[Bioperl-l] overwriting results in bl2seq report
Jason Stajich
jason.stajich at duke.edu
Tue Sep 20 11:05:42 EDT 2005
If you only want the top hit in your report you can also just add the
-v 1 option when you run bl2seq.
It would be more helpful if you provided the bioperl code you are
using rather than the report.
You may also want to read other people's advice on how to best use
BLAST to map probes to a genome:
http://bioinformatics.org/pipermail/bioclusters/2005-April/
002473.html
-jason
On Sep 19, 2005, at 11:31 PM, Usha wrote:
> Hi,
> I am trying to align some probes with a Streptococcus genome using
> local bl2seq. These probes are of 32 nucleotides in length. These
> are matching at multiple positions in the whole genome, but I am
> interseted only in the first match. Could any one help by telling
> me where I can find information about parsing the bl2seq output? I
> want to get the only top hits in a tab delimited text output file.
> I have one problem with regard to my output(report), when I am
> looping the probes I can see only the results for last probe. There
> is a problem of overwrting results in the report. How can I avoid
> this overwriting problem? Attached is my bl2seq output.
> Thanks
> Usha.
>
>
>
> ---------------------------------
> Yahoo! for Good
> Click here to donate to the Hurricane Katrina relief effort.
> Query= gi|22536185|ref|NC_004116.1| Streptococcus agalactiae 2603V/R,
> complete genome
> (2,160,267 letters)
>
>
>
>
>> testquery2
>>
> Length = 32
>
> Score = 63.9 bits (32), Expect = 2e-12
> Identities = 32/32 (100%)
> Strand = Plus / Plus
>
>
> Query: 1 aattaacattgttgattttattcttcaacatc 32
> ||||||||||||||||||||||||||||||||
> Sbjct: 1 aattaacattgttgattttattcttcaacatc 32
>
>
>
> Score = 28.2 bits (14), Expect = 0.13
> Identities = 14/14 (100%)
> Strand = Plus / Minus
>
>
> Query: 1440112 atcaacaatgttaa 1440125
> ||||||||||||||
> Sbjct: 16 atcaacaatgttaa 3
>
>
>
> Score = 28.2 bits (14), Expect = 0.13
> Identities = 14/14 (100%)
> Strand = Plus / Plus
>
>
> Query: 692877 ttgttgattttatt 692890
> ||||||||||||||
> Sbjct: 9 ttgttgattttatt 22
>
>
>
> Score = 28.2 bits (14), Expect = 0.13
>
> Score = 28.2 bits (14), Expect = 0.13
> Identities = 14/14 (100%)
> Strand = Plus / Minus
>
>
> Query: 1079469 gttgaagaataaaa 1079482
> ||||||||||||||
> Sbjct: 29 gttgaagaataaaa 16
>
>
>
> Score = 26.3 bits (13), Expect = 0.51
> Identities = 13/13 (100%)
> Strand = Plus / Minus
>
>
> Query: 1954368 aacaatgttaatt 1954380
> |||||||||||||
> Sbjct: 13 aacaatgttaatt 1
>
>
>
> Score = 26.3 bits (13), Expect = 0.51
> Identities = 13/13 (100%)
> Strand = Plus / Plus
>
>
> Query: 1721632 aattaacattgtt 1721644
> |||||||||||||
> Sbjct: 1 aattaacattgtt 13
>
>
>
> Score = 26.3 bits (13), Expect = 0.51
> Identities = 13/13 (100%)
> Strand = Plus / Plus
>
>
> Query: 554214 acattgttgattt 554226
> |||||||||||||
> Sbjct: 6 acattgttgattt 18
> Score = 26.3 bits (13), Expect = 0.51
> Identities = 13/13 (100%)
> Strand = Plus / Plus
>
>
> Query: 1377395 cattgttgatttt 1377407
> |||||||||||||
> Sbjct: 7 cattgttgatttt 19
>
>
>
> Score = 26.3 bits (13), Expect = 0.51
> Identities = 13/13 (100%)
> Strand = Plus / Minus
>
>
> Query: 1614884 ataaaatcaacaa 1614896
> |||||||||||||
> Sbjct: 21 ataaaatcaacaa 9
>
>
>
> Score = 26.3 bits (13), Expect = 0.51
> Identities = 13/13 (100%)
> Strand = Plus / Minus
>
>
> Query: 1600827 ataaaatcaacaa 1600839
> |||||||||||||
> Sbjct: 21 ataaaatcaacaa 9
>
>
>
> Score = 26.3 bits (13), Expect = 0.51
> Identities = 13/13 (100%)
> Strand = Plus / Plus
>
>
> Query: 846753 tgttgattttatt 846765
> |||||||||||||
> Sbjct: 10 tgttgattttatt 22
> Score = 26.3 bits (13), Expect = 0.51
> Identities = 13/13 (100%)
> Strand = Plus / Plus
>
>
> Query: 933822 ttgattttattct 933834
> |||||||||||||
> Sbjct: 12 ttgattttattct 24
>
>
>
> Score = 26.3 bits (13), Expect = 0.51
> Identities = 13/13 (100%)
> Strand = Plus / Plus
>
>
> Query: 521487 tgattttattctt 521499
> |||||||||||||
> Sbjct: 13 tgattttattctt 25
>
>
>
> Score = 26.3 bits (13), Expect = 0.51
> Identities = 13/13 (100%)
> Strand = Plus / Plus
>
>
> Query: 429120 tttattcttcaac 429132
> |||||||||||||
> Sbjct: 17 tttattcttcaac 29
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 1137089 aattaacattgt 1137100
> ||||||||||||
> Sbjct: 1 aattaacattgt 12
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 1800360 cattgttgattt 1800371
> ||||||||||||
> Sbjct: 7 cattgttgattt 18
