Search to RefSeqBP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-001223
(980 letters)
Database: RefSeq49_BP.fasta
33,088 sequences; 17,681,374 total letters
Searching..................................................done
***** No hits found ******
Database: RefSeq49_BP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 17,681,374
Number of sequences in database: 33,088
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33088
Number of Hits to DB: 35,844,878
Number of extensions: 905450
Number of successful extensions: 2599
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 2592
Number of HSP's successfully gapped: 0
Length of query: 326
Length of database: 17,681,374
Length adjustment: 102
Effective length of query: 224
Effective length of database: 14,306,398
Effective search space: 3204633152
Effective search space used: 3204633152
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqCP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-001223
(980 letters)
Database: RefSeq49_CP.fasta
33,336 sequences; 18,874,504 total letters
Searching..................................................done
***** No hits found ******
Database: RefSeq49_CP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,874,504
Number of sequences in database: 33,336
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33336
Number of Hits to DB: 37,279,950
Number of extensions: 928776
Number of successful extensions: 2432
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 2431
Number of HSP's successfully gapped: 0
Length of query: 326
Length of database: 18,874,504
Length adjustment: 103
Effective length of query: 223
Effective length of database: 15,440,896
Effective search space: 3443319808
Effective search space used: 3443319808
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqHP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-001223
(980 letters)
Database: RefSeq49_HP.fasta
32,964 sequences; 18,297,164 total letters
Searching..................................................done
***** No hits found ******
Database: RefSeq49_HP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,297,164
Number of sequences in database: 32,964
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 32964
Number of Hits to DB: 36,758,366
Number of extensions: 921547
Number of successful extensions: 2560
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 2553
Number of HSP's successfully gapped: 0
Length of query: 326
Length of database: 18,297,164
Length adjustment: 103
Effective length of query: 223
Effective length of database: 14,901,872
Effective search space: 3323117456
Effective search space used: 3323117456
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqMP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-001223
(980 letters)
Database: RefSeq49_MP.fasta
30,036 sequences; 15,617,559 total letters
Searching..................................................done
***** No hits found ******
Database: RefSeq49_MP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 15,617,559
Number of sequences in database: 30,036
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 30036
Number of Hits to DB: 31,327,214
Number of extensions: 785100
Number of successful extensions: 2203
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 2196
Number of HSP's successfully gapped: 0
Length of query: 326
Length of database: 15,617,559
Length adjustment: 102
Effective length of query: 224
Effective length of database: 12,553,887
Effective search space: 2812070688
Effective search space used: 2812070688
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqSP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-001223
(980 letters)
Database: RefSeq49_SP.fasta
24,897 sequences; 11,343,932 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_003360900.1| PREDICTED: hypothetical protein LOC100624077... 135 5e-32
>ref|XP_003360900.1| PREDICTED: hypothetical protein LOC100624077 [Sus scrofa].
