I was trying to sort out a couple of merges between CGs and EG genes
and came across this gnarly thing.
The problem is in the region which the EST GH02584.5prime maps to (this
is in 1B).
Here is a picture of the relevant bit of GeneSeen:
................................................................................
|
CG3176 | EST GH02584.3prime
\-> v <---
\---------------------------------------//--///-------------------------------
<-- <--------- <---- <-------------
CG18275 CG18273 CG18166 CG13372
(annotated as  EG:171D11.6 )
<--
EST GH02584.5prime
................................................................................
1. If you look on GeneSeen, EST GH02584.5prime maps in between annotations.
It is between CG18275 and CG18273 on the bottom strand.
2. However, if you look at the GadFly page for CG18166, homology to EST
GH02584.5prime is given as evidence for this annotation.
(http://fly.ebi.ac. uk:7081 /cgi-bin/annot/gene?CG18166)
(apologies for English URL \!)
3. However, if you look at the EST page for GH02584.5prime, CG3176 is given as
the gene it corresponds to
(http://www.fruitfly.org/cgi-bin/EST/community_query/cloneReport.pl?id_type=0&i
d_value=GH02584&db_name=estlabtrack)
Clone ID: GH02584
Gene: CG3176 (CG3176)
4. I figured I'd use the GH02584.5prime and GH02584.3prime sequences to
BLAST against the genome to see what is going on, and it turns out that
this region is repetitive (which might explain the gaps in the sequence
I guess). This is scaffold AE003417.1
File of BLAST results for GH02584.5prime and GH02584.3prime (called
'BLAST' is attached).
I think that the EST sequences are repeated at least 3-4 times in the
region (both the 3' and 5' sequences are repeated) that spans
approximately from coordinates 233851-250940 of AE003417.1 (this
accession has an October date and is therefore release 2, so the
sequence cannot have changed from release 1 as it has a .1 in the
accession number). The repetitive region includes the following CGs:
CG18275, CG3176, CG18273, CG18166, CG13372.
This explains probably why CG18166 has GH02584.5prime as evidence and
yet GH02584.5prime appears to map to the left of CG18166 on GeneSeen.
It also probably explains why GH02584.3prime appears to be upstream of
GH02584.5prime on GeneSeen :), GeneSeen is probably just showing a
different repeat for the 5' and 3' EST sequences.
I will curate this as an error report, as I guess care should be taken
in annotating this repetitive region and in using EST GH02584 as
evidence and I guess its possible the assembly is not correct.
I have sent this to bdgp, because I think the EST page for GH02584
needs changing \- I don't think it should have the gene as 'CG3176'
regardless of whether or not the region is repeated, because CG3176 is
on the opposite strand from the EST. I thought that the direction of
the match was being taken into account now when matching up ESTs and
CGs ?
Also, how are ESTs being filtered for display on GeneSeen \- if they
match to more than one region, are they still being shown, as seems to
be the case for this EST or are they not being displayed on GeneSeen
(rather like the P-elements, where multiple inserts are not being
displayed). Perhaps this one got through a filter because the repeat
is WITHIN a scaffold rather than the EST hitting more than one scaffold
?
\-------------------------------------------------------------------------------
RID: 974811863-24859-18732
Query= GH02584.5prime
(613 letters)
Database: D. melanogaster genomic nucleotide sequences
1170 sequences; 122,655,632 total letters
Score E
Sequences producing significant alignments: (bits) Value