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Minus
>
>
> Query: 2063737 aaaatcaacaat 2063748
> ||||||||||||
> Sbjct: 19 aaaatcaacaat 8
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 243857 attgttgatttt 243868
> ||||||||||||
> Sbjct: 8 attgttgatttt 19
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Minus
>
>
> Query: 1883050 aaaatcaacaat 1883061
> ||||||||||||
> Sbjct: 19 aaaatcaacaat 8
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Minus
>
>
> Query: 1573828 aaaatcaacaat 1573839
> ||||||||||||
> Sbjct: 19 aaaatcaacaat 8
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 378327 tgttgattttat 378338
> ||||||||||||
> Sbjct: 10 tgttgattttat 21
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Minus
>
>
> Query: 1448800 ataaaatcaaca 1448811
> ||||||||||||
> Sbjct: 21 ataaaatcaaca 10
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 1492953 tgttgattttat 1492964
> ||||||||||||
> Sbjct: 10 tgttgattttat 21
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Minus
>
>
> Query: 1579619 aataaaatcaac 1579630
> ||||||||||||
> Sbjct: 22 aataaaatcaac 11
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 658751 gttgattttatt 658762
> ||||||||||||
> Sbjct: 11 gttgattttatt 22
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Minus
>
>
> Query: 1110879 aataaaatcaac 1110890
> ||||||||||||
> Sbjct: 22 aataaaatcaac 11
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Minus
>
>
> Query: 334763 aataaaatcaac 334774
> ||||||||||||
> Sbjct: 22 aataaaatcaac 11
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 134255 ttgattttattc 134266
> ||||||||||||
> Sbjct: 12 ttgattttattc 23
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 247705 tgattttattct 247716
> ||||||||||||
> Sbjct: 13 tgattttattct 24
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 609508 gattttattctt 609519
> ||||||||||||
> Sbjct: 14 gattttattctt 25
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 756471 gattttattctt 756482
> ||||||||||||
> Sbjct: 14 gattttattctt 25
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Minus
>
>
> Query: 1033051 aagaataaaatc 1033062
> ||||||||||||
> Sbjct: 25 aagaataaaatc 14
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 1035188 ttttattcttca 1035199
> ||||||||||||
> Sbjct: 16 ttttattcttca 27
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 1129234 ttttattcttca 1129245
> ||||||||||||
> Sbjct: 16 ttttattcttca 27
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 1128429 tattcttcaaca 1128440
> ||||||||||||
> Sbjct: 19 tattcttcaaca 30
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 1434633 tattcttcaaca 1434644
> ||||||||||||
> Sbjct: 19 tattcttcaaca 30
>
>
>
> Score = 24.3 bits (12), Expect = 2.0
> Identities = 12/12 (100%)
> Strand = Plus / Plus
>
>
> Query: 1124502 ttcttcaacatc 1124513
> ||||||||||||
> Sbjct: 21 ttcttcaacatc 32
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1202836 acaatgttaat 1202846
> |||||||||||
> Sbjct: 12 acaatgttaat 2
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1181703 attaacattgt 1181713
> |||||||||||
> Sbjct: 2 attaacattgt 12
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1060902 aacaatgttaa 1060912
> |||||||||||
> Sbjct: 13 aacaatgttaa 3
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 224753 taacattgttg 224763
> |||||||||||
> Sbjct: 4 taacattgttg 14
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1961563 taacattgttg 1961573
> |||||||||||
> Sbjct: 4 taacattgttg 14
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 866174 aacattgttga 866184
> |||||||||||
> Sbjct: 5 aacattgttga 15
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 585099 tcaacaatgtt 585109
> |||||||||||
> Sbjct: 15 tcaacaatgtt 5
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 2136590 atcaacaatgt 2136600
> |||||||||||
> Sbjct: 16 atcaacaatgt 6
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 706121 acattgttgat 706131
> |||||||||||
> Sbjct: 6 acattgttgat 16
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1241831 atcaacaatgt 1241841
> |||||||||||
> Sbjct: 16 atcaacaatgt 6
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1049040 atcaacaatgt 1049050
> |||||||||||
> Sbjct: 16 atcaacaatgt 6
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1677419 aatcaacaatg 1677429
> |||||||||||
> Sbjct: 17 aatcaacaatg 7
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1297825 aatcaacaatg 1297835
> |||||||||||
> Sbjct: 17 aatcaacaatg 7
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 38368 attgttgattt 38378
