[Bioperl-l] problem parsing WU-blast output
Joseph Fass
joseph.fass at gmail.com
Wed Oct 24 21:43:08 UTC 2007
Hi Dave,
here's my code, followed by a sample wu-blast report (below).
I'm using bioperl version 1.4
Thanks for looking into it, and I'd be very curious to know what you find.
Joe
***************code***************
#!/usr/bin/perl -w
use strict;
use Bio::SearchIO;
use Bio::SeqIO;
# note: processes only the first result (first query sequence) of the blast
report!
my $usage = "usage: collect_hits.pl <blast report> <sequence database
(fasta)> <output_file>\n";
my $reportfile = shift || die $usage;
# open Blast report for reading in hit IDs
my $in = Bio::SearchIO->new(-file => $reportfile,
-format => 'blast');
# open database (fasta format) for searching for hit IDs
my $databasefile = shift || die $usage;
# open output file (fasta format) for writing out IDs and sequences of Blast
hits
my $hitsfile = shift || die $usage;
my $out = Bio::SeqIO->new(-file => ">$hitsfile",
-format => 'fasta');
# get result from Blast report (only one!)
my $result = $in->next_result(); print "query: " .
$result->query_name()."\n";
#my $dummy = $result->next_hit; print "1st hit: " . $dummy->name() . "\n"; #
for debugging
#$dummy = $result->next_hit; print "2nd hit: " . $dummy->name() . "\n"; #
debugging
# then loop through hits, finding matching IDs in database and writing out
full fasta-format sequences
while (my $hit = $result->next_hit) {
# find hit ID in database file to fill in sequence and write corresponding
sequence to output file
my $seq = Bio::Seq->new( -id => $hit->name() ); # create Seq object with
hit name
print "seq_id: " . $seq->id."\n";
# open database file
my $db = Bio::SeqIO->new(-file => $databasefile,
-format => 'fasta');
# now look through database sequences to pull out correct sequence for ID
from Blast hit
my $still_looking = 1;
do {
my $db_seq = $db->next_seq();
#print $seq->id() . " ... " . $db_seq->id() . "\n";
if ($seq->id() eq $db_seq->id()) {
$seq->seq($db_seq->seq);
$still_looking = 0;
} # if
} while ($still_looking);
# then write sequence (in fasta format) to output_file
$out->write_seq($seq);
print "found a sequence\n";
} # while
********************blast report*************************
BLASTN 2.0MP-WashU [04-May-2006] [linux26-x64-I32LPF64 2006-05-10T17:22:28]
Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.
Reference: Gish, W. (1996-2006) http://blast.wustl.edu
Notice: this program and its default parameter settings are optimized to
find
nearly identical sequences rapidly. To identify weak protein similarities
encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX.
Query= 962_177_14574088_5489_46110_045.ab1
(676 letters)
>Unfiltered+1
TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC
AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
CCCAACAATCCTACTT
>Unfiltered-1
AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
TCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAGCATGG
CCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGGCTTTC
CCTGTAATTAACAAATTGATTACCATTAGGAGAAGCAAGTGTGATGATGTCGAGTGAGAG
TAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAAATCGGCATCAGCATGT
TTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAACACGGTAGTTTTCAAGA
TTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCATATTTG
TTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAGAAGGGGTTGTTTTGTGTTCTT
GAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAAAGGAGACA
GAAAGTGATGCCAGGA
Database: ../Cowpea1X/Cowpea_all_GSS_clean.fasta
260,642 sequences; 158,813,828 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done
Smallest
Sum
High
Expectation
Sequences producing High-scoring Segment Pairs: Score
E(N) N
962_177_14574088_5489_46110_045.ab1 3380 2.0e-147
