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-012346
(975 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: 32,368,501
Number of extensions: 1017178
Number of successful extensions: 2891
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 2889
Number of HSP's successfully gapped: 0
Length of query: 325
Length of database: 17,681,374
Length adjustment: 102
Effective length of query: 223
Effective length of database: 14,306,398
Effective search space: 3190326754
Effective search space used: 3190326754
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)
Animal-Genome cDNA 20110601C-012346
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-012346
(975 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: 32,595,664
Number of extensions: 839030
Number of successful extensions: 2745
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 2743
Number of HSP's successfully gapped: 0
Length of query: 325
Length of database: 18,874,504
Length adjustment: 103
Effective length of query: 222
Effective length of database: 15,440,896
Effective search space: 3427878912
Effective search space used: 3427878912
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-012346
(975 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_003360690.1| PREDICTED: hypothetical protein LOC100624113... 120 1e-27
>ref|XP_003360690.1| PREDICTED: hypothetical protein LOC100624113 [Sus scrofa].
Length = 74
Score = 120 bits (300), Expect = 1e-27
Identities = 61/65 (93%), Positives = 62/65 (95%), Gaps = 2/65 (3%)
Frame = +1
Query: 4 SLCGKLVAGEDGR--RGVRLAFAAKPSPKAGEGAARHICLAAHMQAPGARRKIRSATREC 177
SLCGKL+AGEDG RGVRLAFAAKPSPKAGEGAARHICLAAHMQAPGARRKIRSATREC
Sbjct: 10 SLCGKLLAGEDGDGCRGVRLAFAAKPSPKAGEGAARHICLAAHMQAPGARRKIRSATREC 69
Query: 178 KMSTS 192
KMSTS
Sbjct: 70 KMSTS 74
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: 22,689,541
Number of extensions: 955702
Number of successful extensions: 1825
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 1824
Number of HSP's successfully gapped: 1
Length of query: 325
Length of database: 11,343,932
Length adjustment: 99
Effective length of query: 226
Effective length of database: 8,879,129
Effective search space: 2006683154
Effective search space used: 2006683154
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-012346
(975 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: 27,111,312
Number of extensions: 688149
Number of successful extensions: 2360
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 2357
Number of HSP's successfully gapped: 0
Length of query: 325
Length of database: 15,617,559
Length adjustment: 102
Effective length of query: 223
Effective length of database: 12,553,887
Effective search space: 2799516801
Effective search space used: 2799516801
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-012346
(975 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: 31,982,775
Number of extensions: 811502
Number of successful extensions: 2825
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 2824
Number of HSP's successfully gapped: 0
Length of query: 325
Length of database: 18,297,164
Length adjustment: 103
Effective length of query: 222
Effective length of database: 14,901,872
Effective search space: 3308215584
Effective search space used: 3308215584
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-012346
(975 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|GL892492.1| Sus scrofa unplaced genomic scaffold chrU_scaffol... 488 e-135
Sscrofa_Chr02 220 1e-54
Sscrofa_Chr12 80 3e-12
>gb|GL892492.1| Sus scrofa unplaced genomic scaffold chrU_scaffold1351
Length = 9269
Score = 488 bits (246), Expect = e-135
Identities = 246/246 (100%)
Strand = Plus / Plus
Query: 576 ggtgttgcttttgtgaaatttcagaactttgcagacacaaaaggatgtcctctctggtgt 635
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6919 ggtgttgcttttgtgaaatttcagaactttgcagacacaaaaggatgtcctctctggtgt 6978
Query: 636 tggacagatcttgggagcttcacatctttcctgcattaacacatgggagcagctatcaac 695
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6979 tggacagatcttgggagcttcacatctttcctgcattaacacatgggagcagctatcaac 7038
Query: 696 tcttccgagccaggcgaactgcctagaaatttggggacccttaaatatcaattaggtggt 755
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7039 tcttccgagccaggcgaactgcctagaaatttggggacccttaaatatcaattaggtggt 7098
Query: 756 cttcacttctttacttggttttagcaaaaggattccaataaaatatttaaaagtaaatga 815
