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-014695
(990 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: 30,664,728
Number of extensions: 693955
Number of successful extensions: 2004
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 2004
Number of HSP's successfully gapped: 0
Length of query: 330
Length of database: 18,874,504
Length adjustment: 103
Effective length of query: 227
Effective length of database: 15,440,896
Effective search space: 3505083392
Effective search space used: 3505083392
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-014695
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-014695
(990 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|XP_001787898.1| PREDICTED: POU domain, class 3, transcriptio... 131 8e-31
Alignment gi|XP_002691240.1| PREDICTED: POU class 3 homeobox 3-like [Bos ... 60 5e-15
>ref|XP_001787898.1| PREDICTED: POU domain, class 3, transcription factor 3-like [Bos
taurus].
Length = 828
Score = 131 bits (330), Expect = 8e-31
Identities = 95/219 (43%), Positives = 111/219 (50%), Gaps = 3/219 (1%)
Frame = +3
Query: 15 RSEREGQRANCQIRAERAGXXXXXXXXXXXXAQTRAQSELPRQLGXXXXXXXXXXXXXXE 194
R REG+R + ER G A+T A ELPRQL
Sbjct: 267 RRAREGERERGR---EREGARES--------ARTGAHGELPRQL-RSGTASARAVGAASA 314
Query: 195 PCILPTGVGCVSRIPYMHTHTSTSTNALFF---LLLLQTSAGKKIKHQPQPSAAR*QRNS 365
PC++PTGVGCVSRIPYMHTHTS STNALFF L+LLQTSAGKKIKHQPQPSAAR
Sbjct: 315 PCVVPTGVGCVSRIPYMHTHTSISTNALFFFFLLILLQTSAGKKIKHQPQPSAARKD--- 371
Query: 366 TSFFSCSIFSLLYLFPHFCPKGKMSHQTVTVARRMKKDSCFRGNQELGQ*QLQRNAPSQE 545
P C + + + + R+ + + Q S
Sbjct: 372 --------------VPSDCDCREENERGLLFQRQPRAPAIATSEQ----------CTSAR 407
Query: 546 VFLGQNKT*NARTRGGEQEPASPLGTRAASITTPSRTKK 662
F ++ RT GGE+EPAS LGTRAAS TTPSRTKK
Sbjct: 408 SFPRTEQSRAERTGGGEREPASLLGTRAASTTTPSRTKK 446
>ref|XP_002691240.1| PREDICTED: POU class 3 homeobox 3-like [Bos taurus].
Length = 649
Score = 60.1 bits (144), Expect(2) = 5e-15
Identities = 35/52 (67%), Positives = 39/52 (75%)
Frame = -3
Query: 730 TSRSLTPPFQERSSLVSP*SSKTFFVLEGVVMLAARVPRGEAGSCSPPLVLA 575
T RS P +ER SLVSP KTFFVLEGVV+LAARVP +AGS SPP VL+
Sbjct: 20 TGRSSPAP-RERPSLVSPRRRKTFFVLEGVVVLAARVPSRDAGSRSPPPVLS 70
Score = 39.3 bits (90), Expect(2) = 5e-15
Identities = 22/31 (70%), Positives = 25/31 (80%)
Frame = -1
Query: 591 PLWSSRFKFCSVLGKLLAMVHFSEVAIARAL 499
P+ S+R CSVLGKLLA+VH SEVAIA AL
Sbjct: 67 PVLSARL--CSVLGKLLALVHCSEVAIAGAL 95
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: 29,489,930
Number of extensions: 701729
Number of successful extensions: 2178
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 2175
Number of HSP's successfully gapped: 5
Length of query: 330
Length of database: 17,681,374
Length adjustment: 103
Effective length of query: 227
Effective length of database: 14,273,310
Effective search space: 3240041370
Effective search space used: 3240041370
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-014695
(990 letters)
Database: RefSeq49_SP.fasta
24,897 sequences; 11,343,932 total letters
Searching..................................................done
***** No hits found ******
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: 19,310,033
Number of extensions: 492382
Number of successful extensions: 1355
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 1355
Number of HSP's successfully gapped: 0
Length of query: 330
Length of database: 11,343,932
Length adjustment: 99
Effective length of query: 231
Effective length of database: 8,879,129
Effective search space: 2051078799
Effective search space used: 2051078799
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-014695
(990 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: 25,341,251
