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-013862
(881 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|NP_001040052.1| polymerase (RNA) I polypeptide D [Bos taurus]. 184 7e-47
>ref|NP_001040052.1| polymerase (RNA) I polypeptide D [Bos taurus].
Length = 121
Score = 184 bits (468), Expect = 7e-47
Identities = 95/118 (80%), Positives = 95/118 (80%), Gaps = 1/118 (0%)
Frame = +1
Query: 133 MEEDQELERKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKE 312
MEEDQELERKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKE
Sbjct: 1 MEEDQELERKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKE 60
Query: 313 QDHEPKEASAEPAKSQSQKEEGRQKHRPHPYXXXXXXXXXXXXXXXKR-GQEKPQPRS 483
QDHE KE S EPAKSQSQKEEGRQKHR HPY KR G EK Q RS
Sbjct: 61 QDHEQKEDSKEPAKSQSQKEEGRQKHRSHPYKHSVHTRRSPPGKRGKRGGHEKSQSRS 118
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: 25,667,284
Number of extensions: 658820
Number of successful extensions: 3053
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 3049
Number of HSP's successfully gapped: 1
Length of query: 293
Length of database: 17,681,374
Length adjustment: 101
Effective length of query: 192
Effective length of database: 14,339,486
Effective search space: 2753181312
Effective search space used: 2753181312
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-013862
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-013862
(881 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|XP_534521.2| PREDICTED: similar to RNA polymerase 1-3 isofor... 203 2e-52
>ref|XP_534521.2| PREDICTED: similar to RNA polymerase 1-3 isoform 2 [Canis
familiaris].
Length = 329
Score = 203 bits (516), Expect = 2e-52
Identities = 100/118 (84%), Positives = 101/118 (85%)
Frame = +1
Query: 52 LRPHASRYGAEPSAGRHHLRIPEAAPAMEEDQELERKAIEELLKEAKRGKTRAETMGPMG 231
LRP ASRYG P HHLRIPEA PAMEEDQELERKAIEELLKEAKRGKTRAETMGPMG
Sbjct: 181 LRPRASRYGLAPPLCPHHLRIPEAVPAMEEDQELERKAIEELLKEAKRGKTRAETMGPMG 240
Query: 232 WMKCPLAGTNKRFLINTIKNTLPSHKEQDHEPKEASAEPAKSQSQKEEGRQKHRPHPY 405
WMKCPLAGTNKRFLINTIKNTLPSHKEQD E KE S E KSQ QKEE R+KHR HPY
Sbjct: 241 WMKCPLAGTNKRFLINTIKNTLPSHKEQDPEQKEGSKEATKSQGQKEEKRKKHRGHPY 298
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: 26,213,865
Number of extensions: 576434
Number of successful extensions: 3148
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 3137
Number of HSP's successfully gapped: 1
Length of query: 293
Length of database: 18,874,504
Length adjustment: 102
Effective length of query: 191
Effective length of database: 15,474,232
Effective search space: 2955578312
Effective search space used: 2955578312
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-013862
(881 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_001927023.1| PREDICTED: hypothetical protein LOC100152160... 197 6e-51
>ref|XP_001927023.1| PREDICTED: hypothetical protein LOC100152160 isoform 1 [Sus
scrofa].
Length = 121
Score = 197 bits (501), Expect = 6e-51
Identities = 96/111 (86%), Positives = 96/111 (86%)
Frame = +1
Query: 157 RKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKEQDHEPKEA 336
RKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKEQDHEPKEA
Sbjct: 10 RKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKEQDHEPKEA 69
Query: 337 SAEPAKSQSQKEEGRQKHRPHPYXXXXXXXXXXXXXXXKRGQEKPQPRSHT 489
SAEPAKSQSQKEEGRQKHRPHPY KRGQEKPQPRSHT
Sbjct: 70 SAEPAKSQSQKEEGRQKHRPHPYKPGGRAGGAARRSPGKRGQEKPQPRSHT 120
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: 17,599,999
Number of extensions: 573382
Number of successful extensions: 2016
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 2010
Number of HSP's successfully gapped: 1
Length of query: 293
Length of database: 11,343,932
Length adjustment: 98
Effective length of query: 195
Effective length of database: 8,904,026
Effective search space: 1736285070
Effective search space used: 1736285070
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-013862
(881 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|XP_001472529.1| PREDICTED: hypothetical protein LOC100039220... 162 2e-40
Alignment gi|NP_859419.1| DNA-directed RNA polymerases I and III subunit ... 162 2e-40
>ref|XP_001472529.1| PREDICTED: hypothetical protein LOC100039220 [Mus musculus].
