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-000142
(640 letters)
Database: RefSeq49_BP.fasta
33,088 sequences; 17,681,374 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|YP_209212.2| NADH dehydrogenase subunit 3 [Bos taurus]. 96 2e-20
>ref|YP_209212.2| NADH dehydrogenase subunit 3 [Bos taurus].
Length = 115
Score = 96.3 bits (238), Expect = 2e-20
Identities = 55/102 (53%), Positives = 59/102 (57%)
Frame = +1
Query: 40 ASLLVLIAF*LPQLNAYSEKTSPYECGFDPIGSARLPFSIKFFLVAITXXXXXXXXXXXX 219
A+LLV+IAF LPQLN YSEKTSPYECGFDP+GSARLPFS+KFFLVAIT
Sbjct: 14 ATLLVIIAFWLPQLNVYSEKTSPYECGFDPMGSARLPFSMKFFLVAITFLLFDLEIALLL 73
Query: 220 XXXXXSQTNNXXXXXXXXXXXXXXXXXXXXYE*TQKGLE*AE 345
SQT N YE TQKGLE E
Sbjct: 74 PLPWASQTANLNTMLTMALFLIILLAVSLAYEWTQKGLEWTE 115
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: 18,462,337
Number of extensions: 555711
Number of successful extensions: 1559
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 1541
Number of HSP's successfully gapped: 1
Length of query: 213
Length of database: 17,681,374
Length adjustment: 98
Effective length of query: 115
Effective length of database: 14,438,750
Effective search space: 1660456250
Effective search space used: 1660456250
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: 33 (17.3 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-000142
(640 letters)
Database: RefSeq49_CP.fasta
33,336 sequences; 18,874,504 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_008478.4| NADH dehydrogenase subunit 3 [Canis lupus famil... 95 5e-20
>ref|NP_008478.4| NADH dehydrogenase subunit 3 [Canis lupus familiaris].
Length = 115
Score = 95.1 bits (235), Expect = 5e-20
Identities = 54/102 (52%), Positives = 59/102 (57%)
Frame = +1
Query: 40 ASLLVLIAF*LPQLNAYSEKTSPYECGFDPIGSARLPFSIKFFLVAITXXXXXXXXXXXX 219
ASLLVLIAF LPQLN Y++KTSPYECGFDP+GSARLPFS+KFFLVAIT
Sbjct: 14 ASLLVLIAFWLPQLNIYTDKTSPYECGFDPMGSARLPFSMKFFLVAITFLLFDLEIALLL 73
Query: 220 XXXXXSQTNNXXXXXXXXXXXXXXXXXXXXYE*TQKGLE*AE 345
SQTN YE T+KGLE E
Sbjct: 74 PLPWASQTNKLTTMLIMALLLISLLAASLAYEWTEKGLEWTE 115
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: 19,077,229
Number of extensions: 504757
Number of successful extensions: 1581
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 1568
Number of HSP's successfully gapped: 1
Length of query: 213
Length of database: 18,874,504
Length adjustment: 98
Effective length of query: 115
Effective length of database: 15,607,576
Effective search space: 1794871240
Effective search space used: 1794871240
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: 33 (17.3 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-000142
(640 letters)
Database: RefSeq49_HP.fasta
32,964 sequences; 18,297,164 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|YP_003024033.1| NADH dehydrogenase subunit 3 [Homo sapiens]. 77 1e-14
>ref|YP_003024033.1| NADH dehydrogenase subunit 3 [Homo sapiens].
Length = 115
Score = 77.4 bits (189), Expect = 1e-14
Identities = 44/102 (43%), Positives = 52/102 (50%)
Frame = +1
Query: 40 ASLLVLIAF*LPQLNAYSEKTSPYECGFDPIGSARLPFSIKFFLVAITXXXXXXXXXXXX 219
A LL++I F LPQLN Y EK++PYECGFDP+ AR+PFS+KFFLVAIT
Sbjct: 14 ALLLMIITFWLPQLNGYMEKSTPYECGFDPMSPARVPFSMKFFLVAITFLLFDLEIALLL 73
Query: 220 XXXXXSQTNNXXXXXXXXXXXXXXXXXXXXYE*TQKGLE*AE 345
QT N YE QKGL+ E
Sbjct: 74 PLPWALQTTNLPLMVMSSLLLIIILALSLAYEWLQKGLDWTE 115
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: 18,478,235
Number of extensions: 478581
Number of successful extensions: 1458
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 1425
Number of HSP's successfully gapped: 1
Length of query: 213
Length of database: 18,297,164
Length adjustment: 98
Effective length of query: 115
Effective length of database: 15,066,692
Effective search space: 1732669580
Effective search space used: 1732669580
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: 33 (17.3 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-000142
(640 letters)
Database: RefSeq49_MP.fasta
30,036 sequences; 15,617,559 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_904335.1| NADH dehydrogenase subunit 3 [Mus musculus]. 80 1e-15
>ref|NP_904335.1| NADH dehydrogenase subunit 3 [Mus musculus].
