGAACTATGCGCAGAGGTTACATACCCGAATGCATCTCTGAAATCAGATGCCCCATACTTCCCCCTTACAGGCCCAGTCACTGCTGGTGTCTATCTCTACAACAGAGATACCCACAAGAAATACAAGATGGAGGCCAGATCCACACATAACAAGGCAAGCAACATCCTGCATTTTACCTTTGACACACCAGAATCTCGCATCGACAGACATATTGTCCTAGATCTCAACCTCAACAAACGAGCAACAACCATTGATATGACTTTGAACTCTCCATGGAAGAAGGCAAATCTGCAAGGTGCTATTACAAATGACAAAGGTATCATGGGTATTAACAGCAAGATGTCGGTGGATGGCAAATCTGGTTTCTCGGTCAACTCCAAGTTTGTGAAATCCCGTGTCGGTAACAGCATCAAGTATGTTCCTTCTCTGGAAATCAGTATACCGCAGATGAAGCCCGTGAGCATCCGAGGCATGTTGATGCATAATGGTTACCGGCAGCTGGATTTGGAATATGACATGTCCGGACTGACTGCCGCACCAGTCTCCGCTCAGTTGACCATTAACAACAAACCGGCCCTAAAAGGCGTACGAGGAAGTTTGTCTTTGCAAAAGGACAAGGCCTACTCATTTGACACAAGGGTCATGATTTCATCTGACAACAACAAGATTGGATATAAGCCATTTGTCTCCCTCCGTTCTCCAACAGGGGAGGTCCTTGCATTTGGCGGATCTGCTAATATTATCTTCAACAAGAAGGTTGTTGTAGACCTTGTCCTTGATAAGGCTTTTGCCAAAGCAGTAACACTCAAAGGTTTCGTAACCAAGACAACGAAGAACCGAGGTCGTGTTATATACAACACTAAGATGACTTATACATCCAGTCCAGTGGATCTTCTGCTGAAAGCCAAGATAGACAACAGAAACTCTCGTGCAGTTGCGACAGTTGTAGACTTCACCTACGTCATTCGCAAAATTGCCCGTAACAACATCAAACTTGTGTCAAAGGTCACGAACCTCAGCAGTAAATACCTTACCAAGGCCAAAGCTTCAGCGAATGTACTAGTAAAAAGGAATCCTGAGTTGAACTTGAAATTTATGGGTAATCTAGAGCACAACAAGAAACACTCCGAGTTTGACGTCGATGTTCGCTATGGTCGTGACTTCAAAGATGAAAGCAAACATATCGACATGAGTTTTGAGATGAATAGAAAGTTCAAGGACATTACGGCAGCATCTGCCAATCTCCAGACAAGATTAACATTCCCTGGACAGGGTCTTAATATAATCGTAAAGGGTAATCACAAACACAGCAGTAAGGAACTTGATTCCAACATCTTCCTGCGTCTTGGTAAAGGACAACCTATTGAGAGCAGTTTGCTCATACAGGACAAAACAGAACAATTGGTGAAGGTCGTCAGTGAATACAAGCTTAGTTATCCAGGCAGGGAAGTCATCTTCAATCATACATTAGCACAGACAGATAAAACCACTTTTGTTAGTTCCTTCAAATCTCAACTGGAGAAAAATGGAAAGAATACCATTATTACAACACTGAAAACTTACCCTGACAAGGAAAGGGTTTCCATCTCATCAGATTTGAAACTAAGCAAACAAACACCAGTCCATTTGCAAGGAGACTTTGATTTCAATCCAGCAGACTTTATCACCAGTATGTCATATGAGAAAGATTTAAAAAAATATTCTGGATCATTGACATCTCTGACCAAGGGAACTGAGTCATCAAGCTTAACAATTGATTTGCAACACCCAGAAAGACGCATTGTCATGGACCTTAGTGGCAAGAGCATGATGAAGAAATACCAGGTTGAGGCAGATTTAAAGTGGAATGCAGGCAGAAATGATTCTGAAAATGTGCATATATCATCTTGGATTGAGCCACCGACAGAAGAAAAATTGAATGGCTCCATAACCATCACTTATCCGACAAGAACACTCACTTTGAACGCCCATCAATTACTATCAGACAAATATAACATGCATGCTGATTTTACATGGGAAACTGACAAGAAAGTTACTATGGATACAATCGTCTTATACAAAAACAACATGATGATAAACACCTTAAAGTTGACCTCTCCATTTAGTAAGATGCGTAGACTTGACCTAGCTGTAAACCATAAAGATGACCACGAAGAATATGCAACTAACGTTGAGGTCAAGTGGAACAAAGGTGAATCTGTAACTTCTGAGCTCATACTTAAAAAGCCCGCCAGTCTTAAAACCGTTGTTGGTAGTGTCTTCATGAAAACAAGCTTCAAGGTTCTGAAGAAGATAAGATTAGACGTAAATCATAAATTAAGTGACTCCCTGGCTTCGTCTGTGAAATTTGCATGGAACAGGCAACTCATTAATGTAGATGTAAACCTGAAAAACACAACCAAAGGTAAGAAGATGGGATTTAATGGAAATGTTGATGTTAAGACCTCCTTTGCCTACTTGAAGAAGGGACAACTTAAAATCTCCCATGATAACAATGGTAAGACATTCAACACTTTGACGACTTTGATGAAGAACAAGAAAACATACAAAATCGACAGTAAGATAACTCACATCCCCACAGCTAATAAATATGAAAACACTGGAGCTATTTCTATTTCTGCACCTACTGGAAAGTCTGATATAGTATGGAGTCATATGCACACTTCAGAAAAAGTCACGTCCATGTTCGCTTCATCACAGGGAAAGAAGGGTGATAAGAATATAACAGTGAGACTAAATGGAGAATTTAAAGACCTATATGCTGCCAGTCTTAGCATTCAAACACCATATAAGTCTGCTCGTGATGCCTTGCTGGAGGTTAGTATGAAGCATGATGGGTATGTTATGGTTGACAGCAAGGCTAACGTAAATGTAAATGGTGCGAAAGTTGCTGCTGCTACCATTAGCTACAACTTGCGGAGCCCTGCTACCATTACTACACTTAATATTCCTGCCCTTGATATCAACTGCAGGATTCAAGGTAATGCAACATCAGAGAAAAACTCAGAAACTGTTATAATGGAGGTTGTTCTTACACCAGAAATTAGTATGGCCCTCTCAGCATCACAGAAATTTTTTGATGTCACTGGTAACCCTGATGCTTTTGCCCAGTCTCTCATTTCATGGAAATCTTCCTTCCCAGGATATGAGCATGCCAAATTCGTTTACGAAATTAGTGATAACAAAGACGAGTCCAGTGTTACAACACATACAAAACTTGAGTATAGCCAGGGTAAAGTCATAGAAGTTAAATCTGAATTAGATAAAAACAGTTACTATTCATCACTGGCTACACCTTATGAATCGTTGCCATTTATGGAAGGAAAAATCAGTTTCGTTGGCAAACCAGAATCTTTCAGAAGCTCTGCATTTATCAAGATACTACCTGTATTGGAGAAAACGTCTGCATCTGTATCATGGAGCACCCTTGATGGATTGAAAACTGAACTGAGAGTGGATACACCATCTACCCAGTATCCTTATATTCAGGTTAACTTGGAGGCAAAGAAAACGGAAAACGGAAAAACAACCGGTGATCTTGTAGTTGAATATCTTCCCAGAGAAACTGTCCGAGTGGAGGTGATGAGCGATATTAGTGATATTGTCAACCTCTCTGCAAAGGTGACATCACCATTTGTAATGATTGATCTATACCACAGTGGAAACCTACAATCATTTAAATCCAGTGCAGAGATTGAGGGGACACCTGGCAAGAAATATGGTCTCATTGTAGGCTATACAAATGGTACAACGATTGAAGGCTATGCAACTATATCTGTGCCAGGAAGAAGAGACATAAATGCAGTCTTCTCACACCAAGGATCTGCAATGAACTTTATCACTCATGCAGAAATAACACACAACAGAATGAACCAATTCACCTCTGACTTTAAATTTGCAGCAGGCAACTCAATAACTGTGTCTGCATCCACTTCACTTAGGTCTTTGCTCCTCATATCAGAAGACAAATATAGAGCAGCTTTTACTACGAAGGTCATCCCATTGAAAAAGATGTCTGCTCATGGAGAATTTGTGACAACAACCATAGGAAAGTCTGAAGCAGATGTGTCTTTTGACCTGACTAAAGATATTGAGGGTAGTCTTACTGTTAAATCACCTTTGATTAAAAACATTGAAGCTTCTTTTAATCATCATCAGAGTGAAAAATATATAAACAGTAGAGCAGAAATCGTCCATGACGGTAAAAAAAATATTGATGTGCAGGCCTCTCTAAATGTTGATGAAGATTCTGTTGTTGGTGAAATAGGTATCAAATCCCCATTGTCTGATGATATCCAGGTCCTGTCTAGGTTTGATGGTGGTAAAGACAACTTTGTTGTTCATTTTGAAGGCTCTGTCGGTGTTAACAAATCTGAAATTGATTTATCCCACAAATGGGTTGAGAGAAACAGCCAGCAGACGATAAGTGTGAGATCGACAGGGATGAAGGACGTGACAGCAGAGATAAGTAACACCGGTGATTACTATAACTTAAGATCATATGCTGAGTTAAATCATGGACTTGAAAAACATAGAATTGATTCTACATTTAAACATCTGATAGGCAACACTGAAGGAAGTATTTCCATATCTTCTCCCCTGGGTGATCCACTATCCACAAACTTCTTTGTAAAGGTCACTGAGGCAAATTTAGAGTCAAATGTTGAACTGAACATAGGCTCAGACAAGAGTGAAGTTCATGTTTCTGTTGGTTCAAAACCAAATCTGGAAGGAAGCATTCGTGTCAATTCACCTTACGTCACTGATGTCTCAGCTGGATTTGATCACACTGGAGAGTTTCCAAATATTGTTTCTCACGCACAAGTGAACATAGCCAATAAAGACATTGTTGATGTTAAGTTGATGTCACAATCCACAGAGAGGGGAATAGCTGGATCATTTGCACTGCAGACACCATTGAAAAACTATTCAAGTATTGAGACATCTTTCTTCCACCAAGGCATGTCTAACAATTTCAGAAGTCATGGAGATTTTGCCATTAATTCTGATAAGTCTGAAATTAATCTTTTCTACAGTTCAATGTACAAGTATGAGGGTATGGTCTCCATCAAATCTCATCTCATTGATGACCTTAAGATTGGCTTTGAACATGATGGAACAAAAACTAACTTTGACTCTCATGGGGAAATCAGTGTTGGATTTGAGAAATATGAACTCGATGTTAATGCAAATGTAGATTCAGATGTCATATTGAGCATGATTGTAAAATCTCCCAGAAATGAAGATATCATTGCTAGGTTTTCACACTCGGGTAATTTCTCAGATTTTAGATGCCATGCAGAACTAATGCATGATAAAGACAGCAAATGGGAGGGAGATGTCAGTTTTTCTGCTGGTGATGAAATAAGAGGAGAGATTGTTTTCAAACCATGTCATCATCTTCACAAAGTTTTCATTTTCGATTCTAATATCAAGTTTGAATTCAGTAAATACCATGCTGAAATAAATGGAGATTTACCATTTTTAGGAGAAGTACTTCTGAATTTCAAACGCACAGGAGAACTAAATGACTTTAACATACATGCAGATGCTAGTTTCAGAAATAAGAAATCAGATGCAGATGTCACTTTCCAGCTTGCAAAGAAATTACTCTCTTCATCTGTAAACCTTAGATTTCCACATATGGAAGATGTGTCTTTTAGTTTCAATCACAATGGAGGTTTGAAAAACTTCAACACAAAAACTGAAATGACAATTGGACAGAATAGAACCCAAGGAGCTGTAAGGGTGAGAATCACTGGTTCATCCATTTATTCAAACTTAGCAATTCAATCCCATTACATGGACAGGATAAATGTTAACTTCAACCACAATGGACAATTTGGAGATTTCACCACCAGTGGAGATGTCACTATTGGCAACATGAAAAATGAAGCAGACATGGCATTCCACCTTTCTGGCAAAGTTATGTCATCATCAGCCAGTGTCAAATCGCCTTTAATGGATAGTGTCAGCATAGACTTTAACCACAATGGAGCACCAACAGACTTTACTACCAAAGCTTCTGTGACCATAGGTGATAAAAAAAATGAAGGAGACATTACATTCCAGATTACAGAAAAGGCTGTCATCTCTTCACTTAATATCAAATCACCATACATGGACAACATCAATGCTAATTTCAATCACGAAGGATTTGCTACGAAATTCACTACCAAGGCTGATGTAACAATTGGTGTTGAAAAAAGTGAAGGTGATGTTTCATTCCAGTGGTCCAACACTTCTACGACAATCTCTGGGAACCTGAAATCGCCATCAATGGAAGATATTACTTTTAACCAGTACACCTTATCTATGCCAACAAAGTATACGTATCATCAGGATTACTCGGTTGGTGATGCAAAAACTGAAACTGATATGATGCTGGACTACACCAACCTGAAGGCCACCTTTGCTTTGACTTCGCCAAAAACTTCCCTAAATTTTGACCACTCTGGTGATATTAAGAATTTCATCTCCGCATTGGACCTAACAACTGAAATGGGAAGATATTCTTCTGAAGCAAAATTCACACTGAATGATAATGTAGAAGCAAGCTTCAAACTCACTTCCCCTGTTGAAGGAATGGAGTCAATTTCAGCACTTTATACCCACAATGGCAAACCATCCAACTTCAGATGCCATGGGGAGTTATCTCTTCCAAATAAAGCTAATGTTGCTGATTTAATTATCAATGTTGAGCAACTAACAAATATGAAAGGAAGTCTTCAAATTAAATCTGAAATCATTCCAGACTTCACAGCGAAATTCTCCAACATACTCACAGAAACATCTCTGCAGTCAATGTCTGAGATCAGTGTTGATGATGAAGTACTCTATGGTATAGCTGTCTCTTTCACCAACAATTCATTCCTTAAAGCTGAACTGGAAGTGAAAACACCAGTAACAGAATATCGTGTTATTAGGCTGTCAGGAATTAATCAAATGGACAAAGACCAGGTAAAAGCATCTGCAGAGCTTCTTATTGGAAGTGATAGCAGTGTAATGGAACTTTCATTTTCTTCTAAACCAAATGTTGCGGGCGTTTTCGAACTCAGATCTGTATACCTACCTCATCTTAAGGCTACCCTAGATGCTACTGGAACACCAACTAATTTTAGAGGAAACTCAGAACTTATTTTTGATGGTGAAAAGAAAGGAAGTGTTGATGCTTCTTTCAATATGGAAGGTATATTAGATGCAAATCTCAAGATGGAACTGCCCCTGGAAAATTACACAAGGATAAATGGAGACATCTCAATTAGGAGCAGTAGTGACTTACTTGACATAAAATCTGCACTGAGTATTGAAGATAGAGAGTTAGTTGACGGCAGTGTTCGAATTACAAACCAAAATCAGCTCTCAGGAGAAATATCTCTGAAATCTATTTACATTAACCCTTTGACTGTGAGCTTTGATTTATCTGGGGATCTTAAAGACTTCAGTACAACAGCCGACATAAGCTACAATAATGAGAAACTGGCTGCAAGTAGTATGAAATTCAATTTCAACCCAACTCCTTTGAAAACATCTGGGTTTGCATCGTTCAACAAGATGTCTTTTGCATACAGCTTAGATAATGCCCCAAAAGATTTTAAATCCCATGCAGAGGTAAAAGTAGAAGAAAAGATGTGGTCTCTTGATGCAACCTGCACTAGAAAGCAAGACATTGATGCTTCATTTAAGGTCATTATTCCAGAGATTGATCCAATTTCTGGAAAATTGTCTCATAGCCAGAGACAGTTCAGATGTGCATCTCATGTCGAGCTTAAAACAGATTCCTCAACAAAATACCAGTATGACATGCTTCTCAAGTGGAGACGTGCCTTGGAAGGAACTTTCAGTGTCAAAACACCCATCAAAGGAATGGAAATTACAAAAGTTGTCCTCAATCATGATGGCACTTTCCCAAACATCAAATCTTCAGCTGAAGTCAATTTCAACAAGACAGACATTTCAGCCGCTGTCAGTCTGATGCATGGTGATTTAACCAAAGGAGATGTTTCCATTAAAACTCCATTTGAAGGATTGGAAGATGTCAGTGTAACATTCTATTCTGAAGGTGATATTGAAAAATTCCAAGCAGGTGGAAAGGTTTTGTATGCTCCAGGAAAAGATATTGAGGCAGGAGTGGAACATAGTTTGTCTGACAATAAGCTGCAGTCCCGCATCCATTTTATGTCACCCTTCACCGATGAAATCGTTGTCAGTGCTAACCATACTGGGGTTCCTATGAATTTTGTGTCAAGTTATGAATTAGCCATGGGTTCAGATAATAGAATCAAATCTGAGACATCTTTGAAAACTGGATTCCAGTATGTTCAATTCAAATCTTCTGTCACTACAACAATGAGTGGGGAAACATTTGTACAAAAGGTTGAGCTAAAGCATGATGGCGCTATAGAGAAGTTCAAAACAGAGGCAATGGTACAAGCAATGGAGAAATTAGTAAGAGTTGATACATCCTTCCAGCTTGAACCAGTCATTGAAGGATCAGCCTCAATCATTACACCATTCTTTGAAAAGTCAGAGGAAATAAAGGTAATCTTTTCACATAGTGGTAGTACTAGTGGATTCCTCTCAACTGGAGAGTTACAGTATTCTCCAAAGAAAAAGATAAGTGGAAAAATTGATTTCCTCAATAATGGTTGGAGGAGGAGAGTTGCAACTGTCGAAGTAAGAACGCCATTTAAGGGCATGGAGGTGAACAAGGTTACCTACCAGCATACAGGCAACTCGGACAGCTTTGATTGTGATGCAGATATTTTTGTTGCTTCCCAGCCACTCAGCGCTACTTTCAAAGGATCTAAAGCACCTTTAAGCATGGATCTGAACATCAAAACACCATTTGAAGGATATGAGAGTTTTGGACTTAACGGGAACTTCCTAAACAACACAATGGGCAGATATAGCGGCAGAATGGAAGCCTCATGGCACCCAAATCAGGCAGTCATTTTTGAAAGTTCATTTGCTGCATTGAGAAATAAAATTGAAGGAAGTGCCTCACTAACAACTCCATTTGTCATGCTCCAACGGTCCTCAATTGAATTCTCACACCAGGAGCTCTCTCAAAAATTCATTGAAAATCTAAAAGCAACTTTCAATGGAAGTAGAATTGTGGATGTTGAGGTTGATCACAGCCTGATGAATGAACGCAAACATGCCATTATTACAATGCGTGCTCCACGCTCCATGAAATTTGACATGAGTGGTGATTTCACTCTGGAAAGTTCAGCAGTTGATGCATCTGCCAACTGGAACACTGAAGATAGTAAAAGTAATCTGAAACTTGAGGGAGTTTATGACATAAGAACAGACAAGAGAATGAACTTCAAACTGACCCGACCTGGACAGGTGATTTCCTATTCCGGATTATTGGACAGAAGACACAGTAAATCTGACCTTGTCTGGGGTATAGGATCAACACAAAAAGCAGGCTATGAAGTCGCAATCAATGATTATGACTCCAGACTGAAACTTATACTTCCAACACGAAGCCTAGAGCTAACCGGGTCCCATCGATCAAAGGTCACAGAAGGGTCATTTCTATGGGATGCTGATGTGGATGAAACAAAGAAGGTTGGCTTCCGTTCTGTGATAGTGCCATCAGATGATGCTATTAAGGCCGATGTTACATTCCAGCTTCCAAGCTTAGGAAAGAGAGTACAAGTCGGTTCAGAGGTTGTGGTCAATAGAGGACGTGTAATTTTCGACGGCAAGACAGAGTTCTCTTACTCTCCTGATGAGAGAAAGAAGATTGTGTTTTCATCAAGGCTTGAGGATAAGTCCCTTGGAGCCACGAAAAACTACAGCTTCAGCATGGGTCTAAGTCATCCATACACGACTGTTGATATCAAACTGGCATCACATGTTGGCAAATCCAAGAACAGATATTCCGCTGGTATGGGGCTTGAGTACCTTAACACACACAGACAGACCAAGACCTTCCAAGTCAATGGACAGATTAACAAACTCAGGAAAACCATCAGCTTCGAGCTGCAGAGTCCAGTCAAATCTATCAGTATTTCGGGCAGTGCTCAGACTGAAGACAAGTTCCGTGTGTCTATCCTCAACATCTATGACCAGAAGATGCCACTGACGACTGTTTTCACCGTCGACCCTGCCACCAGATCACTTGACTTTTACATTAATTATGACCTTGAGAACCCAAGTAGTGAGTTCCACATAAATGCCAAGTATGTGAACAGTTCTGCATTGGCTGCCGAGGTGTTCCATATCGTCAACCGTGAACGAGTGACTGACATTCTGGTTACTGCCAGACTCAACAACTCTCACCTCCTTCACACAAGAGTTCACTGGAGACCGGAAATGATCAAGGAATACGAGACTGTTCGAGAGAGGAAACTTGAGGACTACAAGAGACGCCTGGAAATTTCAGCAGTTAAAGTAGAGGCTGCTGTAATTGAGGAAACTGTTGAGAAGTTTAAGATGATCTGGGAAGCTGTTGTAGAGGAGATTGGCCAAGACAATGCTCTAGCTATAGAGGCTGCTGTTATCCCCATGTTTGAAGATGGACTGAGGACATATGCACAAGTGCAGGGACATGTGCAGGCAAACTTCCTTCCATTTGCCTTGGATTTGGCCAACATAACACAGTACAAGTACAACAGATTTGTACAAACATACAGAGAGTTTTCACAGGCAGTAAAGCTTCCAGAAACAATGAAGGATCTTGACTTCCTGTCGTCTGCCAGACAACCATTGGAGAAGCCCTTTAATTATGCACTGGATCTGATCAAGATCCCTGCGAAGCACCTTCCAACCCAGGTGACCGGAGCACTGAAATACCCGGCCAAATATATGTTTTCTAATATGGATACTGCTATGTTGGAGCAGCTTAACAAGAACTGGGAACTTGAACACCATCTAGAATCTGTCATTGAAACCATTCTTCTTGCAATTGAGGAGGAAGCTGAGGAAGGCATACTTAAATTGAAGAGTATCATTCTCAACTCGGCACAATCCCCAATCACTGTGTACGACCCAACCCACGGGGAGATCCAGGCAGAATTTCACTCACCCATACCACTGAAGTCTCTGGATGAGCTACCTGTTATCAATATTGAAAGATATATTAACATGGTTATGAAAACTCGCAGTAGAAAGACAGAAAATGTTCCCAGCAAGACATCAGAATGGTTGCCACCATTTACTGGTGTTGCCAGTATTACCAGCGGTCATAAAATCACAACTTTCGACGGGTATATCTATGACCTTGATGCTGACTGCACGTTTGTGCTTGTCCGTGATTTCAGGAATGGCAACTTCAGTATTATTCTGAACAACAATGATGGGACAACTCTGTCAATCCTTTCACATGGAAAACCAATAGAAATCAAGCAGAGCGGAGAGATCTCTGTTGCCATGGAGCCTGTCACTCTCCCATACAAAGAAAACAACATCACAATTACATCATCAGATGACGGAATCATCAGCATTGATGGGGCTAACCACTTCAAGGTAGATTATGACCTCTCAGTCGATCACATCGATGTAGAGATCAATGGATGGTATTACGGCAAAACTGCAGGACTTCTTGGTACCTTTGACAACGAGCCCTCAAATGACCTTATGACCTCCTTTGGAAAAATCATCAATAATCCTAAACGTTTCGCCAGAACTTGGGATGTTGGAAACACAAATTGCCGTTAA PRIMER_TASK=generic PRIMER_PICK_LEFT_PRIMER=3 PRIMER_PICK_RIGHT_PRIMER=3 PRIMER_OPT_SIZE=18 PRIMER_MIN_SIZE=15 PRIMER_MAX_SIZE=21 PRIMER_MAX_NS_ACCEPTED=1 PRIMER_PRODUCT_SIZE_RANGE=75-150 P3_FILE_FLAG=1 PRIMER_EXPLAIN_FLAG=1 PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/home/sam/software/primer3-2.4.0/src/primer3_config/ PRIMER_LEFT_NUM_RETURNED=5 PRIMER_RIGHT_NUM_RETURNED=5 PRIMER_INTERNAL_NUM_RETURNED=0 PRIMER_PAIR_NUM_RETURNED=5 PRIMER_PAIR_0_PENALTY=0.160101 PRIMER_LEFT_0_PENALTY=0.109387 PRIMER_RIGHT_0_PENALTY=0.050714 PRIMER_LEFT_0_SEQUENCE=TTACGCCACGGCAACTGT PRIMER_RIGHT_0_SEQUENCE=CGCAGTGCCAACAAGCTG PRIMER_LEFT_0=1347,18 PRIMER_RIGHT_0=1471,18 PRIMER_LEFT_0_TM=59.891 PRIMER_RIGHT_0_TM=60.051 PRIMER_LEFT_0_GC_PERCENT=55.556 PRIMER_RIGHT_0_GC_PERCENT=61.111 PRIMER_LEFT_0_SELF_ANY_TH=9.11 PRIMER_RIGHT_0_SELF_ANY_TH=10.11 PRIMER_LEFT_0_SELF_END_TH=0.13 PRIMER_RIGHT_0_SELF_END_TH=0.00 PRIMER_LEFT_0_HAIRPIN_TH=42.06 PRIMER_RIGHT_0_HAIRPIN_TH=0.00 PRIMER_LEFT_0_END_STABILITY=3.5500 PRIMER_RIGHT_0_END_STABILITY=4.2400 PRIMER_PAIR_0_COMPL_ANY_TH=10.66 PRIMER_PAIR_0_COMPL_END_TH=0.00 