gb|AE003417.1|AE003417 Drosophila melanogaster genomic scaf... 650 0.0
Alignments
>gb|AE003417.1|AE003417 Drosophila melanogaster genomic scaffold
142000013386054 section 1 of 35,
complete sequence
Length = 314661
Score = 650 bits (328), Expect = 0.0
Identities = 331/332 (99%)
Strand = Plus / Minus
Query: 194 aggaccctcttcatctttcgtggtccgcgggggtcgcccatttctgttcaagattgtctg 253
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237566 aggaccctcttcatctttcgtggtccgcgggggtcgcccatttctgttcaagattgtctg
237507
Query: 254 cccatggttctcagctctgagctgctccaggatgccctgcggtccagcaacaagcttcta 313
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237506 cccatggttctcagctctgagctgctccaggatgccctgcggtccagcaacaagcttcta
237447
Query: 314 ttcgaatgctatggcagcctgatcagatgctatcaggagtgcgttgaacttcgcaaggat 373
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237446 ttcgaatgctatggcagcctgatcagatgctatcaggagtgcgttgaacttcgcaaggat
237387
Query: 374 aacaaggatcggactaagagccaagactactgggatgcagagtttgtaggttctgtgatc 433
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237386 aacaaggatcggactaagagccaagactactgggatgcagagtttgtaggttctgtgatc
237327
Query: 434 aagcagctggcagagatggttcgccgctctcaggagcctgaaaagctgttagaagagaac 493
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237326 aagcagctggcagagatggttcgccgctctcaggagcctgaaaagctgttagaagagaac
237267
Query: 494 aattcgaaaactgttcgtcctcttggcactcg 525
||||||||||||||||||||||||| ||||||
Sbjct: 237266 aattcgaaaactgttcgtcctcttgtcactcg 237235
Score = 611 bits (308), Expect = e-174
Identities = 327/332 (98%), Gaps = 1/332 (0%)
Strand = Plus / Minus
Query: 194 aggaccctcttcatctttcgtggtccgcgggggtcgcccatttctgttcaagattgtctg 253
||||||||||||||||||||||||| |||||||||| |||||||||||||||||||||||
Sbjct: 246212 aggaccctcttcatctttcgtggtctgcgggggtcggccatttctgttcaagattgtctg
246153
Query: 254 cccatggttctcagctctgagctgctccaggatgccctgcggtccagcaacaagcttcta 313
|||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 246152 cccatggt-ctcagctctgagctactccaggatgccctgcggtccagcaacaagcttcta
246094
Query: 314 ttcgaatgctatggcagcctgatcagatgctatcaggagtgcgttgaacttcgcaaggat 373
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 246093 ttcgaatgctatggcagcctgatcagatgctatcaggagtgcgttgaacttcgcaaggat
246034
Query: 374 aacaaggatcggactaagagccaagactactgggatgcagagtttgtaggttctgtgatc 433
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 246033 aacaaggatcggactaagagccaagactactgggatgcagagtttgtaggttctgtgatc
245974
Query: 434 aagcagctggcagagatggttcgccgctctcaggagcctgaaaagctgttagaagagaac 493
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 245973 aagcagctggcagagatggttcgccgctctcaggagcctgaaaagctgttagaagagaac
245914
Query: 494 aattcgaaaactgttcgtcctcttggcactcg 525
||||||||||||||||||||||||| ||||||
Sbjct: 245913 aattcgaaaactgttcgtcctcttgtcactcg 245882
Score = 593 bits (299), Expect = e-168
Identities = 305/307 (99%)
Strand = Plus / Minus
Query: 194 aggaccctcttcatctttcgtggtccgcgggggtcgcccatttctgttcaagattgtctg 253
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 240648 aggaccctcttcatctttcgtggtccgcgggggtcgcccatttctgttcaagattgtctg
240589
Query: 254 cccatggttctcagctctgagctgctccaggatgccctgcggtccagcaacaagcttcta 313
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 240588 cccatggttctcagctctgagctgctccaggatgccctgcggtccagcaacaagcttcta
240529
Query: 314 ttcgaatgctatggcagcctgatcagatgctatcaggagtgcgttgaacttcgcaaggat 373
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 240528 ttcgaatgctatggcagcctgatcagatgctatcaggagtgcgttgaacttcgcaaggat
240469
Query: 374 aacaaggatcggactaagagccaagactactgggatgcagagtttgtaggttctgtgatc 433
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 240468 aacaaggatcggactaagagccaagactactgggatgcagagtttgtaggttctgtgatc