Length = 121
Score = 135 bits (339), Expect = 5e-32
Identities = 66/67 (98%), Positives = 66/67 (98%)
Frame = +3
Query: 6 HFAQGCVLGLAPFSRPETQLYRRPSPALQRTPSPSRTRIFSRSQAVDEACTWVKLAPDPT 185
HFAQGCVLGLAPFSRPETQLYRRPSPALQRTPSPSRTRIFSRSQAVDEA TWVKLAPDPT
Sbjct: 55 HFAQGCVLGLAPFSRPETQLYRRPSPALQRTPSPSRTRIFSRSQAVDEAGTWVKLAPDPT 114
Query: 186 ANLVLSS 206
ANLVLSS
Sbjct: 115 ANLVLSS 121
Database: RefSeq49_SP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 11,343,932
Number of sequences in database: 24,897
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24897
Number of Hits to DB: 23,028,026
Number of extensions: 577950
Number of successful extensions: 1534
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 1530
Number of HSP's successfully gapped: 1
Length of query: 326
Length of database: 11,343,932
Length adjustment: 99
Effective length of query: 227
Effective length of database: 8,879,129
Effective search space: 2015562283
Effective search space used: 2015562283
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to Sscrofa10_2
BLASTN 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-001223
(980 letters)
Database: Sscrofa_10.2.fasta
4582 sequences; 2,808,509,378 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
gb|GL893011.1| Sus scrofa unplaced genomic scaffold chrU_scaffol... 1534 0.0
Sscrofa_Chr09 113 2e-22
Sscrofa_Chr06 66 4e-08
>gb|GL893011.1| Sus scrofa unplaced genomic scaffold chrU_scaffold1819
Length = 98757
Score = 1534 bits (774), Expect = 0.0
Identities = 840/854 (98%), Gaps = 6/854 (0%)
Strand = Plus / Plus
Query: 128 caggagtcaagctgtggatgaagcatgcacgtgggtgaagctggctcctgacccaactgc 187
||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct: 85102 caggagtcaagctgtggatgaagcaggcacgtgggtgaagctggctcctgacccaactgc 85161
Query: 188 gaacctagtcctcagcagttacagaaaagataaccacaaggctggctgaaagccagtgct 247
||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct: 85162 gaacctagtcctcagcagttaaagaaaagataaccacaaggctggctgaaagccagtgct 85221
Query: 248 ccttcctgcaagtctggacccaggctccagttaaagttgaagaaattatcttagataagt 307
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 85222 ccttcctgcaagtctggacccaggctccagttaaagttgaagaaattatcttagataagt 85281
Query: 308 agtcaaggacgtgtggccattcataatagcatttataatcagctggagcacttttccgat 367
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 85282 agtcaaggacgtgtggccattcataatagcatttataatcagctggagcacttttccgat 85341
Query: 368 ttatcatttgcttaggtccctttgcttgcttcctgattcatcattttacctgcctgttat 427
||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct: 85342 ttatcatttgcttaggtccctttgcttgcttcctgattcatcactttacctgcctgttat 85401
Query: 428 tgcagtcaatcagatctgttatttgttgtaatattgataacaggagatacttatctcttg 487
||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct: 85402 tgcagtcaatcagatctgttatttgttgtgatattgataacaggagatacttatctcttg 85461
Query: 488 ctctattttaatttaacccttgtggtaatagggttagtaccaaagtttagggccaccact 547
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 85462 ctctattttaatttaacccttgtggtaatagggttagtaccaaagtttagggccaccact 85521
Query: 548 cttttcccatataagctgttggccccaactgtaatgatggctcttgttgttctttactgt 607
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 85522 cttttcccatataagctgttggccccaactgtaatgatggctcttgttgttctttactgt 85581
Query: 608 ctcatctcactggtgtctgctacttcctggaaggaaaatactctagttaagttgtctcag 667
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 85582 ctcatctcactggtgtctgctacttcctggaaggaaaatactctagttaagttgtctcag 85641
Query: 668 agtgtagccgatggtgggaatttaaataattgttggatatgtcatatgagccctcatgcc 727
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 85642 agtgtagccgatggtgggaatttaaataattgttggatatgtcatatgagccctcatgcc 85701
Query: 728 agccatggacagtatctcccatcagtggtccccatcactgattttgataccataccagac 787