1
962_191_14579666_5489_46288_070.ab1 2705 6.4e-117
1
962_307_14625348_5489_47135_029.ab1 2314 2.8e-99
1
962_370_14650238_5489_47797_032.ab1 2054 1.8e-87
1
962_400_14670294_5489_48184_096.ab1 2040 7.2e-87
1
962_79_14536329_16654_45346_033.ab1 1928 7.8e-82
1
962_187_14578095_5489_46263_022.ab1 1764 2.3e-74
1
962_309_14626130_16654_47155_078.ab1 1263 1.1e-51
1
962_45_14523164_5489_45006_087.ab1 1160 3.7e-47
1
962_394_14659720_16654_47971_045.ab1 1146 1.6e-46
1
962_61_14529390_16654_45210_020.ab1 1077 2.1e-43
1
962_177_14574088_16654_46114_045.ab1 955 7.5e-38
1
962_282_14615493_16654_46934_055.ab1 891 1.3e-34
1
962_248_14601477_16654_46676_055.ab1 687 1.0e-25
1
962_196_14581545_16654_48111_005.ab1 633 3.0e-23
1
>962_177_14574088_5489_46110_045.ab1
Length = 676
Plus Strand HSPs:
Score = 3380 (513.2 bits), Expect = 2.0e-147, P = 2.0e-147
Identities = 676/676 (100%), Positives = 676/676 (100%), Strand = Plus /
Plus
Query: 1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
Query: 61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120
Query: 121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180
Query: 181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240
Query: 241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300
Query: 301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360
Query: 361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420
Query: 421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480
Query: 481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540
Query: 541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600
Query: 601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660
Query: 661 CCCAACAATCCTACTT 676
||||||||||||||||
Sbjct: 661 CCCAACAATCCTACTT 676
>962_191_14579666_5489_46288_070.ab1
Length = 664
Plus Strand HSPs:
Score = 2705 (411.9 bits), Expect = 6.4e-117, P = 6.4e-117
Identities = 541/541 (100%), Positives = 541/541 (100%), Strand = Plus /
Plus
Query: 136 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA
195
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA 60
Query: 196 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
255
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
120
Query: 256 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
315
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
180
Query: 316 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
375
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
240
Query: 376 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
435
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
300
Query: 436 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
495
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
360
Query: 496 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
555
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
420
Query: 556 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
615
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 421 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
480
Query: 616 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
675
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 481 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
540
Query: 676 T 676
|
Sbjct: 541 T 541
>962_307_14625348_5489_47135_029.ab1
Length = 687
Minus Strand HSPs:
Score = 2314 (353.2 bits), Expect = 2.8e-99, P = 2.8e-99
Identities = 558/629 (88%), Positives = 558/629 (88%), Strand = Minus /
Plus
Query: 676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
||||||||||||||||||||||||||||| ||||||||||||| ||| ||||||||||
Sbjct: 72 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
131
Query: 617 -ATTT-A-GAGA-GAAA---TTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGA
565
|| | | | || |||| || |||||||||||||||||| | |||||| | ||
Sbjct: 132 CATCTCATGTGAAGAAAAATTTACAAGTTAGAATAAAAAAAAAT-TAGTTC-G-----GA
184
Query: 564 AAAAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTC
505
|| || |||||||||||||||||| |||||||| |||| ||||||||||| |||||
Sbjct: 185 AAGCAG----TACTTGAAATCTGTGAGGATTGTTAACGGGTACGGCGAGTTTGACTATTC
240
Query: 504 TGAGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
445
||||||||||||| || | |||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 TGAGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
300
Query: 444 GAGCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
385
||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 301 GAGCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
360
Query: 384 TGGCTTTCCCTGTAATTAACAAATTGATTAC---CA-T--T--AGGAGAAGCAAGTGTGA
333
||||| ||||||||||||||||||||||||| || | | |||||||||||||||||
Sbjct: 361 TGGCTCTCCCTGTAATTAACAAATTGATTACAATCAATGGTGCAGGAGAAGCAAGTGTGA
420
Query: 332 TGATGTCGAGTGAGAGTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAA
273
|||| | ||||||| ||| ||||||||||||||||||||||||||||||| ||||||||
Sbjct: 421 TGATTTTGAGTGAG--TAGCGATTAGTTGATTACTTACCATTAAGGACAACTAGGAGGAA
478
Query: 272 ATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
213
||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 479 ATCGGCATCAGCATGGTGAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
538
Query: 212 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCG
153
|||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||
Sbjct: 539 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTCTGGAGGACACG
598
Query: 152 AAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAA 96
|||||||||||||| ||| ||||||||||||||||||| |||| ||| |||||||||
Sbjct: 599 AAGGTGACCATATTGGTTTCTGAATAGAGTGTGGAACCACCTGTCAGAGTCGAAGTAGAA
658
Query: 95 GGGGTTGTTTTGTGTTCTTGAATCAGACT 67
|||||| |||||| |||||| || |||
Sbjct: 659 GGGGTTATTTTGTCCTCTTGATTCCAACT 687
>962_370_14650238_5489_47797_032.ab1
Length = 581
Plus Strand HSPs:
Score = 2054 (314.2 bits), Expect = 1.8e-87, P = 1.8e-87
Identities = 468/514 (91%), Positives = 468/514 (91%), Strand = Plus / Plus
Query: 1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
|||| |||||||||||||||||||| ||||||||||||||| | | ||||| |||||||
Sbjct: 74 TCCTTGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGGGA--A-CACCAAGAGAGCC
130
Query: 61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
| |||||||| || |||||| |||||| ||||||||||||||| ||| ||||||| |
Sbjct: 131 AAGAAGAGTCGGAATCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
190
Query: 119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct: 191 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
250
Query: 178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 251 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
310
Query: 238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct: 311 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
370
Query: 298 AGTAATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCT--A--AT-
352
||||||||||||||| |||||| |||| | ||||||||||||||||||||| | ||
Sbjct: 371 AGTAATCAACTAATCGCTACTC--ACTCAAAATCATCACACTTGCTTCTCCTGCACCATT
428
Query: 353 G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGG
409
| ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct: 429 GATTGTAATCAATTTGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGG
488
Query: 410 CAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
469
||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct: 489 CAGAGACTCCTACATTCTTGAGCAGGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
548
Query: 470 CTTTTTGGTTAACCCTAATGAAAACGAGAATCTC 503
||||||||| |||||| | || ||||||||||||
Sbjct: 549 CTTTTTGGT-AACCCTGACGACAACGAGAATCTC 581
>962_400_14670294_5489_48184_096.ab1