> |||||||||||
> Sbjct: 8 attgttgattt 18
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 358991 attgttgattt 359001
> |||||||||||
> Sbjct: 8 attgttgattt 18
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1757703 aaatcaacaat 1757713
> |||||||||||
> Sbjct: 18 aaatcaacaat 8
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 495597 attgttgattt 495607
> |||||||||||
> Sbjct: 8 attgttgattt 18
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1541827 aaatcaacaat 1541837
> |||||||||||
> Sbjct: 18 aaatcaacaat 8
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1022497 aaatcaacaat 1022507
> |||||||||||
> Sbjct: 18 aaatcaacaat 8
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 651482 aaatcaacaat 651492
> |||||||||||
> Sbjct: 18 aaatcaacaat 8
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 241085 aaatcaacaat 241095
> |||||||||||
> Sbjct: 18 aaatcaacaat 8
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1538020 aaaatcaacaa 1538030
> |||||||||||
> Sbjct: 19 aaaatcaacaa 9
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1452215 aaaatcaacaa 1452225
> |||||||||||
> Sbjct: 19 aaaatcaacaa 9
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1427497 aaaatcaacaa 1427507
> |||||||||||
> Sbjct: 19 aaaatcaacaa 9
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1166874 aaaatcaacaa 1166884
> |||||||||||
> Sbjct: 19 aaaatcaacaa 9
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 948551 aaaatcaacaa 948561
> |||||||||||
> Sbjct: 19 aaaatcaacaa 9
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1299221 ttgttgatttt 1299231
> |||||||||||
> Sbjct: 9 ttgttgatttt 19
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1445881 ttgttgatttt 1445891
> |||||||||||
> Sbjct: 9 ttgttgatttt 19
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 387873 aaaatcaacaa 387883
> |||||||||||
> Sbjct: 19 aaaatcaacaa 9
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1225643 taaaatcaaca 1225653
> |||||||||||
> Sbjct: 20 taaaatcaaca 10
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 988731 tgttgatttta 988741
> |||||||||||
> Sbjct: 10 tgttgatttta 20
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1033545 tgttgatttta 1033555
> |||||||||||
> Sbjct: 10 tgttgatttta 20
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 109598 taaaatcaaca 109608
> |||||||||||
> Sbjct: 20 taaaatcaaca 10
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 159566 ataaaatcaac 159576
> |||||||||||
> Sbjct: 21 ataaaatcaac 11
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1699447 aataaaatcaa 1699457
> |||||||||||
> Sbjct: 22 aataaaatcaa 12
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1658995 aataaaatcaa 1659005
> |||||||||||
> Sbjct: 22 aataaaatcaa 12
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1622012 aataaaatcaa 1622022
> |||||||||||
> Sbjct: 22 aataaaatcaa 12
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1605728 aataaaatcaa 1605738
> |||||||||||
> Sbjct: 22 aataaaatcaa 12
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1590211 aataaaatcaa 1590221
> |||||||||||
> Sbjct: 22 aataaaatcaa 12
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 754682 ttgattttatt 754692
> |||||||||||
> Sbjct: 12 ttgattttatt 22
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 789992 ttgattttatt 790002
> |||||||||||
> Sbjct: 12 ttgattttatt 22
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1358216 aataaaatcaa 1358226
> |||||||||||
> Sbjct: 22 aataaaatcaa 12
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 952297 ttgattttatt 952307
> |||||||||||
> Sbjct: 12 ttgattttatt 22
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1015262 ttgattttatt 1015272
> |||||||||||
> Sbjct: 12 ttgattttatt 22
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 698859 aataaaatcaa 698869
> |||||||||||
> Sbjct: 22 aataaaatcaa 12
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 684509 aataaaatcaa 684519
> |||||||||||
> Sbjct: 22 aataaaatcaa 12
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 216359 aataaaatcaa 216369
> |||||||||||
> Sbjct: 22 aataaaatcaa 12
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1469332 gaataaaatca 1469342
> |||||||||||
> Sbjct: 23 gaataaaatca 13
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1328838 gaataaaatca 1328848
> |||||||||||
> Sbjct: 23 gaataaaatca 13
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1721248 tgattttattc 1721258
> |||||||||||