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7099 cttcacttctttacttggttttagcaaaaggattccaataaaatatttaaaagtaaatga 7158
Query: 816 aaaata 821
||||||
Sbjct: 7159 aaaata 7164
Score = 404 bits (204), Expect = e-110
Identities = 204/204 (100%)
Strand = Plus / Plus
Query: 375 gcccgagagctccttatctttgaagcccagccaggggctgtccctttcagagatctgggc 434
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6424 gcccgagagctccttatctttgaagcccagccaggggctgtccctttcagagatctgggc 6483
Query: 435 tagactggaaagattctggaaggcctaaggtttggaattctcttgaagagctgacaggat 494
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6484 tagactggaaagattctggaaggcctaaggtttggaattctcttgaagagctgacaggat 6543
Query: 495 ggctgtggtgcccatatagtggttcctgccacttgaacaggctgtgagaagtggagaaga 554
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6544 ggctgtggtgcccatatagtggttcctgccacttgaacaggctgtgagaagtggagaaga 6603
Query: 555 tgccttcagcttgggttctgtggt 578
||||||||||||||||||||||||
Sbjct: 6604 tgccttcagcttgggttctgtggt 6627
Score = 210 bits (106), Expect = 1e-51
Identities = 129/137 (94%), Gaps = 6/137 (4%)
Strand = Plus / Plus
Query: 3 ctctttgtgcggtaaactcgtggctggtgaggatgg------ccgtcgcggagttcgcct 56
||||||||||||||||||| |||||||||||||||| | ||||||||||||||||
Sbjct: 4987 ctctttgtgcggtaaactcctggctggtgaggatggngatggctgtcgcggagttcgcct 5046
Query: 57 ggcttttgctgcgaaaccgtccccaaaggcgggggagggtgccgcccggcacatttgctt 116
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 5047 ggcttttgctgcgaaaccgtccccaaaggcgggggagggtgccgcccggcacatttgctt 5106
Query: 117 agctgcgcacatgcagg 133
|||||||||||||||||
Sbjct: 5107 agctgcgcacatgcagg 5123
Score = 115 bits (58), Expect = 5e-23
Identities = 58/58 (100%)
Strand = Plus / Plus
Query: 171 ggagtgtaagatgtccacatcttaaatggccgcactcgccgcgtaagtccagggccaa 228
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 5694 ggagtgtaagatgtccacatcttaaatggccgcactcgccgcgtaagtccagggccaa 5751
Score = 91.7 bits (46), Expect = 7e-16
Identities = 65/70 (92%), Gaps = 1/70 (1%)
Strand = Plus / Plus
Query: 906 tgatagttgaggtttttatgagactgttaccacagttatcccttttggcttttgatgaat 965
|||||||||||||||||||||||||||||| |||||||| || ||||||||||||||| |
Sbjct: 7249 tgatagttgaggtttttatgagactgttacaacagttat-ccatttggcttttgatgagt 7307
Query: 966 tgggtgaaaa 975
| ||||||||
Sbjct: 7308 ttggtgaaaa 7317
Score = 85.7 bits (43), Expect = 4e-14
Identities = 43/43 (100%)
Strand = Plus / Plus
Query: 130 caggcccctggtgctcgaaggaagatccgcagcgcgacgaggg 172
|||||||||||||||||||||||||||||||||||||||||||
Sbjct: 5379 caggcccctggtgctcgaaggaagatccgcagcgcgacgaggg 5421
>Sscrofa_Chr02
|| Length = 162569375
Score = 220 bits (111), Expect = 1e-54
Identities = 190/214 (88%), Gaps = 3/214 (1%)
Strand = Plus / Minus
Query: 599 gaactttgcagacacaaaaggatgtcctctctggtgttggacagatcttgggagcttcac 658
|||||| ||||||||| | |||||||||||||||||| ||||||||||| || ||||
Sbjct: 72006042 gaacttggcagacacaca-ggatgtcctctctggtgtcggacagatcttagggacttcgt 72005984
Query: 659 atctttcctgcattaacacatgggagcagctatcaactcttccgagccaggcgaactgcc 718
||||||||||||||||||||| |||||||||||||| | || ||| || |||| |||
Sbjct: 72005983 atctttcctgcattaacacattggagcagctatcaatt--tctgaggggggagaaccgcc 72005926
Query: 719 tagaaatttggggacccttaaatatcaattaggtggtcttcacttctttacttggtttta 778
||||||| | ||||||||||||||||||||||||||||||||||||||||||||||| ||
Sbjct: 72005925 tagaaatgtagggacccttaaatatcaattaggtggtcttcacttctttacttggttgta 72005866
Query: 779 gcaaaaggattccaataaaatatttaaaagtaaa 812
|||||||||||| ||||||||| |||||||||||
Sbjct: 72005865 gcaaaaggattctaataaaataattaaaagtaaa 72005832
>Sscrofa_Chr12
|| Length = 63588571
Score = 79.8 bits (40), Expect = 3e-12
Identities = 61/68 (89%)
Strand = Plus / Plus
Query: 741 tatcaattaggtggtcttcacttctttacttggttttagcaaaaggattccaataaaata 800
|||||| ||||| | ||| ||||||||||||||||||| ||||||||| ||||||||||
Sbjct: 51993737 tatcaactaggtaggctttacttctttacttggttttatcaaaaggataacaataaaata 51993796
Query: 801 tttaaaag 808
||||||||
Sbjct: 51993797 tttaaaag 51993804
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: 24,850,326
Number of extensions: 251
Number of successful extensions: 251
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 250
Number of HSP's successfully gapped: 10
Length of query: 975
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 954
Effective length of database: 2,808,413,156
Effective search space: 2679226150824
Effective search space used: 2679226150824
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)