Length = 115
Score = 80.5 bits (197), Expect = 1e-15
Identities = 46/99 (46%), Positives = 51/99 (51%)
Frame = +1
Query: 49 LVLIAF*LPQLNAYSEKTSPYECGFDPIGSARLPFSIKFFLVAITXXXXXXXXXXXXXXX 228
L+L+AF LPQ+N YSEK +PYECGFDP SARLPFS+KFFLVAIT
Sbjct: 17 LILVAFWLPQMNLYSEKANPYECGFDPTSSARLPFSMKFFLVAITFLLFDLEIALLLPLP 76
Query: 229 XXSQTNNXXXXXXXXXXXXXXXXXXXXYE*TQKGLE*AE 345
QT YE TQKGLE E
Sbjct: 77 WAIQTIKTSTMMIMAFILVTILSLGLAYEWTQKGLEWTE 115
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: 15,597,209
Number of extensions: 397925
Number of successful extensions: 1135
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 1117
Number of HSP's successfully gapped: 1
Length of query: 213
Length of database: 15,617,559
Length adjustment: 97
Effective length of query: 116
Effective length of database: 12,704,067
Effective search space: 1473671772
Effective search space used: 1473671772
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: 32 (16.9 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-000142
(640 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|NP_008641.1| NADH dehydrogenase subunit 3 [Sus scrofa]. 104 4e-23
>ref|NP_008641.1| NADH dehydrogenase subunit 3 [Sus scrofa].
Length = 115
Score = 104 bits (259), Expect = 4e-23
Identities = 60/102 (58%), Positives = 62/102 (60%)
Frame = +1
Query: 40 ASLLVLIAF*LPQLNAYSEKTSPYECGFDPIGSARLPFSIKFFLVAITXXXXXXXXXXXX 219
ASLLVLIAF LPQLNAYSEKTSPYECGFDP+GSARLPFS+KFFLVAIT
Sbjct: 14 ASLLVLIAFWLPQLNAYSEKTSPYECGFDPMGSARLPFSMKFFLVAITFLLFDLEIALLL 73
Query: 220 XXXXXSQTNNXXXXXXXXXXXXXXXXXXXXYE*TQKGLE*AE 345
SQTNN YE TQKGLE AE
Sbjct: 74 PLPWASQTNNLKTMLTMALFLLILLAASLAYEWTQKGLEWAE 115
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: 12,641,802
Number of extensions: 474055
Number of successful extensions: 971
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 958
Number of HSP's successfully gapped: 1
Length of query: 213
Length of database: 11,343,932
Length adjustment: 95
Effective length of query: 118
Effective length of database: 8,978,717
Effective search space: 1059488606
Effective search space used: 1059488606
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: 32 (16.9 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-000142
(640 letters)
Database: Sscrofa_10.2.fasta
4582 sequences; 2,808,509,378 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Sscrofa_Chr02 416 e-114
Sscrofa_Chr07 96 3e-17
Sscrofa_Chr03 74 1e-10
Sscrofa_Chr11 58 6e-06
>Sscrofa_Chr02
|| Length = 162569375
Score = 416 bits (210), Expect = e-114
Identities = 288/314 (91%)
Strand = Plus / Minus
Query: 33 aaccctagcctccctactcgtactaatcgcattctgactaccccaactaaacgcatattc 92
||||||||||||| ||||| || |||||||||||||||||||||| ||||| ||||| ||
Sbjct: 96268987 aaccctagcctccttactcatattaatcgcattctgactaccccagctaaatgcatactc 96268928
Query: 93 agaaaaaacaagcccatatgaatgtggatttgaccccataggatcagcacgcctcccatt 152
|||||||||||||||||| ||||||||||||||||||||||||||||||||||| |||||