PRIMER_PAIR_0_PRODUCT_SIZE=125 PRIMER_PAIR_1_PENALTY=0.233503 PRIMER_LEFT_1_PENALTY=0.107750 PRIMER_RIGHT_1_PENALTY=0.125753 PRIMER_LEFT_1_SEQUENCE=CGTGAGCATCCGAGGCAT PRIMER_RIGHT_1_SEQUENCE=CTGAGCGGAGACTGGTGC PRIMER_LEFT_1=3266,18 PRIMER_RIGHT_1=3362,18 PRIMER_LEFT_1_TM=59.892 PRIMER_RIGHT_1_TM=60.126 PRIMER_LEFT_1_GC_PERCENT=61.111 PRIMER_RIGHT_1_GC_PERCENT=66.667 PRIMER_LEFT_1_SELF_ANY_TH=7.91 PRIMER_RIGHT_1_SELF_ANY_TH=0.00 PRIMER_LEFT_1_SELF_END_TH=0.00 PRIMER_RIGHT_1_SELF_END_TH=0.00 PRIMER_LEFT_1_HAIRPIN_TH=31.82 PRIMER_RIGHT_1_HAIRPIN_TH=0.00 PRIMER_LEFT_1_END_STABILITY=4.4000 PRIMER_RIGHT_1_END_STABILITY=5.0100 PRIMER_PAIR_1_COMPL_ANY_TH=0.78 PRIMER_PAIR_1_COMPL_END_TH=0.78 PRIMER_PAIR_1_PRODUCT_SIZE=97 PRIMER_PAIR_2_PENALTY=0.251305 PRIMER_LEFT_2_PENALTY=0.125552 PRIMER_RIGHT_2_PENALTY=0.125753 PRIMER_LEFT_2_SEQUENCE=CGCAGATGAAGCCCGTGA PRIMER_RIGHT_2_SEQUENCE=CTGAGCGGAGACTGGTGC PRIMER_LEFT_2=3253,18 PRIMER_RIGHT_2=3362,18 PRIMER_LEFT_2_TM=60.126 PRIMER_RIGHT_2_TM=60.126 PRIMER_LEFT_2_GC_PERCENT=61.111 PRIMER_RIGHT_2_GC_PERCENT=66.667 PRIMER_LEFT_2_SELF_ANY_TH=0.00 PRIMER_RIGHT_2_SELF_ANY_TH=0.00 PRIMER_LEFT_2_SELF_END_TH=0.00 PRIMER_RIGHT_2_SELF_END_TH=0.00 PRIMER_LEFT_2_HAIRPIN_TH=0.00 PRIMER_RIGHT_2_HAIRPIN_TH=0.00 PRIMER_LEFT_2_END_STABILITY=4.3500 PRIMER_RIGHT_2_END_STABILITY=5.0100 PRIMER_PAIR_2_COMPL_ANY_TH=0.00 PRIMER_PAIR_2_COMPL_END_TH=0.00 PRIMER_PAIR_2_PRODUCT_SIZE=110 PRIMER_PAIR_3_PENALTY=0.299294 PRIMER_LEFT_3_PENALTY=0.173382 PRIMER_RIGHT_3_PENALTY=0.125912 PRIMER_LEFT_3_SEQUENCE=CGGCGCGAAAGTTGAAGG PRIMER_RIGHT_3_SEQUENCE=CCTTCAGCTCGACCACCG PRIMER_LEFT_3=1922,18 PRIMER_RIGHT_3=2053,18 PRIMER_LEFT_3_TM=59.827 PRIMER_RIGHT_3_TM=60.126 PRIMER_LEFT_3_GC_PERCENT=61.111 PRIMER_RIGHT_3_GC_PERCENT=66.667 PRIMER_LEFT_3_SELF_ANY_TH=12.10 PRIMER_RIGHT_3_SELF_ANY_TH=0.00 PRIMER_LEFT_3_SELF_END_TH=0.00 PRIMER_RIGHT_3_SELF_END_TH=0.00 PRIMER_LEFT_3_HAIRPIN_TH=0.00 PRIMER_RIGHT_3_HAIRPIN_TH=40.25 PRIMER_LEFT_3_END_STABILITY=3.4600 PRIMER_RIGHT_3_END_STABILITY=4.9400 PRIMER_PAIR_3_COMPL_ANY_TH=11.23 PRIMER_PAIR_3_COMPL_END_TH=14.04 PRIMER_PAIR_3_PRODUCT_SIZE=132 PRIMER_PAIR_4_PENALTY=0.299294 PRIMER_LEFT_4_PENALTY=0.173382 PRIMER_RIGHT_4_PENALTY=0.125912 PRIMER_LEFT_4_SEQUENCE=CCGGCGCGAAAGTTGAAG PRIMER_RIGHT_4_SEQUENCE=CCTTCAGCTCGACCACCG PRIMER_LEFT_4=1921,18 PRIMER_RIGHT_4=2053,18 PRIMER_LEFT_4_TM=59.827 PRIMER_RIGHT_4_TM=60.126 PRIMER_LEFT_4_GC_PERCENT=61.111 PRIMER_RIGHT_4_GC_PERCENT=66.667 PRIMER_LEFT_4_SELF_ANY_TH=12.10 PRIMER_RIGHT_4_SELF_ANY_TH=0.00 PRIMER_LEFT_4_SELF_END_TH=0.00 PRIMER_RIGHT_4_SELF_END_TH=0.00 PRIMER_LEFT_4_HAIRPIN_TH=0.00 PRIMER_RIGHT_4_HAIRPIN_TH=40.25 PRIMER_LEFT_4_END_STABILITY=3.0200 PRIMER_RIGHT_4_END_STABILITY=4.9400 PRIMER_PAIR_4_COMPL_ANY_TH=5.41 PRIMER_PAIR_4_COMPL_END_TH=9.34 PRIMER_PAIR_4_PRODUCT_SIZE=133 =