240409
Query: 434 aagcagctggcagagatggttcgccgctctcaggagcctgaaaagctgttagaagagaac 493
|||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Sbjct: 240408 aagcagctggcagagatggttcgccgctctcaggagcctgaaaagctgttagaagaaaac
240349
Query: 494 aattcga 500
| |||||
Sbjct: 240348 atttcga 240342
Score = 420 bits (212), Expect = e-116
Identities = 254/268 (94%)
Strand = Plus / Minus
Query: 251 ctgcccatggttctcagctctgagctgctccaggatgccctgcggtccagcaacaagctt 310
||||||||||||||||| ||||||||||||||||||||| ||||||||||||||||||||
Sbjct: 251207 ctgcccatggttctcagttctgagctgctccaggatgccttgcggtccagcaacaagctt
251148
Query: 311 ctattcgaatgctatggcagcctgatcagatgctatcaggagtgcgttgaacttcgcaag 370
|||||||||||||||||||||||| |||||||| |||| ||||||| ||||||||||||
Sbjct: 251147 ctattcgaatgctatggcagcctgttcagatgccatcaaaagtgcgtcgaacttcgcaag
251088
Query: 371 gataacaaggatcggactaagagccaagactactgggatgcagagtttgtaggttctgtg 430
|||||||||||||||||| ||||||||||| ||||||||||||||||||||| | |||||
Sbjct: 251087 gataacaaggatcggactgagagccaagaccactgggatgcagagtttgtagttcctgtg
251028
Query: 431 atcaagcagctggcagagatggttcgccgctctcaggagcctgaaaagctgttagaagag 490
|||||||||||| ||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct: 251027 atcaagcagctgacagagatggttcgccgctctcaggagcctgaaaagcttttagaagag
250968
Query: 491 aacaattcgaaaactgttcgtcctcttg 518
|||||||||||||||||||||||||||
Sbjct: 250967 tacaattcgaaaactgttcgtcctcttg 250940
Score = 389 bits (196), Expect = e-107
Identities = 196/196 (100%)
Strand = Plus / Minus
Query: 1 tttattgccaatctcttcgtggggttatccccgtaaatttgtggtcgctgctttgctcca 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237798 tttattgccaatctcttcgtggggttatccccgtaaatttgtggtcgctgctttgctcca
237739
Query: 61 ttttttgttctcgtgtttaacggtttaaactgaactcatctttgcattgagcaacaacaa 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237738 ttttttgttctcgtgtttaacggtttaaactgaactcatctttgcattgagcaacaacaa
237679
Query: 121 gcccgacataactgcactctgagcggcgcttcctctccgatctaccacccgctccattac 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237678 gcccgacataactgcactctgagcggcgcttcctctccgatctaccacccgctccattac
237619
Query: 181 aggaagtaggagtagg 196
||||||||||||||||
Sbjct: 237618 aggaagtaggagtagg 237603
Score = 389 bits (196), Expect = e-107
Identities = 196/196 (100%)
Strand = Plus / Minus
Query: 1 tttattgccaatctcttcgtggggttatccccgtaaatttgtggtcgctgctttgctcca 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 240880 tttattgccaatctcttcgtggggttatccccgtaaatttgtggtcgctgctttgctcca
240821
Query: 61 ttttttgttctcgtgtttaacggtttaaactgaactcatctttgcattgagcaacaacaa 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 240820 ttttttgttctcgtgtttaacggtttaaactgaactcatctttgcattgagcaacaacaa
240761
Query: 121 gcccgacataactgcactctgagcggcgcttcctctccgatctaccacccgctccattac 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 240760 gcccgacataactgcactctgagcggcgcttcctctccgatctaccacccgctccattac
240701
Query: 181 aggaagtaggagtagg 196
||||||||||||||||
Sbjct: 240700 aggaagtaggagtagg 240685
Score = 337 bits (170), Expect = 2e-91
Identities = 182/186 (97%)
Strand = Plus / Minus
Query: 1 tttattgccaatctcttcgtggggttatccccgtaaatttgtggtcgctgctttgctcca 60
|||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct: 246443 tttattgccaatctcttcgtggggttatcctcgtaaatttgtggtcgctgctttgctcca
246384
Query: 61 ttttttgttctcgtgtttaacggtttaaactgaactcatctttgcattgagcaacaacaa 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 246383 ttttttgttctcgtgtttaacggtttaaactgaactcatctttgcattgagcaacaacaa
246324
Query: 121 gcccgacataactgcactctgagcggcgcttcctctccgatctaccacccgctccattac 180
|||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||
Sbjct: 246323 gcccgacataactgcactctgagcggcgctgtctctccgatctcccacccgctccattac