> Sbjct: 13 tgattttattc 23
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 147481 gaataaaatca 147491
> |||||||||||
> Sbjct: 23 gaataaaatca 13
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 289194 attttattctt 289204
> |||||||||||
> Sbjct: 15 attttattctt 25
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 654632 attttattctt 654642
> |||||||||||
> Sbjct: 15 attttattctt 25
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1149811 attttattctt 1149821
> |||||||||||
> Sbjct: 15 attttattctt 25
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 682457 aagaataaaat 682467
> |||||||||||
> Sbjct: 25 aagaataaaat 15
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 333994 aagaataaaat 334004
> |||||||||||
> Sbjct: 25 aagaataaaat 15
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 2015203 attttattctt 2015213
> |||||||||||
> Sbjct: 15 attttattctt 25
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1786838 gaagaataaaa 1786848
> |||||||||||
> Sbjct: 26 gaagaataaaa 16
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1115801 gaagaataaaa 1115811
> |||||||||||
> Sbjct: 26 gaagaataaaa 16
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 907480 tttattcttca 907490
> |||||||||||
> Sbjct: 17 tttattcttca 27
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1440630 tttattcttca 1440640
> |||||||||||
> Sbjct: 17 tttattcttca 27
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 155543 ttattcttcaa 155553
> |||||||||||
> Sbjct: 18 ttattcttcaa 28
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 180330 ttattcttcaa 180340
> |||||||||||
> Sbjct: 18 ttattcttcaa 28
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1081696 ttgaagaataa 1081706
> |||||||||||
> Sbjct: 28 ttgaagaataa 18
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 816592 ttgaagaataa 816602
> |||||||||||
> Sbjct: 28 ttgaagaataa 18
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 931476 tattcttcaac 931486
> |||||||||||
> Sbjct: 19 tattcttcaac 29
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 844976 gttgaagaata 844986
> |||||||||||
> Sbjct: 29 gttgaagaata 19
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 1855993 tgttgaagaat 1856003
> |||||||||||
> Sbjct: 30 tgttgaagaat 20
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 758581 attcttcaaca 758591
> |||||||||||
> Sbjct: 20 attcttcaaca 30
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1153478 attcttcaaca 1153488
> |||||||||||
> Sbjct: 20 attcttcaaca 30
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 810368 tgttgaagaat 810378
> |||||||||||
> Sbjct: 30 tgttgaagaat 20
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1669608 attcttcaaca 1669618
> |||||||||||
> Sbjct: 20 attcttcaaca 30
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 70059 tgttgaagaat 70069
> |||||||||||
> Sbjct: 30 tgttgaagaat 20
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1132162 ttcttcaacat 1132172
> |||||||||||
> Sbjct: 21 ttcttcaacat 31
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Plus
>
>
> Query: 1380017 ttcttcaacat 1380027
> |||||||||||
> Sbjct: 21 ttcttcaacat 31
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 492657 atgttgaagaa 492667
> |||||||||||
> Sbjct: 31 atgttgaagaa 21
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 358577 atgttgaagaa 358587
> |||||||||||
> Sbjct: 31 atgttgaagaa 21
>
>
>
> Score = 22.3 bits (11), Expect = 8.0
> Identities = 11/11 (100%)
> Strand = Plus / Minus
>
>
> Query: 341438 atgttgaagaa 341448
> |||||||||||
> Sbjct: 31 atgttgaagaa 21
> Lambda K H
> 1.37 0.711 1.31
>
> Gapped
> Lambda K H
> 1.37 0.711 1.31
>
>
> Matrix: blastn matrix:1 -3
> Gap Penalties: Existence: 5, Extension: 2
> Number of Sequences: 1
> Number of Hits to DB: 2088
> Number of extensions: 115
> Number of successful extensions: 115
> Number of sequences better than 10.0: 1
> Number of HSP's better than 10.0 without gapping: 1
> Number of HSP's gapped: 115
> Number of HSP's successfully gapped: 115
> Length of query: 2160267
> Length of database: 32
> Length adjustment: 13
> Effective length of query: 2160254
> Effective length of database: 19
> Effective search space: 41044826
> Effective search space used: 41044826
> X1: 7 (13.9 bits)
> X2: 15 (29.7 bits)
> X3: 25 (49.6 bits)
> S1: 7 (14.4 bits)
> S2: 11 (22.3 bits)
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
--
Jason Stajich
Duke University
http://www.duke.edu/~jes12
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