[Feedback] Site Feedback: BLAST & sequence download problem

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URL         : http://ensembl.gramene.org/Oryza_sativa/Tools/Blast/Ticket?db=core;tl=JrHlxNQB6bbe5SvV-35769-26299854

Subject     : Site Feedback: BLAST & sequence download  problem

Name        : Pankaj

Email       : jaiswalp at oregonstate.edu

Organization: 

Comments    : 

Hi Everyone,

I am trying to BLAST the following sequence against the O. sativa japonica genome (unmasked). 
>Pokkali_32265
ATCATCTTTAGCTATACCAACAATACCTACTAGGCGATCACCAGAATTTGCGGTGTCAATTTTTAACCTACCGAGGCCGGTGGCTGCATTCAGGAGCTGTTGTTCATCATCACAAATGGAACGGAGTCAAGTTGTAACTTGTAACTCAAGACACATAAGCAGTCACATGAATGAACTAATAGCCAGGTCATGAATTTAAAAATATATACATACACATTTCATGACGGCACGCGTTGATTTGCTATCTAACATGGAGCAACAGATCTAACTGATGTGTCCATGTGAGATCAAACTGATGTGCGGGGTAACCTAAAACAGCCTCTGGCTTTCCTAACTTGCTGCAAGGGCTACTTCTACCAATGCTACTTTGGTTTCTTAAGCTATGGCACAATTCTTTCCTTTCTAAAAATAATGCTCTACGGAACATGAGCAGAGTCAGTGTGGTGCAGTTAGTTGTCCCCCTCAAATGGTCGTTGCATTTCATTCTTGCGCAGCAGAAAAGCTCGCAGATAAGTGTTGCTTCAGGCAAAAAGTGCATAAAGCTCCGAGGAATGATAGTCAGTACTCAGTAGAGGACTCCAAGATAAGCACGGAACAGGACAGTTCCCATCGCTTAACCAAATCCATGGAAGCCACTTACTTTCCCATCTTACTCGCAAAGGTCTTCCTCTCATCTTTATGCTTCTTGTGAAGTGTCCTAAATTTCGTTTCTTGCTTTGCTCGGACAAGCATCCAATCCAAGGCCAAATCATACTCCATTGTATTGGGTTGAGAACAATGCGAGGTTGAAACTGCCTTCTTCTGTTCTTCTCGTTGTCTTATACCCATTCTAATATTGTTGATTGTTAAGTGCCCGAGAAGAGTTTCTGAAGGTTTTGGAACCTTAAGCAATCCTTTGCTGCAATAAAGGGGTCTTCCACCGACCACCAAGCCTGAATTAATTTTTGAAATAGCAGAGTCTGCGGCACTTTTTGTTTTGAATATAGCATATGCTTTTCCATTGTTTGGATCATCATAAGTTGGGTGGTTAATAGGCTTAGCGATACAATTTAGTTGTAAAGCATCACGTATAAGCTCCTCTATGTCAGCAGCTGCAAACTGTATGTCAAGATTTTGAATGTACACAAGTGTCCCCTGCTCATCAGCATTTCGTAGTCTGGTATCCCATGGAATCTTGAACCATTTGCTTCTGTCAGCTTGTCTACCTGCTAGTTCCAAAGGTCCAGTGCGACTTGGTCTTTCAGGAACATCTAATGGCACATTTTGCACTGTAACATTTTCAGAAAATTTGACCCTCTTTGGTGGCCTCTCCCCAGGGAGAACTTTCTGTGCAGGTTTGGTAATGTTCTCTGTAGATTTGGACACACTCTCCTCTTTCAGTGCTACATGGGGAGGGGGAATGGCAGCAGCCGCACTTTCCTCCTTGACCACTGGCTGGGGAAAGGGAATGGCTGAAGCCACATTTTCCTCCTTGAATACTGACGGGGGAAGGGAAACTGCAGCAACTGGACTTTCATCCTCCATAACCGTTGACTGGGGAAGGGGAACTGGGACATTAAGCATCTTCTGATCAACACCATGCACTTCCTGGTCTGAACAGGATGTCACTTGCTCAACTTTTGAATTAAGCAAAAGATTTCCTTCCACCCCTGCAATTTTCTCAGGTAATTGTTCAGAAAGTGTGCAACTGTTAACATCAAAAAACCTGTAGAAGATATAATCAGCCATTGCTAGTTCCCTGGGGGAAGGTTGACGATTCCTCTCATCCTTTGAAATGCAAAGCACAGTGCATTTCCCACCAATAGCTTCCAATGGGTTGATATCAGCAAGGCCAACGCCTTCACCACAAGCAAGAAATATCTCCTTTTCCATTACAGGGCCACTTAAATGTTTTTGAATCTCATCCGGGAGAAAAAACCAAAGAATCTTTACTTTCTTAGCCTGATTTTGCTGCCATATCTTTATTATCTTTCCAATGTAAGGTTCAGACTCACCACTCTTAAAAAGATATACATTGTCATACAGTGAGTACTTCACATTGTCAAATGTGAAGGAGTCATAAAACTGTGTATCCATCTTAATACCACCTTTTGCTCTCTTCTTCCCCCATGAGAATTGGATATTCTCATTACTACCATCCATTCTGATAATGGTAACTTGTAGCTCACTGTGCACTCACCATAAGCGCGTGGCGGCCGCCGGCGAGGAGGGCGGCGAGGTGGAGGCCGGGGGCGCGTGGCTCCCAGGTAGCAGGAGGAGGCCGCGGTGGGAGAGGGAGGAGGAGGAGGAGGAGGAGGTTGG