246264
Query: 181 aggaag 186
||||||
Sbjct: 246263 aggaag 246258
Score = 337 bits (170), Expect = 2e-91
Identities = 182/186 (97%)
Strand = Plus / Minus
Query: 1 tttattgccaatctcttcgtggggttatccccgtaaatttgtggtcgctgctttgctcca 60
|||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct: 235311 tttattgccaatctcttcgtggggttatcctcgtaaatttgtggtcgctgctttgctcca
235252
Query: 61 ttttttgttctcgtgtttaacggtttaaactgaactcatctttgcattgagcaacaacaa 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 235251 ttttttgttctcgtgtttaacggtttaaactgaactcatctttgcattgagcaacaacaa
235192
Query: 121 gcccgacataactgcactctgagcggcgcttcctctccgatctaccacccgctccattac 180
|||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||
Sbjct: 235191 gcccgacataactgcactctgagcggcgctgtctctccgatctcccacccgctccattac
235132
Query: 181 aggaag 186
||||||
Sbjct: 235131 aggaag 235126
Score = 234 bits (118), Expect = 2e-60
Identities = 131/134 (97%), Gaps = 1/134 (0%)
Strand = Plus / Minus
Query: 392 agccaagactactgggatgcagagtttgtaggttctgtgatcaagcagctggcagagatg 451
||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||
Sbjct: 242941 agccaagactactggaat-cagagtttgtaggttctgtgatcaagcagctggcagagatg
242883
Query: 452 gttcgccgctctcaggagcctgaaaagctgttagaagagaacaattcgaaaactgttcgt 511
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 242882 gttcgccgctctcaggagcctgaaaagctgttagaagagaacaattcgaaaactgttcgt
242823
Query: 512 cctcttggcactcg 525
||||||| ||||||
Sbjct: 242822 cctcttgtcactcg 242809
Score = 210 bits (106), Expect = 3e-53
Identities = 125/130 (96%), Gaps = 1/130 (0%)
Strand = Plus / Minus
Query: 194 aggaccctcttcatctttcgtggtccgcgggggtcgcccatttctgttcaagattgtctg 253
||||||||||||||||||||||||| |||||||||| |||||||||||||||||||||||
Sbjct: 235080 aggaccctcttcatctttcgtggtctgcgggggtcggccatttctgttcaagattgtctg
235021
Query: 254 cccatggttctcagctctgagctgctccaggatgccctgcggtccagcaacaagcttcta 313
||||||| ||||||||||||||| ||||||||||||||||||||||||| ||||||||||
Sbjct: 235020 cccatgg-tctcagctctgagctactccaggatgccctgcggtccagcaccaagcttcta
234962
Query: 314 ttcgaatgct 323
||||||||||
Sbjct: 234961 ttcgaatgct 234952
Score = 153 bits (77), Expect = 6e-36
Identities = 86/89 (96%)
Strand = Plus / Minus
Query: 525 gttgaactatcgcgatgctaatgcgacacgcttgctgaatgtggggcttacccatcgtta 584
|||||||||||||||||||||||||||||||||||||||||||| ||| ||||||||| |
Sbjct: 237172 gttgaactatcgcgatgctaatgcgacacgcttgctgaatgtggcgctcacccatcgtca
237113
Query: 585 acgtttgcatttggatccggatgagatag 613
|||||||||||||||||||||||||||||
Sbjct: 237112 acgtttgcatttggatccggatgagatag 237084
Score = 153 bits (77), Expect = 6e-36
Identities = 86/89 (96%)
Strand = Plus / Minus
Query: 525 gttgaactatcgcgatgctaatgcgacacgcttgctgaatgtggggcttacccatcgtta 584
|||||||||||||||||||||||||||||||||||||||||||| ||| ||||||||| |
Sbjct: 248347 gttgaactatcgcgatgctaatgcgacacgcttgctgaatgtggcgctcacccatcgtca
248288
Query: 585 acgtttgcatttggatccggatgagatag 613
|||||||||||||||||||||||||||||
Sbjct: 248287 acgtttgcatttggatccggatgagatag 248259
Score = 153 bits (77), Expect = 6e-36
Identities = 86/89 (96%)
Strand = Plus / Minus
Query: 525 gttgaactatcgcgatgctaatgcgacacgcttgctgaatgtggggcttacccatcgtta 584
|||||||||||||||||||||||||||||||||||||||||||| ||| ||||||||| |
Sbjct: 240249 gttgaactatcgcgatgctaatgcgacacgcttgctgaatgtggcgctcacccatcgtca
240190
Query: 585 acgtttgcatttggatccggatgagatag 613
|||||||||||||||||||||||||||||
Sbjct: 240189 acgtttgcatttggatccggatgagatag 240161
Score = 153 bits (77), Expect = 6e-36
Identities = 86/89 (96%)
Strand = Plus / Minus
Query: 525 gttgaactatcgcgatgctaatgcgacacgcttgctgaatgtggggcttacccatcgtta 584
|||||||||||||||||||||||||||||||||||||||||||| ||| ||||||||| |
Sbjct: 245819 gttgaactatcgcgatgctaatgcgacacgcttgctgaatgtggcgctcacccatcgtca