Length = 641
Plus Strand HSPs:
Score = 2040 (312.1 bits), Expect = 7.2e-87, P = 7.2e-87
Identities = 488/564 (86%), Positives = 488/564 (86%), Strand = Plus / Plus
Query: 123 ACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCC
182
||||||||||| ||| |||||||||||||||| |||||||| ||||||||||||||||||
Sbjct: 1 ACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAACGCTCC 60
Query: 183 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
242
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
120
Query: 243 CTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAA
302
|||||||||||| | ||||||||||||||||||||||| |||||||||||||||||||||
Sbjct: 121 CTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTAAGTAA
180
Query: 303 TCAACTAATCACTACTCTCACTCGA-CATCATCACA--CTTGCTTCT-C-CTAATG---G
354
|||||||||| |||||| | | | | ||||| ||| ||| || || | | | || |
Sbjct: 181 TCAACTAATCGCTACTCACTCACAATCATCA-CACTTTCTTTCTCCTGCACCATTGATTG
239
Query: 355 TAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
414
||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct: 240 TAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
299
Query: 415 ACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
474
|||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 300 ACTCCTACATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
359
Query: 475 TGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACA
534
||||||||||| | || |||||||||||||||||| |||||||||||||||| |||||||
Sbjct: 360 TGGTTAACCCTGACGACAACGAGAATCTCAGAATAGTCAAACTCGCCATACCCGTTAACA
419
Query: 535 ACCCTCACAGATTTCAAGTAGCGCCTTTTTT-CTGATCCTGAACTATAACTTTTTTTATT
593
| |||||||||||||||||| ||||| || || | | | ||| | ||
Sbjct: 420 ATCCTCACAGATTTCAAGTACTGCCTTCCGAACTAATTTTTT--T-TCCCTTCTAACATG
476
Query: 594 CTAACTTGCAATTTCTCTCTAAAT-TAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAG
652
| | || | || | | | |||||||||| ||| ||||||||||||| |||||
Sbjct: 477 CGATTTTTCTCCA-CT-TGTGATGATAAATGCTTGGCCTGTAGGACTTTTTCCTATCTAG
534
Query: 653 CACAGAAGCCCAACAATCCTACTT 676
||||||||||||||||||||||||
Sbjct: 535 CACAGAAGCCCAACAATCCTACTT 558
>962_79_14536329_16654_45346_033.ab1
Length = 675
Plus Strand HSPs:
Score = 1928 (295.3 bits), Expect = 7.8e-82, P = 7.8e-82
Identities = 472/553 (85%), Positives = 472/553 (85%), Strand = Plus / Plus
Query: 77 AAGAA-CACAAAACAACCCCTTCTACTTCAGCTCCGACA-G-G-TTCCACACTCTATTCA
132
|||| || || |||||||||||||||||| |||||||| | | ||||||||||||| ||
Sbjct: 6 AAGAGTCAGAAGACAACCCCTTCTACTTCAACTCCGACAAGTGGTTCCACACTCTATACA 65
Query: 133 GCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTC
192
| ||| |||||||||||||||| || ||||| |||||||||||||||||| |||||||||
Sbjct: 66 GAAACCAATATGGTCACCTTCGTGTGCTCCAGAGGTTCGACCAACGCTCCGAACAAATTC
125
Query: 193 AGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
252
|||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct: 126 AGAATCTTGAAAACTACCGTCTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
185
Query: 253 CTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATC
312
|| | || |||||||||||||| ||||| |||||||||| |||||||||| |||||||
Sbjct: 186 CTCACCACGCTGATGCCGATTTGCTCCTATTTGTCCTTAACGGTAAGTAATAAACTAATA
245
Query: 313 ACTACTC-TCACTCGACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTT
364
| || | || || | | ||| | |||||||||| || || || ||||| ||
Sbjct: 246 ATCGCTAGTAACA-GA-A-CTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTT
302
Query: 365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
|||||||||||| | || || |||| |||||||||||||| |||||||| |||| |||
Sbjct: 303 GTTAATTACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACAT
362
Query: 425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
||||||||||||| |||| ||||| |||||||||||||||| |||||||||| |||||||
Sbjct: 363 TCTTGAGCAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCC
422
Query: 485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
| | || |||||| |||||||||||||||||||||||||||| ||||||||||||||||
Sbjct: 423 TGACGACAACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAT
482
Query: 545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
|||||||||| ||||||| ||||| | ||||| | |||||||| || |||||||||
Sbjct: 483 ATTTCAAGTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCAT
539
Query: 605 TTTCTCTCTAAAT 617
|||||||||||||
Sbjct: 540 TTTCTCTCTAAAT 552
Score = 1188 (184.3 bits), Expect = 2.1e-48, P = 2.1e-48
Identities = 358/471 (76%), Positives = 358/471 (76%), Strand = Plus / Plus
Query: 220 AGTTCAAGTCCAAACCCAACACCCTCCTTCTTC-CTAAACATGCTGATGCCGATTTCCTC
278
||| ||| |||| || | || || ||| || | | | || || | ||||
Sbjct: 159 AGTCCAAACCCAACACC--CTCCTTC-TTCCTCACCACGC-TGATGCCGATTTGCTCCTA
214
Query: 279 CTTGTTGTCCTTAATG-GTAAGTAATCAACTAATCACTACTCTCACTCGACATCATCACA
337
|||| | | |||| ||| | | ||||| ||| | || || ||||
Sbjct: 215 TTTGTCCTTAACGGTAAGTAA-TAAACTAATAATCGCTAGTAACAGA--ACTTCATATTT
271
Query: 338 -CTTGCTTCTCCTAA-TGGTA---ATCAATTTGTTAATTACAGGGAAAGCCATACTCACC
392
||| || | | || || || ||||| |||||||||||||| | || || ||||
Sbjct: 272 GCTT-CTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGGACCCGTAATCACA
330
Query: 393 TTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATC
452
|||||||||||||| |||||||| |||| |||||||||||||||| |||| ||||| |||
Sbjct: 331 TTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGATGCCCAGAAAATC
390
Query: 453 CCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATC
512
||||||||||||| |||||||||| |||||||| | || |||||| ||||||||||||||
Sbjct: 391 CCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGATCTCAGAATAATC
450
Query: 513 AAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCCTTTTTTCTGATCC
572
|||||||||||||| |||||||||||||||| |||||||||| ||||||| ||||| |
Sbjct: 451 AAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCCTTTT--CTGATTC
508
Query: 573 TGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T----A-AA-TGCT
625
||||| | |||||||| || ||||||||| ||||||||||||| | | || || |
Sbjct: 509 CCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGTGACGATAAATGTT
567
Query: 626 TGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACTT 676
|| ||| ||||||||||| | |||||||||||||||||||| ||||||||
Sbjct: 568 TGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCTACTT 618
>962_187_14578095_5489_46263_022.ab1
Length = 590
Plus Strand HSPs:
Score = 1764 (270.7 bits), Expect = 2.3e-74, P = 2.3e-74
Identities = 410/453 (90%), Positives = 410/453 (90%), Strand = Plus / Plus
Query: 1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
||||||||||||||||||||||||| ||||||||||||||| | ||||||| |||||||
Sbjct: 144 TCCTGGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGG--G-AGCACCAAGAGAGCC
200
Query: 61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
| |||||||| || ||||| |||||| ||||||||||||||| ||| ||||||| |
Sbjct: 201 AAGAAGAGTCGGAACCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
260
Query: 119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct: 261 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
320
Query: 178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 321 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
380
Query: 238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct: 381 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
440
Query: 298 AGTAATCAACTAATCACTACTCTCACTCGACA-TCATCACACTTGCTT-CTCCT--A--A
351
||||||||||||||| |||||| |||| ||| ||||||||||| ||| ||||| | |
Sbjct: 441 AGTAATCAACTAATCGCTACTC--ACTC-ACAATCATCACACTTTCTTTCTCCTGCACCA
497
Query: 352 T-G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGAC
407
| | |||||||||| |||||||||||||| ||||||||||||||||||||||||||||