Number of extensions: 570161
Number of successful extensions: 1779
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 1778
Number of HSP's successfully gapped: 0
Length of query: 330
Length of database: 15,617,559
Length adjustment: 102
Effective length of query: 228
Effective length of database: 12,553,887
Effective search space: 2862286236
Effective search space used: 2862286236
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-014695
(990 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: 29,909,260
Number of extensions: 676525
Number of successful extensions: 2028
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 2028
Number of HSP's successfully gapped: 0
Length of query: 330
Length of database: 18,297,164
Length adjustment: 103
Effective length of query: 227
Effective length of database: 14,901,872
Effective search space: 3382724944
Effective search space used: 3382724944
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-014695
(990 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|GL893854.2| Sus scrofa unplaced genomic scaffold ChrUScaf1739 908 0.0
>gb|GL893854.2| Sus scrofa unplaced genomic scaffold ChrUScaf1739
Length = 44412
Score = 908 bits (458), Expect = 0.0
Identities = 461/462 (99%)
Strand = Plus / Plus
Query: 319 taaaacaccaaccccaaccttcagcagcaaggtaacagagaaactcgacctcgtttttct 378
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 305 taaaacaccaaccccaaccttcagcagcaaggtaacagagaaactcgacctcgtttttct 364
Query: 379 cctgttcaattttttccttgttatatttgtttcctcatttctgcccaaagggaaagatgt 438
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 365 cctgttcaattttttccttgttatatttgtttcctcatttctgcccaaagggaaagatgt 424
Query: 439 cgcatcagactgtgactgttgcgaggagaatgaaaaaggactcttgtttcagaggcaacc 498
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 425 cgcatcagactgtgactgttgcgaggagaatgaaaaaggactcttgtttcagaggcaacc 484
Query: 499 aagagctcgggcaatagcaacttcagagaaatgcaccatcgcaagaagttttcctaggac 558
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 485 aagagctcgggcaatagcaacttcagagaaatgcaccatcgcaagaagttttcctaggac 544
Query: 559 agaacaaaacttgaaacgcgaggaccagagggggagagcaggagccagcctctcctctcg 618
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 545 agaacaaaacttgaaacgcgaggaccagagggggagagcaggagccagcctctcctctcg 604
Query: 619 gcacgcgtgcagccagcatcaccacgccttcaaggacgaaaaaagttttactactctaag 678
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 605 gcacgcgtgcagccagcatcaccacgccttcaaggacgaaaaaagttttactactctaag 664
Query: 679 gggagacgagtgagctgcgttcctgaaaaggaggcgtcaaggagcggctggtcgctggtc 738
|||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Sbjct: 665 gggagacgagtgagctgcgttcctgagaaggaggcgtcaaggagcggctggtcgctggtc 724
Query: 739 gtccacggttcggtgaagaagaaaggagcggcttctttcttt 780
||||||||||||||||||||||||||||||||||||||||||
Sbjct: 725 gtccacggttcggtgaagaagaaaggagcggcttctttcttt 766
Score = 157 bits (79), Expect = 1e-35
Identities = 79/79 (100%)
Strand = Plus / Plus
Query: 107 cgcgcaaaccagggcgcagagcgagctcccgcggcaactcggctccagcacggccagcgc 166
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 32 cgcgcaaaccagggcgcagagcgagctcccgcggcaactcggctccagcacggccagcgc 91
Query: 167 cagcgccgccgtcggtgca 185
|||||||||||||||||||
Sbjct: 92 cagcgccgccgtcggtgca 110
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: 22,402,451
Number of extensions: 190
Number of successful extensions: 190
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 190
Number of HSP's successfully gapped: 2
Length of query: 990
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 969
Effective length of database: 2,808,413,156
Effective search space: 2721352348164
Effective search space used: 2721352348164
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)