245760
Query: 585 acgtttgcatttggatccggatgagatag 613
|||||||||||||||||||||||||||||
Sbjct: 245759 acgtttgcatttggatccggatgagatag 245731
Score = 153 bits (77), Expect = 6e-36
Identities = 86/89 (96%)
Strand = Plus / Minus
Query: 525 gttgaactatcgcgatgctaatgcgacacgcttgctgaatgtggggcttacccatcgtta 584
|||||||||||||||||||||||||||||||||||||||||||| ||| ||||||||| |
Sbjct: 242744 gttgaactatcgcgatgctaatgcgacacgcttgctgaatgtggcgctcacccatcgtca
242685
Query: 585 acgtttgcatttggatccggatgagatag 613
|||||||||||||||||||||||||||||
Sbjct: 242684 acgtttgcatttggatccggatgagatag 242656
Score = 83.8 bits (42), Expect = 4e-15
Identities = 57/62 (91%)
Strand = Plus / Minus
Query: 453 ttcgccgctctcaggagcctgaaaagctgttagaagagaacaattcgaaaactgttcgtc 512
|||| |||||||||| |||||||||||||| ||||||| |||||||| ||||||||||||
Sbjct: 234908 ttcgacgctctcaggggcctgaaaagctgtaagaagagtacaattcgcaaactgttcgtc
234849
Query: 513 ct 514
||
Sbjct: 234848 ct 234847
Score = 69.9 bits (35), Expect = 7e-11
Identities = 56/63 (88%)
Strand = Plus / Minus
Query: 32 cgtaaatttgtggtcgctgctttgctccattttttgttctcgtgtttaacggtttaaact 91
|||||||| | |||||||||||||||| |||||||||||||| || |||| ||| |||||
Sbjct: 233471 cgtaaattagaggtcgctgctttgctcaattttttgttctcgcgtctaactgttcaaact
233412
Query: 92 gaa 94
|||
Sbjct: 233411 gaa 233409
Score = 61.9 bits (31), Expect = 2e-08
Identities = 37/39 (94%)
Strand = Plus / Minus
Query: 354 gcgttgaacttcgcaaggataacaaggatcggactaaga 392
|||||||| ||||||||||||| ||||||||||||||||
Sbjct: 234947 gcgttgaatttcgcaaggataataaggatcggactaaga 234909
Score = 60.0 bits (30), Expect = 6e-08
Identities = 61/70 (87%), Gaps = 1/70 (1%)
Strand = Plus / Minus
Query: 115 caacaagcccgacataactgcactctgagcggcgcttcctctccgatctaccacccgctc 174
||||||| ||| |||||||| |||||||||||||| |||||| |||| |||||| |||
Sbjct: 233403 caacaagtccgggataactgcgctctgagcggcgctatctctccaatctcccaccc-ctc
233345
Query: 175 cattacagga 184
||||||||||
Sbjct: 233344 cattacagga 233335
Database: D. melanogaster genomic nucleotide sequences
Posted date: Nov 13, 2000  4:43  PM
Number of letters in database: 122,655,632
Number of sequences in database: 1170
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 Hits to DB: 36288
Number of Sequences: 1170
Number of extensions: 36288
Number of successful extensions: 34
Number of sequences better than 10.0: 14
length of query: 613
length of database: 122,655,632
effective HSP length: 18
effective length of query: 595
effective length of database: 122,634,572
effective search space: 72967570340
effective search space used: 72967570340
T: 0
A: 0
X1: 6 (11.9 bits)
X2: 10 (19.8 bits)
S1: 12 (24.3 bits)
S2: 17 (34.2 bits)
================================================================================
RID: 974814393-18387-30096
Query= GH02584.3prime
(541 letters)
Database: D. melanogaster genomic nucleotide sequences
1170 sequences; 122,655,632 total letters
Score E
Sequences producing significant alignments: (bits) Value
gb|AE003417.1|AE003417 Drosophila melanogaster genomic scaf... 1072 0.0
>gb|AE003417.1|AE003417 Drosophila melanogaster genomic scaffold
142000013386054 section 1 of 35,
complete sequence
Length = 314661
Score = 1072 bits (541), Expect = 0.0
Identities = 541/541 (100%)
Strand = Plus / Plus
Query: 1 gcgtgatggatctctgcgaggagtgtggctactcctgcggcgagtgcgccaagtttattt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 235866 gcgtgatggatctctgcgaggagtgtggctactcctgcggcgagtgcgccaagtttattt
235925
Query: 61 gccgcaactgcgtgactttattgtgagttaagtcccagaaggaagaagcatccccctagg 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 235926 gccgcaactgcgtgactttattgtgagttaagtcccagaaggaagaagcatccccctagg
235985