Sbjct: 96268927 agaaaaaacaagcccatacgaatgtggatttgaccccataggatcagcacgccttccatt 96268868
Query: 153 ctcaataaaatttttcctagtagccattacatttctcctttttgatctagaaatcgccct 212
||||||||||| ||||||||||| |||||||| ||||| |||||||||||||| |||||
Sbjct: 96268867 ttcaataaaattcttcctagtagcaattacattcctcctctttgatctagaaattgccct 96268808
Query: 213 tctccttcccctaccatgagcatcccaaacaaacaatctaaaaacaatacttacaatagc 272
||||| || ||||||||||||||||||||||||| |||||||||||||| ||||||||
Sbjct: 96268807 cctcctccctttaccatgagcatcccaaacaaacaacctaaaaacaatactcacaatagc 96268748
Query: 273 actattccttcttatcctactagcagcaagcctagcatacgaatgaacccaaaaaggcct 332
|||||| ||||||| ||||||||||||||| ||||||| ||||||||||||||||||||
Sbjct: 96268747 actatttcttcttacactactagcagcaagcttagcatatgaatgaacccaaaaaggcct 96268688
Query: 333 agaatgagcagaat 346
||||||| ||||||
Sbjct: 96268687 agaatgaacagaat 96268674
Score = 408 bits (206), Expect = e-111
Identities = 311/346 (89%)
Strand = Plus / Plus
Query: 1 ataaatattatactaacactactcacaaacgtaaccctagcctccctactcgtactaatc 60
|||||||| ||| |||||||||||||||| ||||||||||||||| |||||||| |||||
Sbjct: 120056081 ataaatatcatattaacactactcacaaatgtaaccctagcctccttactcgtattaatc 120056140
Query: 61 gcattctgactaccccaactaaacgcatattcagaaaaaacaagcccatatgaatgtgga 120
||||||||||||||||| ||||||||||| | |||||||||||||||||| |||||||||
Sbjct: 120056141 gcattctgactaccccagctaaacgcatactgagaaaaaacaagcccatacgaatgtgga 120056200
Query: 121 tttgaccccataggatcagcacgcctcccattctcaataaaatttttcctagtagccatt 180
||||| | |||||||||||||||||| ||||| ||||||||||| ||||||||||| |||
Sbjct: 120056201 tttgatctcataggatcagcacgccttccattttcaataaaattcttcctagtagcaatt 120056260
Query: 181 acatttctcctttttgatctagaaatcgcccttctccttcccctaccatgagcatcccaa 240
||||| ||||| |||| || |||||| ||||| ||||| || |||||||||||||||||
Sbjct: 120056261 acattcctcctctttgttccagaaattgccctcctcctccctttaccatgagcatcccaa 120056320
Query: 241 acaaacaatctaaaaacaatacttacaatagcactattccttcttatcctactagcagca 300
|||||||| |||||||||||||| |||||||||||||| || || | |||||| |||||
Sbjct: 120056321 acaaacaacctaaaaacaatactcacaatagcactatttctcctaacactactaacagca 120056380
Query: 301 agcctagcatacgaatgaacccaaaaaggcctagaatgagcagaat 346
||| ||||||| ||||||||||||||||||||||||||| ||||||
Sbjct: 120056381 agcttagcatatgaatgaacccaaaaaggcctagaatgaacagaat 120056426
Score = 309 bits (156), Expect = 1e-81
Identities = 198/212 (93%)
Strand = Plus / Plus
Query: 1 ataaatattatactaacactactcacaaacgtaaccctagcctccctactcgtactaatc 60
|||||||||||| |||||||||||||||| |||| |||||||||| ||||||||||||||
Sbjct: 136868930 ataaatattatattaacactactcacaaatgtaatcctagcctccttactcgtactaatc 136868989
Query: 61 gcattctgactaccccaactaaacgcatattcagaaaaaacaagcccatatgaatgtgga 120
||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||||
Sbjct: 136868990 gcattctgactaccccagctaaacgcatattcagaaaaaacaagcccatacgaatgtgga 136869049
Query: 121 tttgaccccataggatcagcacgcctcccattctcaataaaatttttcctagtagccatt 180
|||||||||||||||||||||||||| ||||| |||||| |||||||| ||||||| |||
Sbjct: 136869050 tttgaccccataggatcagcacgccttccattttcaatataatttttcttagtagcaatt 136869109