Sbjct: 498 TTGATTGTAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGAC
557
Query: 408 GGCAGAGACTCCTTCATTCTTGAGCAAGGCCAT 440
||||||||||||| |||||||||||||||||||
Sbjct: 558 GGCAGAGACTCCTACATTCTTGAGCAAGGCCAT 590
>962_309_14626130_16654_47155_078.ab1
Length = 531
Plus Strand HSPs:
Score = 1263 (195.6 bits), Expect = 1.1e-51, P = 1.1e-51
Identities = 281/312 (90%), Positives = 281/312 (90%), Strand = Plus / Plus
Query: 365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
|||||||||||| | ||||||||||||||||||||||||||||||||||||||| |||||
Sbjct: 1 GTTAATTACAGGAAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCATTCAT 60
Query: 425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
||||||||||||||||| ||| | ||||||||||||||||||||||||||||||||||||
Sbjct: 61 TCTTGAGCAAGGCCATGTTCAAAGGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
120
Query: 485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
||| || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct: 121 TAACGACAACGACAATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAA
180
Query: 545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
|||||||||| ||||| | | ||| | ||||||||| ||||||||||||||| |||
Sbjct: 181 ATTTCAAGTACTGCCTTCTGT--GATTCCATACTATAACTGTTTTTATTCTAACTTTCAA
238
Query: 605 TTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
||||||||||||| ||||| || | ||| ||||||||||||| |||||||||||||| ||
Sbjct: 239 TTTCTCTCTAAAT-AAATGTTTCTCCTGTAGGACTTTTTCCTATCTAGCACAGAAGCTCA
297
Query: 665 ACAATCCTACTT 676
|||||||||||
Sbjct: 298 GCAATCCTACTT 309
>962_45_14523164_5489_45006_087.ab1
Length = 697
Plus Strand HSPs:
Score = 1160 (180.1 bits), Expect = 3.7e-47, P = 3.7e-47
Identities = 302/364 (82%), Positives = 302/364 (82%), Strand = Plus / Plus
Query: 327 ACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTTGTTAATTACAGGGAA
379
| | | ||| | |||||||||| || || || ||||| ||||||||||||||
Sbjct: 13 AGAACTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGG 72
Query: 380 AGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCA
439
| || || |||| |||||||||||||| |||||||| |||| |||||||||||||||| |
Sbjct: 73 ACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGA
132
Query: 440 TGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAA
499
||| ||||| |||||||||||||||| |||||||||| |||||||| | || |||||| |
Sbjct: 133 TGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGA
192
Query: 500 TCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCC
559
||||||||||||||||||||||||||| |||||||||||||||| |||||||||| |||
Sbjct: 193 TCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCC
252
Query: 560 TTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T
618
|||| ||||| | ||||| | |||||||| || ||||||||| ||||||||||||| |
Sbjct: 253 TTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGT
309
Query: 619 -A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCT
672
| | | || ||| ||| ||||||||||| | |||||||||||||||||||| ||||
Sbjct: 310 GACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCT
369
Query: 673 ACTT 676
||||
Sbjct: 370 ACTT 373
>962_394_14659720_16654_47971_045.ab1
Length = 708
Minus Strand HSPs:
Score = 1146 (178.0 bits), Expect = 1.6e-46, P = 1.6e-46
Identities = 284/333 (85%), Positives = 284/333 (85%), Strand = Minus /
Plus
Query: 676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
||||||||||||||||||||||||||||| ||||||||||||| ||| ||||||||||
Sbjct: 374 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
433
Query: 617 -ATTTAGAGAGAAATTGCAAGTTAGAA-T-A-AA-AAAAGTTATAGTTCAGGATCAGAAA
563
|| | | ||| || ||| || | | || |||| | | | || || ||||
Sbjct: 434 CATCTCATGTGAAGAAA-AATTTACAAGTTAGAATAAAAAAAAAAAAT-AGT-TCGGAAA
490
Query: 562 AAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTG
503
|| ||||||||||||||||||||||||||| |||| ||||||||||| |||||||