Query: 121 gaaacccgttagtttaaaaatcaatcgaccatcatcttatttccagtggtaatcgaattg 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 235986 gaaacccgttagtttaaaaatcaatcgaccatcatcttatttccagtggtaatcgaattg
236045
Query: 181 aagaagaggaggctccgctgtgcgagcactgccagatgttcctcagctagggcatcaaac 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 236046 aagaagaggaggctccgctgtgcgagcactgccagatgttcctcagctagggcatcaaac
236105
Query: 241 aatcaagcaaatgtcaaatgtattacgttttaaagaatatagagctatatagtatttaac 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 236106 aatcaagcaaatgtcaaatgtattacgttttaaagaatatagagctatatagtatttaac
236165
Query: 301 attaagcaaaaatctttgatctattctttggaatgctagaaaacttaaatcatgaccttg 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 236166 attaagcaaaaatctttgatctattctttggaatgctagaaaacttaaatcatgaccttg
236225
Query: 361 agttggccaatggcgtttccttaacgtaaaacacaccttttcgaacagcgtcgtgggcct 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 236226 agttggccaatggcgtttccttaacgtaaaacacaccttttcgaacagcgtcgtgggcct
236285
Query: 421 ttcggttgctaccatttggcgaatggtgaagataagcaggaagggtgcgacttttcacgg 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 236286 ttcggttgctaccatttggcgaatggtgaagataagcaggaagggtgcgacttttcacgg
236345
Query: 481 ccagtgcctgcgtggcgcgcactgtggccattacagtggccagtttcagacccaagtccg 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 236346 ccagtgcctgcgtggcgcgcactgtggccattacagtggccagtttcagacccaagtccg
236405
Query: 541 c 541
|
Sbjct: 236406 c 236406
Score = 1072 bits (541), Expect = 0.0
Identities = 541/541 (100%)
Strand = Plus / Plus
Query: 1 gcgtgatggatctctgcgaggagtgtggctactcctgcggcgagtgcgccaagtttattt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241436 gcgtgatggatctctgcgaggagtgtggctactcctgcggcgagtgcgccaagtttattt
241495
Query: 61 gccgcaactgcgtgactttattgtgagttaagtcccagaaggaagaagcatccccctagg 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241496 gccgcaactgcgtgactttattgtgagttaagtcccagaaggaagaagcatccccctagg
241555
Query: 121 gaaacccgttagtttaaaaatcaatcgaccatcatcttatttccagtggtaatcgaattg 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241556 gaaacccgttagtttaaaaatcaatcgaccatcatcttatttccagtggtaatcgaattg
241615
Query: 181 aagaagaggaggctccgctgtgcgagcactgccagatgttcctcagctagggcatcaaac 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241616 aagaagaggaggctccgctgtgcgagcactgccagatgttcctcagctagggcatcaaac
241675
Query: 241 aatcaagcaaatgtcaaatgtattacgttttaaagaatatagagctatatagtatttaac 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241676 aatcaagcaaatgtcaaatgtattacgttttaaagaatatagagctatatagtatttaac
241735
Query: 301 attaagcaaaaatctttgatctattctttggaatgctagaaaacttaaatcatgaccttg 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241736 attaagcaaaaatctttgatctattctttggaatgctagaaaacttaaatcatgaccttg
241795
Query: 361 agttggccaatggcgtttccttaacgtaaaacacaccttttcgaacagcgtcgtgggcct 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241796 agttggccaatggcgtttccttaacgtaaaacacaccttttcgaacagcgtcgtgggcct
241855
Query: 421 ttcggttgctaccatttggcgaatggtgaagataagcaggaagggtgcgacttttcacgg 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241856 ttcggttgctaccatttggcgaatggtgaagataagcaggaagggtgcgacttttcacgg
241915
Query: 481 ccagtgcctgcgtggcgcgcactgtggccattacagtggccagtttcagacccaagtccg 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241916 ccagtgcctgcgtggcgcgcactgtggccattacagtggccagtttcagacccaagtccg
241975
Query: 541 c 541
|
Sbjct: 241976 c 241976
Score = 1059 bits (534), Expect = 0.0
Identities = 541/542 (99%), Gaps = 1/542 (0%)
Strand = Plus / Plus
Query: 1 gcgtgatggatctctgcgagg-agtgtggctactcctgcggcgagtgcgccaagtttatt 59
||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct: 246999 gcgtgatggatctctgcgagggagtgtggctactcctgcggcgagtgcgccaagtttatt