Parses out sequence id, left, and right primers and creates the proper tab-delimited primer sequences file needed by primersearch
Runs primersearch using the newly created primer sequences file and the target FastA file that was used to generate our primers in Primer3
%%bash
cd /home/sam/analyses/20181129_geoduck_vtg_primers/
seq_id=$(grep "SEQUENCE_ID=" /home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_primers_default_format.txt | sed 's/SEQUENCE_ID=//')
left_primer=$(grep "PRIMER_LEFT_0_SEQUENCE=" /home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_primers_default_format.txt | sed 's/PRIMER_LEFT_0_SEQUENCE=//')
right_primer=$(grep "PRIMER_RIGHT_0_SEQUENCE=" /home/sam/analyses/20181129_geoduck_vtg_primers/20181129_primer3_primers_default_format.txt | sed 's/PRIMER_RIGHT_0_SEQUENCE=//')
printf "%s\t" "${seq_id}" "${left_primer}" "${right_primer}" > /home/sam/analyses/20181129_geoduck_vtg_primers/20181129_emboss_primers.txt
# Add newline to end of file
printf "\n" >> /home/sam/analyses/20181129_geoduck_vtg_primers/20181129_emboss_primers.txt
/home/sam/software/EMBOSS-6.6.0/emboss/primersearch \
-auto \
/home/sam/data/geoduck/transcriptomes/transdecoder_fasta_splits/TRINITY_DN51983_c0_g1_i8.p1.cds \
/home/sam/analyses/20181129_geoduck_vtg_primers/20181129_emboss_primers.txt
cat /home/sam/analyses/20181129_geoduck_vtg_primers/TRINITY_DN51983_c0_g1_i8.primersearch
cat: /home/sam/analyses/20181129_geoduck_vtg_primers/TRINITY_DN51983_c0_g1_i8.primersearch: No such file or directory
%%bash
cd /home/sam/analyses/20181129_geoduck_vtg_primers/
ls
20181129_emboss_primers.txt 20181129_primer3_params.txt 20181129_primer3_primers_default_format.txt 20181129_primer3_primers.txt TRINITY_DN51983_c0_g1_i8.p1.cds.for TRINITY_DN51983_c0_g1_i8.p1.cds.rev trinity_dn51983_c0_g1_i8.primersearch
%%bash
cat /home/sam/analyses/20181129_geoduck_vtg_primers/trinity_dn51983_c0_g1_i8.primersearch
Primer name TRINITY_DN51983_c0_g1_i8.p1.cds Amplimer 1 Sequence: TRINITY_DN51983_c0_g1_i8.p1 TTACGCCACGGCAACTGT hits forward strand at 1348 with 0 mismatches CGCAGTGCCAACAAGCTG hits reverse strand at [13013] with 0 mismatches Amplimer length: 125 bp
Primers match up to their source sequence, as expected. Now, to test the primers on the rest of the transcriptome to ensure specificity.