Sbjct: 491 GCAG----TACTTGAAATCTGTGAGGGTTGTTAACGGGTACGGCGAGTTTGACTATTCTG
546
Query: 502 AGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
443
||||||||||| || | |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 547 AGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
606
Query: 442 GCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
383
||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct: 607 GCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
666
Query: 382 GCTTTCCCTGTAATTAACAAATTGATTACCATT 350
||| |||||||||||||| |||||||||| | |
Sbjct: 667 GCTCTCCCTGTAATTAACGAATTGATTACAAAT 699
>962_61_14529390_16654_45210_020.ab1
Length = 696
Plus Strand HSPs:
Score = 1077 (167.6 bits), Expect = 2.1e-43, P = 2.1e-43
Identities = 265/312 (84%), Positives = 265/312 (84%), Strand = Plus / Plus
Query: 372 ACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAG
431
||||| | || || |||| |||||||||||||| |||||||| |||| ||||||||||
Sbjct: 1 ACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAG 60
Query: 432 CAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAA
491
|||||| |||| ||||| |||||||||||||||| |||||||||| |||||||| | ||
Sbjct: 61 CAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGAC
120
Query: 492 AACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAA
551
|||||| |||||||||||||||||||||||||||| |||||||||||||||| |||||||
Sbjct: 121 AACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAA
180
Query: 552 GTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCT
611
||| ||||||| ||||| | ||||| | |||||||| || ||||||||| |||||||
Sbjct: 181 GTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCT
237
Query: 612 CTAAAT-T-A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
|||||| | | | | || ||| ||| ||||||||||| | |||||||||||||||||
Sbjct: 238 CTAAATGTGACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCA
297
Query: 665 ACAATCCTACTT 676
||| ||||||||
Sbjct: 298 ACAGTCCTACTT 309
>962_177_14574088_16654_46114_045.ab1
Length = 625
Minus Strand HSPs:
Score = 955 (149.3 bits), Expect = 7.5e-38, P = 7.5e-38
Identities = 191/191 (100%), Positives = 191/191 (100%), Strand = Minus /
Plus
Query: 676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
617
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 435 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
494
Query: 616 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
557
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 495 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
554
Query: 556 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
497
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 555 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
614
Query: 496 TCGTTTTCATT 486
|||||||||||
Sbjct: 615 TCGTTTTCATT 625
>962_282_14615493_16654_46934_055.ab1
Length = 274
Minus Strand HSPs:
Score = 891 (139.7 bits), Expect = 1.3e-34, P = 1.3e-34
Identities = 191/207 (92%), Positives = 191/207 (92%), Strand = Minus /
Plus
Query: 561 AAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGA
502
||||| |||||||||||||||||| |||||||| |||||||||||||||| ||||||||
Sbjct: 68 AAGGCAGTACTTGAAATCTGTGAGGATTGTTAACGGGTATGGCGAGTTTGACTATTCTGA
127
Query: 501 GATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
442
|||||||||| || | |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 128 GATTCTCGTTGTCGTCTGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
187
Query: 441 CATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGG
382
||||||||||||||| |||| ||||||||||||||||||||||| |||||||||||||||
Sbjct: 188 CATGGCCTTGCTCAATAATGTAGGAGTCTCTGCCGTCAGGGTTCCCCAAGGTGAGTATGG
247
Query: 381 CTTTCCCTGTAATTAACAAATTGATTA 355
|| |||||| ||||||| | |||||||
Sbjct: 248 CTCTCCCTGCAATTAACGATTTGATTA 274
>962_248_14601477_16654_46676_055.ab1
Length = 566
Minus Strand HSPs:
Score = 687 (109.1 bits), Expect = 1.0e-25, P = 1.0e-25
Identities = 203/273 (74%), Positives = 203/273 (74%), Strand = Minus /
Plus
Query: 333 ATGATGTCGAGTGAGA-GTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGG
275
|||| | | | ||| ||||| | ||| |||||| ||| ||||||| | ||||||
Sbjct: 1 ATGAAATTTAATCAGAAGTAGT-A--AGTA-ATTACTGACCGCTAAGGACGAGGAGGAGG 56
Query: 274 AAATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACA
215
||||| || || ||||| | ||| ||||| ||||||| |||| |||||| |||||| |||
Sbjct: 57 AAATCAGCGTCTGCATGGTGAGGGAGAAGAAGGGTGTGGGGTCTGGACTCGAACTCCACA
116
Query: 214 ACACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGC---GTTGGTCGAACCTGTGGAGG
158
|||||||||| | ||| ||||||| ||| |||||| ||||||| || || || |||
Sbjct: 117 ACACGGTAGTCTCGAAGGTTCTGAAGCTGTGTGGAGCTTCGTTGGTCAAAGCTCTGAAGG
176
Query: 157 ACCCGAAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAG 98
| || | |||||| | || ||| |||| |||||| |||| || | || ||||||
Sbjct: 177 ATACGGATGTGACCGTGTTGGTTCTTGAAAAGAGTGCGGAATCTATTCGACATGAAGTGA
236
Query: 97 AAGGGGTTGTTTTGTGTTCTTGAATCAGACTCT 65
|| |||||| | |||||| ||| || || |||
Sbjct: 237 AAAGGGTTGGTCTGTGTTTGTGAGTCTGAGTCT 269
>962_196_14581545_16654_48111_005.ab1
Length = 538
Minus Strand HSPs:
Score = 633 (101.0 bits), Expect = 3.0e-23, P = 3.0e-23
Identities = 169/204 (82%), Positives = 169/204 (82%), Strand = Minus /
Plus
Query: 201 CAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCAT
142
||||||||||||||||||| | |||||||||||||| ||||||||||| || |||||||
Sbjct: 2 CAAGATTCTGAATTTGTTTCGTACGTTGGTCGAACCTCTGGAGGACCCGGAGATGACCAT 61
Query: 141 ATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAAGGGGTTGTTTT 85
||| ||| |||||||||||||||||| | ||||||||||||| ||| ||||| ||||
Sbjct: 62 ATTGGTTTTTGAATAGAGTGTGGAACCACCTATCGGAGCTGAAGTGGAAAGGGTTATTTT
121
Query: 84 GTGTTCTTGAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAA 25
|| ||| | | ||||||| ||||| || ||||||| | | | ||||||||||| |
Sbjct: 122 GT--TCTCG--T--GACTCTTGTTGGCTTTCTTGGTGCT-C-GT-GATGTACAATGCCTA
172
Query: 24 AGGAGACAGAAAGTGATGCCAGGA 1
|||| ||||||| |||||||||||
Sbjct: 173 AGGAAACAGAAACTGATGCCAGGA 196
Parameters:
E=1e-20
evalues
echofilter
-o Cowpea962_177_14574088_5489_46110_045.ab1.wu.n
ctxfactor=2.00
Query ----- As Used ----- ----- Computed
----
Strand MatID Matrix name Lambda K H Lambda K H
+1 0 +5,-4 0.192 0.182 0.357 same same same
Q=10,R=10 0.104 0.0151 0.0600 n/a n/a n/a
-1 0 +5,-4 0.192 0.182 0.357 same same same
Q=10,R=10 0.104 0.0151 0.0600 n/a n/a n/a
Query
Strand MatID Length Eff.Length E S W T X E2 S2
+1 0 676 676 9.9e-21 611 11 n/a 73 0.049 80
134 0.048 119
-1 0 676 676 9.9e-21 611 11 n/a 73 0.049 80
134 0.048 119
Statistics:
Database: ../../Cowpea1X/Cowpea_all_GSS_clean.fasta
Title: ../Cowpea1X/Cowpea_all_GSS_clean.fasta
Posted: 2:44:50 PM PDT Oct 19, 2007
Created: 2:44:50 PM PDT Oct 19, 2007
Format: XDF-1
# of letters in database: 158,813,828
# of sequences in database: 260,642
# of database sequences satisfying E: 15
No. of states in DFA: 245 (490 KB)
Total size of DFA: 548 KB (2076 KB)
Time to generate neighborhood: 0.00u 0.00s 0.00t Elapsed: 00:00:00
No. of threads or processors used: 2
Search cpu time: 1.19u 0.04s 1.23t Elapsed: 00:00:00
Total cpu time: 1.20u 0.04s 1.24t Elapsed: 00:00:00
Start: Fri Oct 19 14:51:16 2007 End: Fri Oct 19 14:51:16 2007
On 10/24/07, Dave Messina <David.Messina at sbc.su.se> wrote:
>
> Hi Joseph,
>
> Could you post the blast report that's giving you trouble? And also could
> you tell us what version of WU-BLAST you're running and what version of
> BioPerl you're using?
>
> I'd like to try and reproduce your problem.
>
> Thanks,
> Dave
>
>
--
Joseph Fass
joseph.fass at gmail.com || joefass at hotmail.com
970.227.5928 (c) || 530.754.7978 (w)
More information about the Bioperl-l
mailing list