247058
Query: 60 tgccgcaactgcgtgactttattgtgagttaagtcccagaaggaagaagcatccccctag 119
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 247059 tgccgcaactgcgtgactttattgtgagttaagtcccagaaggaagaagcatccccctag
247118
Query: 120 ggaaacccgttagtttaaaaatcaatcgaccatcatcttatttccagtggtaatcgaatt 179
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 247119 ggaaacccgttagtttaaaaatcaatcgaccatcatcttatttccagtggtaatcgaatt
247178
Query: 180 gaagaagaggaggctccgctgtgcgagcactgccagatgttcctcagctagggcatcaaa 239
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 247179 gaagaagaggaggctccgctgtgcgagcactgccagatgttcctcagctagggcatcaaa
247238
Query: 240 caatcaagcaaatgtcaaatgtattacgttttaaagaatatagagctatatagtatttaa 299
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 247239 caatcaagcaaatgtcaaatgtattacgttttaaagaatatagagctatatagtatttaa
247298
Query: 300 cattaagcaaaaatctttgatctattctttggaatgctagaaaacttaaatcatgacctt 359
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 247299 cattaagcaaaaatctttgatctattctttggaatgctagaaaacttaaatcatgacctt
247358
Query: 360 gagttggccaatggcgtttccttaacgtaaaacacaccttttcgaacagcgtcgtgggcc 419
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 247359 gagttggccaatggcgtttccttaacgtaaaacacaccttttcgaacagcgtcgtgggcc
247418
Query: 420 tttcggttgctaccatttggcgaatggtgaagataagcaggaagggtgcgacttttcacg 479
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 247419 tttcggttgctaccatttggcgaatggtgaagataagcaggaagggtgcgacttttcacg
247478
Query: 480 gccagtgcctgcgtggcgcgcactgtggccattacagtggccagtttcagacccaagtcc 539
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 247479 gccagtgcctgcgtggcgcgcactgtggccattacagtggccagtttcagacccaagtcc
247538
Query: 540 gc 541
||
Sbjct: 247539 gc 247540
Score = 634 bits (320), Expect = 0.0
Identities = 326/328 (99%)
Strand = Plus / Plus
Query: 1 gcgtgatggatctctgcgaggagtgtggctactcctgcggcgagtgcgccaagtttattt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 238354 gcgtgatggatctctgcgaggagtgtggctactcctgcggcgagtgcgccaagtttattt
238413
Query: 61 gccgcaactgcgtgactttattgtgagttaagtcccagaaggaagaagcatccccctagg 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 238414 gccgcaactgcgtgactttattgtgagttaagtcccagaaggaagaagcatccccctagg
238473
Query: 121 gaaacccgttagtttaaaaatcaatcgaccatcatcttatttccagtggtaatcgaattg 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 238474 gaaacccgttagtttaaaaatcaatcgaccatcatcttatttccagtggtaatcgaattg
238533
Query: 181 aagaagaggaggctccgctgtgcgagcactgccagatgttcctcagctagggcatcaaac 240
|||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 238534 aagaagaggaggatccgctgtgcgagcactgccagatgttcctcagctagggcatcaaac
238593
Query: 241 aatcaagcaaatgtcaaatgtattacgttttaaagaatatagagctatatagtatttaac 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 238594 aatcaagcaaatgtcaaatgtattacgttttaaagaatatagagctatatagtatttaac
238653
Query: 301 attaagcaaaaatctttgatctattctt 328
|||| |||||||||||||||||||||||
Sbjct: 238654 attaggcaaaaatctttgatctattctt 238681
Score = 605 bits (305), Expect = e-172
Identities = 311/313 (99%)
Strand = Plus / Plus
Query: 1 gcgtgatggatctctgcgaggagtgtggctactcctgcggcgagtgcgccaagtttattt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 243924 gcgtgatggatctctgcgaggagtgtggctactcctgcggcgagtgcgccaagtttattt
243983
Query: 61 gccgcaactgcgtgactttattgtgagttaagtcccagaaggaagaagcatccccctagg 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 243984 gccgcaactgcgtgactttattgtgagttaagtcccagaaggaagaagcatccccctagg
244043
Query: 121 gaaacccgttagtttaaaaatcaatcgaccatcatcttatttccagtggtaatcgaattg 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 244044 gaaacccgttagtttaaaaatcaatcgaccatcatcttatttccagtggtaatcgaattg
244103
Query: 181 aagaagaggaggctccgctgtgcgagcactgccagatgttcctcagctagggcatcaaac 240