Query: 181 acatttctcctttttgatctagaaatcgccct 212
||||| ||||| |||||||||||||| |||||
Sbjct: 136869110 acattcctcctctttgatctagaaattgccct 136869141
>Sscrofa_Chr07
|| Length = 134764511
Score = 95.6 bits (48), Expect = 3e-17
Identities = 135/164 (82%)
Strand = Plus / Plus
Query: 92 cagaaaaaacaagcccatatgaatgtggatttgaccccataggatcagcacgcctcccat 151
|||||||| ||||||| ||||||||| ||||||| ||||||||||| | |||| || |
Sbjct: 35447485 cagaaaaaccaagcccctatgaatgtagatttgattccataggatcaccctgcctacctt 35447544
Query: 152 tctcaataaaatttttcctagtagccattacatttctcctttttgatctagaaatcgccc 211
| || ||||||||||||||||||||||| |||| ||||| ||| |||||||||| | ||
Sbjct: 35447545 tttccataaaatttttcctagtagccatcccattcctcctgtttaatctagaaattgtcc 35447604
Query: 212 ttctccttcccctaccatgagcatcccaaacaaacaatctaaaa 255
| |||| || ||| |||| |||||||||||| || ||||||
Sbjct: 35447605 tcttcctacctctatgctgagtatcccaaacaaataacctaaaa 35447648
>Sscrofa_Chr03
|| Length = 144787322
Score = 73.8 bits (37), Expect = 1e-10
Identities = 221/281 (78%), Gaps = 1/281 (0%)
Strand = Plus / Plus
Query: 55 ctaatcgcattctgactaccccaactaaacgcatattcagaaaaaacaagcccatatgaa 114
|||||| ||||||||||||||||| |||| ||| ||||| || | | || || |||
Sbjct: 44483164 ctaatcacattctgactaccccaattaaatatttatacagaagaatccaatccctaggaa 44483223
Query: 115 tgtggatttgaccccataggatcagcacgcctcccattctcaataaaatttttcctagta 174
||||||||||| |||||||||||| |||||| | || || ||||| |||||| |||||
Sbjct: 44483224 tgtggatttgatgccataggatcagaacgcctacacttttccataaattttttcttagta 44483283
Query: 175 gccattacatttctcctttttgatctagaaatcgcccttctccttcccctaccatgagca 234
|||||| ||||||| | |||||| || | || ||||| || || | | |||| ||||
Sbjct: 44483284 gccattgcatttcttatctttgatttatatattgccctcct-tttacttttccataagca 44483342
Query: 235 tcccaaacaaacaatctaaaaacaatacttacaatagcactattccttcttatcctacta 294
||||||||||| | ||||||||| ||||| || ||||||||||| | | ||||||
Sbjct: 44483343 tcccaaacaaatatcctaaaaacagtacttgttatggcactattcctaatattactacta 44483402
Query: 295 gcagcaagcctagcatacgaatgaacccaaaaaggcctaga 335
||| |||| | || || ||||||||||||||||| |||||
Sbjct: 44483403 gcaacaagaccggcctatgaatgaacccaaaaaggactaga 44483443
>Sscrofa_Chr11
|| Length = 87690581
Score = 58.0 bits (29), Expect = 6e-06
Identities = 44/49 (89%)
Strand = Plus / Plus
Query: 291 actagcagcaagcctagcatacgaatgaacccaaaaaggcctagaatga 339
|||||||||||| || ||||| ||||| || ||||||||||||||||||
Sbjct: 47926469 actagcagcaagtctggcatatgaatggacacaaaaaggcctagaatga 47926517
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: 14,910,392
Number of extensions: 525
Number of successful extensions: 525
Number of sequences better than 1.0e-05: 4
Number of HSP's gapped: 525
Number of HSP's successfully gapped: 6
Length of query: 640
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 619
Effective length of database: 2,808,413,156
Effective search space: 1738407743564
Effective search space used: 1738407743564
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 17 (34.2 bits)
S2: 29 (58.0 bits)