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 85702 agccatggacagtatctcccatcagtggtccccatcactgattttgataccataccagac 85761
Query: 788 cctgagaccttctataatctttctcctccacgactcacattccaagttcagatagccagt 847
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 85762 cctgagaccttctataatctttctcctccacgactcacattccaagttcagatagccagt 85821
Query: 848 ggggcctccgaataccccaactccttggcttccacctgtctgaggtaaatt-catcgcag 906
||||||||||||||||||||||||| ||||||||||||||||||||| || ||||||||
Sbjct: 85822 -gggcctccgaataccccaactcctt-gcttccacctgtctgaggtaatttccatcgcag 85879
Query: 907 gaaaaaatgactactgggttcccaaaggtcccctcaaatttcttctgagaaaatgtgatg 966
| ||||||||||||| ||| ||| ||||| ||||||||||||||||||||||||||||||
Sbjct: 85880 g-aaaaatgactact-ggtcccccaaggt-ccctcaaatttcttctgagaaaatgtgatg 85936
Query: 967 cccaaaaacccccc 980
||||||| ||||||
Sbjct: 85937 cccaaaaccccccc 85950
Score = 167 bits (84), Expect = 1e-38
Identities = 84/84 (100%)
Strand = Plus / Plus
Query: 48 aggcctgagacgcagctctacaggagaccaagtcctgctctgcagagaactccttctcct 107
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 82070 aggcctgagacgcagctctacaggagaccaagtcctgctctgcagagaactccttctcct 82129
Query: 108 tccagaacaaggatcttcagcagg 131
||||||||||||||||||||||||
Sbjct: 82130 tccagaacaaggatcttcagcagg 82153
Score = 93.7 bits (47), Expect = 2e-16
Identities = 47/47 (100%)
Strand = Plus / Plus
Query: 4 ctcactttgctcagggctgcgtccttgggctggcgcccttctccagg 50
|||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 81310 ctcactttgctcagggctgcgtccttgggctggcgcccttctccagg 81356
>Sscrofa_Chr09
|| Length = 153670197
Score = 113 bits (57), Expect = 2e-22
Identities = 105/121 (86%)
Strand = Plus / Minus
Query: 524 gtaccaaagtttagggccaccactcttttcccatataagctgttggccccaactgtaatg 583
|||||||| |||||| || |||| ||||| ||||||||||| |||| |||| |||||||
Sbjct: 6227253 gtaccaaaacttagggtcatcactgttttcacatataagctgctggctccaaatgtaatg 6227194
Query: 584 atggctcttgttgttctttactgtctcatctcactggtgtctgctacttcctggaaggaa 643
|||||| || || ||||||||||||||||||||||||||| ||| |||||||||| |||
Sbjct: 6227193 atggctattatttctctttactgtctcatctcactggtgtcagctgcttcctggaaagaa 6227134
Query: 644 a 644
|
Sbjct: 6227133 a 6227133
>Sscrofa_Chr06
|| Length = 157765593
Score = 65.9 bits (33), Expect = 4e-08
Identities = 78/93 (83%)
Strand = Plus / Plus
Query: 560 aagctgttggccccaactgtaatgatggctcttgttgttctttactgtctcatctcactg 619
||||||||| ||| || ||||||||||| ||| ||| ||||||||| || ||| ||||
Sbjct: 53641351 aagctgttgaccctaattgtaatgatggttctggtttctctttactgcttcctcttactg 53641410
Query: 620 gtgtctgctacttcctggaaggaaaatactcta 652
||||||| || |||||| |||| ||||||||||
Sbjct: 53641411 gtgtctggtatttcctgaaaggcaaatactcta 53641443
Score = 65.9 bits (33), Expect = 4e-08
Identities = 78/93 (83%)
Strand = Plus / Plus
Query: 560 aagctgttggccccaactgtaatgatggctcttgttgttctttactgtctcatctcactg 619
||||||||| ||| || ||||||||||| ||| ||| ||||||||| || ||| ||||
Sbjct: 53964149 aagctgttgaccctaattgtaatgatggttctggtttctctttactgcttcctcttactg 53964208
Query: 620 gtgtctgctacttcctggaaggaaaatactcta 652
||||||| || |||||| |||| ||||||||||
Sbjct: 53964209 gtgtctggtatttcctgaaaggcaaatactcta 53964241
Database: Sscrofa_10.2.fasta
Posted date: Nov 16, 2011 10:34 AM
Number of letters in database: 2,808,509,378
Number of sequences in database: 4582
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: 4582
Number of Hits to DB: 32,636,994
Number of extensions: 193
Number of successful extensions: 193
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 190
Number of HSP's successfully gapped: 6
Length of query: 980
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 959
Effective length of database: 2,808,413,156
Effective search space: 2693268216604
Effective search space used: 2693268216604
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 18 (36.2 bits)
S2: 29 (58.0 bits)