|||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 244104 aagaagaggaggatccgctgtgcgagcactgccagatgttcctcagctagggcatcaaac
244163
Query: 241 aatcaagcaaatgtcaaatgtattacgttttaaagaatatagagctatatagtatttaac 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 244164 aatcaagcaaatgtcaaatgtattacgttttaaagaatatagagctatatagtatttaac
244223
Query: 301 attaagcaaaaat 313
|||| ||||||||
Sbjct: 244224 attaggcaaaaat 244236
Score = 347 bits (175), Expect = 2e-94
Identities = 250/274 (91%), Gaps = 2/274 (0%)
Strand = Plus / Plus
Query: 270 ttaaagaatatagagctatatagtatttaacattaagcaaaaatctttgatctattcttt 329
|||||||||||||| | ||||| | |||||| || |||||||| |||||||||||||
Sbjct: 239143 ttaaagaatatagaaccatatacttcttaacacgaaacaaaaatcgttgatctattcttc
239202
Query: 330 ggaatgctagaaaacttaaatcatgaccttgagttggccaatggcgtttccttaacgtaa 389
|||||||| |||||| ||| |||| | || ||||||||||||||| |||||||||||
Sbjct: 239203 ggaatgctgcgaaacttgaattttgacttcgacttggccaatggcgttcccttaacgtaa
239262
Query: 390 aacacaccttttcgaacagcgtcgtgggcctttcggttgctaccatttggcgaatggtga 449
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 239263 aacacaccttttcgaacagcgtcgtgggcctttcggttgctaccatttggcgaatggtga
239322
Query: 450 agataagcaggaagggtgcga--cttttcacggccagtgcctgcgtggcgcgcactgtgg 507
||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||
Sbjct: 239323 agataagcaggaagggtgcgactctcttcacggccagtgcctgcgtggcgcgcactgtgg
239382
Query: 508 ccattacagtggccagtttcagacccaagtccgc 541
|||||||||| |||||||||||||||||||||||
Sbjct: 239383 ccattacagtagccagtttcagacccaagtccgc 239416
Score = 262 bits (132), Expect = 8e-69
Identities = 207/230 (90%), Gaps = 4/230 (1%)
Strand = Plus / Plus
Query: 1 gcgtgatggatctctgcgaggagtgtggctactcctgcggcgagtgcgccaagtttattt 60
||||||||||||||||||||||||||||||||||||||||||||||| ||| ||| ||||
Sbjct: 233851 gcgtgatggatctctgcgaggagtgtggctactcctgcggcgagtgctccaggttcattt
233910
Query: 61 gccgcaactgcgtgactttattgtgagttaagtcccagaaggaagaagcatccccctagg 120
|||||| |||||||||||||||||||||||||||| | ||||||||||||||| ||
Sbjct: 233911 gccgcagctgcgtgactttattgtgagttaagtccttaa---aagaagcatcccccttgg
233967
Query: 121 gaaacccgttagtttaaaaatcaatcgaccatcatctta-tttccagtggtaatcgaatt 179
||| || || ||| ||||||||||||||||||||||| ||||||||||||||||| ||
Sbjct: 233968 gaacaccttttatttgaaaatcaatcgaccatcatcttattttccagtggtaatcgagtt
234027
Query: 180 gaagaagaggaggctccgctgtgcgagcactgccagatgttcctcagcta 229
||||||||| ||| ||| |||||||||||||||||||||||| |||||||
Sbjct: 234028 gaagaagagaaggatcccctgtgcgagcactgccagatgttcttcagcta 234077
Score = 44.1 bits (22), Expect = 0.003
Identities = 25/26 (96%)
Strand = Plus / Plus
Query: 196 cgctgtgcgagcactgccagatgttc 221
||||||||||| ||||||||||||||
Sbjct: 238688 cgctgtgcgagtactgccagatgttc 238713
Score = 34.2 bits (17), Expect = 3.3
Identities = 17/17 (100%)
Strand = Plus / Plus
Query: 250 aatgtcaaatgtattac 266
|||||||||||||||||
Sbjct: 234161 aatgtcaaatgtattac 234177
Database: D. melanogaster genomic nucleotide sequences
Posted date: Nov 13, 2000  4:43  PM
Number of letters in database: 122,655,632
Number of sequences in database: 1170
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 Hits to DB: 39600
Number of Sequences: 1170
Number of extensions: 39600
Number of successful extensions: 82
Number of sequences better than 10.0: 18
length of query: 541
length of database: 122,655,632
effective HSP length: 18
effective length of query: 523
effective length of database: 122,634,572
effective search space: 64137881156
effective search space used: 64137881156
T: 0
A: 0
X1: 6 (11.9 bits)
X2: 10 (19.8 bits)
S1: 12 (24.3 bits)
S2: 17 (34.2 bits)
\-------------------------------------------------------------------------------