Sets variables for file/folder paths
Runs for loop over all individual CDS FastA files:
tr to convert filenames to lowercaseprimersearch on each CDS FastA filegrep to evaluate if the word "Amplimer" is found in the resulting output file; if it is not, the file is deleted.%%bash
cd /home/sam/analyses/20181129_geoduck_vtg_primers/
fasta_loc="/home/sam/data/geoduck/transcriptomes/transdecoder_fasta_splits/"
primersearch="/home/sam/software/EMBOSS-6.6.0/emboss/primersearch"
primers="/home/sam/analyses/20181129_geoduck_vtg_primers/20181129_emboss_primers.txt"
time \
for fasta in ${fasta_loc}*.cds
do
fasta_no_path=$(echo ${fasta##*/})
fasta_no_ext=$(echo ${no_path%%.*})
fasta_no_ext_lower=$(echo ${fasta_no_ext} | tr '[:upper:]' '[:lower:]')
${primersearch} -auto ${fasta} ${primers}
if ! grep --quiet "Amplimer" "${fasta_no_ext_lower}.primersearch"
then rm ${fasta_no_ext_lower}.primersearch
fi
done
Process is interrupted.
Killed it to change code to allow primer mismatches.
Also fix extension removal.
%%bash
cd /home/sam/analyses/20181129_geoduck_vtg_primers/
fasta_loc="/home/sam/data/geoduck/transcriptomes/transdecoder_fasta_splits/"
primersearch="/home/sam/software/EMBOSS-6.6.0/emboss/primersearch"
primers="/home/sam/analyses/20181129_geoduck_vtg_primers/20181129_emboss_primers.txt"
time \
for fasta in ${fasta_loc}*.cds
do
fasta_no_path=$(echo ${fasta##*/})
fasta_no_ext=$(echo ${fasta_no_path%%.*})
fasta_no_ext_lower=$(echo ${fasta_no_ext} | tr '[:upper:]' '[:lower:]')
${primersearch} -auto ${fasta} ${primers} 20
if ! grep --quiet "Amplimer" "${fasta_no_ext_lower}.primersearch"
then rm ${fasta_no_ext_lower}.primersearch
fi
done
real 208m42.396s user 76m45.956s sys 79m27.744s
%%bash
cd /home/sam/analyses/20181129_geoduck_vtg_primers/
# Check contents of files with matches
for file in *.primersearch
do
echo "FILE: ${file}"
echo ""
cat ${file}
echo "----------------------------------"
echo ""
done
# Copy data to Gannet
cd /home/sam/analyses/
rsync \
--archive \
--relative \
./20181129_geoduck_vtg_primers/ gannet:/volume1/web/Atumefaciens
FILE: trinity_dn51983_c0_g1_i4.primersearch Primer name TRINITY_DN51983_c0_g1_i8.p1.cds Amplimer 1 Sequence: TRINITY_DN51983_c0_g1_i4.p1 TTACGCCACGGCAACTGT hits forward strand at 1348 with 0 mismatches CGCAGTGCCAACAAGCTG hits reverse strand at [12569] with 0 mismatches Amplimer length: 125 bp ---------------------------------- FILE: trinity_dn51983_c0_g1_i8.primersearch Primer name TRINITY_DN51983_c0_g1_i8.p1.cds Amplimer 1 Sequence: TRINITY_DN51983_c0_g1_i8.p1 TTACGCCACGGCAACTGT hits forward strand at 1348 with 0 mismatches CGCAGTGCCAACAAGCTG hits reverse strand at [13013] with 0 mismatches Amplimer length: 125 bp ----------------------------------