I get one of the following regions aligned almost 100%
1 24143770 to 24144455 (+)

However when I click on the 'sequence' link next to the genome location it provides a sequence from a very different region, even though the header says the genome location same as the BLAST query result. Also the BLAST result say forward strand, but the following view spits out the minus strand.


BLAST Genomic Sequence

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BLAST/BLAT type

BLASTN
Query location

Query_1 686 to 1 (-)
Database location 1 24143770 to 24144455 (+)
Genomic location 1 24143770 to 24144455 (+)
Alignment score 99.0
E-value 0.0
Alignment length 686
Percentage identity 99.0

Exons          All exons

>chromosome:IRGSP-1.0:1:24143470:24144755:-1 
24144755 GGGACCTCATGTGCACTGGTTTTGATAGTTGAGGGACTTGTTGAATCTGGTTTTCTGGTT 24144696
24144695 GAAGAACGAAAATCGGATTCGTTGATAAGTTAAGGGACCTCAGATGAACTTATTCCTTTC 24144636
24144635 ACTTTGGGAGAAAAGGAAAGCAGGGCATCTCCTGTTAGACTTTAGCAGGTAACACATGTT 24144576
24144575 GGTCCAAGACAACTCAAAAGTGTACATTGATTTACTTCAAGAATGAGTATGCATGTCTCA 24144516
24144515 TGAAGCTAGATCTCAAGAACCAGCATATGGTTCACCAAGAGCATCCAAAACGAAGACATG 24144456
24144455 ATCATCTTTAGCTATACCAACAATACCTACCAGGCGATCACCAGAATTTGCGGTGTCAAT 24144396
24144395 TTTTAACCTACCGAGGCCGGTGGCTGCATTCAGGAGCTGTTGTTCATCATCACAAATGGA 24144336
24144335 ACGGAGTCAAGTTGTAACTTGTAACTCAAGACACATAAGCAGTCACATGAATGAACTAAT 24144276
24144275 AGCCAGGTCATGAATTTAAAAATATATACATACACATTTCATGACGGCACGCGTTGATTT 24144216
24144215 GCTATCTAACATGGAGCAACAGATCTAACTGATGTGTCCATGTGAGATCAAATTGATGTG 24144156
24144155 CGGGGTAACCTAAAACAGCCTCTGGCTTTCCTAACTTGCTGCAAGGGCTACTTCTACCAA 24144096
24144095 TGTTACTTTGGTTTCTTAAGCTATGGCACAATTCTTTCCTTTCTAAAAATAATGCTCTAC 24144036
24144035 GGAACATGAGCAGAGTCAGTGTGGTGCAGTTAGTTGTCCCCCTCAAATGGTCGTTGCATT 24143976
24143975 TCATTCTTGCGCAGCAGAAAAACTCGCAGATAAGTGTTGCTTCAGGCAAAAAGTGCATAA 24143916
24143915 AGCTCCGAGGAATGATAGTCAGTACTCAGTAGAGGACTCCAAGATAAGCACGGAACAGGA 24143856
24143855 CAGTTCCCATCGCTTAACCAAATCCATGGAAGCCACTTACTTTCCCATCTTACTCGCAAA 24143796
24143795 GGTCTTCCTCTCATCTTTATGCTTCTATAGATATAAATTGAGCATTCAAAATTTAAGGTC 24143736
24143735 TGTATGGATAAAACTGAAAGCTGGTATACACAGAGATCTCCAGTGGAAGTGCACATACCT 24143676
24143675 TGTGAAGTGTCCTAAATTTCGTTTCTTGCTTTGCTCGGACAAGCATCCAATCCAAGGCCA 24143616
24143615 AATCATACTCCATTGTATTGGGTTGAGAACAATGCGAGGTTGAAACTGCCTTCTTCTGGA 24143556
24143555 GAAAGAATAATGGTTGTGCAAAAATATTAAGACAGAGAAAAGAAATAGAGCAAACTTCAT 24143496
24143495 AGGACAACATCAGCACCTGTTCTTCT                                   24143470

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http://www.warelab.org/bugs/view.php?id=5205