Length = 126
Score = 162 bits (411), Expect = 2e-40
Identities = 78/91 (85%), Positives = 81/91 (89%)
Frame = +1
Query: 133 MEEDQELERKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKE 312
ME+DQELERKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKE
Sbjct: 1 MEDDQELERKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKE 60
Query: 313 QDHEPKEASAEPAKSQSQKEEGRQKHRPHPY 405
QDHE KE S EP KSQ QKE +K+R H Y
Sbjct: 61 QDHEQKEGSKEPGKSQDQKEASGKKYRSHSY 91
>ref|NP_859419.1| DNA-directed RNA polymerases I and III subunit RPAC2 isoform 2 [Mus
musculus].
Length = 126
Score = 162 bits (411), Expect = 2e-40
Identities = 78/91 (85%), Positives = 81/91 (89%)
Frame = +1
Query: 133 MEEDQELERKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKE 312
ME+DQELERKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKE
Sbjct: 1 MEDDQELERKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKE 60
Query: 313 QDHEPKEASAEPAKSQSQKEEGRQKHRPHPY 405
QDHE KE S EP KSQ QKE +K+R H Y
Sbjct: 61 QDHEQKEGSKEPGKSQDQKEASGKKYRSHSY 91
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: 21,569,288
Number of extensions: 463833
Number of successful extensions: 2396
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 2386
Number of HSP's successfully gapped: 2
Length of query: 293
Length of database: 15,617,559
Length adjustment: 101
Effective length of query: 192
Effective length of database: 12,583,923
Effective search space: 2416113216
Effective search space used: 2416113216
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-013862
(881 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|NP_689918.1| DNA-directed RNA polymerases I and III subunit ... 169 2e-42
Alignment gi|NP_001193488.1| DNA-directed RNA polymerases I and III subun... 117 1e-26
>ref|NP_689918.1| DNA-directed RNA polymerases I and III subunit RPAC2 isoform 2
[Homo sapiens].
Length = 122
Score = 169 bits (429), Expect = 2e-42
Identities = 81/91 (89%), Positives = 83/91 (91%)
Frame = +1
Query: 133 MEEDQELERKAIEELLKEAKRGKTRAETMGPMGWMKCPLAGTNKRFLINTIKNTLPSHKE 312
MEEDQELERKAIEELLKEAKRGKTRAETMGPMGWMKCPLA TNKRFLINTIKNTLPSHKE
Sbjct: 1 MEEDQELERKAIEELLKEAKRGKTRAETMGPMGWMKCPLASTNKRFLINTIKNTLPSHKE 60
Query: 313 QDHEPKEASAEPAKSQSQKEEGRQKHRPHPY 405
QDHE KE EPAKSQ+QKEE +KHR HPY
Sbjct: 61 QDHEQKEGDKEPAKSQAQKEENPKKHRSHPY 91
>ref|NP_001193488.1| DNA-directed RNA polymerases I and III subunit RPAC2 isoform 3
[Homo sapiens].
Length = 94
Score = 117 bits (294), Expect = 1e-26
Identities = 53/63 (84%), Positives = 55/63 (87%)
Frame = +1
Query: 217 MGPMGWMKCPLAGTNKRFLINTIKNTLPSHKEQDHEPKEASAEPAKSQSQKEEGRQKHRP 396
MGPMGWMKCPLA TNKRFLINTIKNTLPSHKEQDHE KE EPAKSQ+QKEE +KHR
Sbjct: 1 MGPMGWMKCPLASTNKRFLINTIKNTLPSHKEQDHEQKEGDKEPAKSQAQKEENPKKHRS 60
Query: 397 HPY 405
HPY
Sbjct: 61 HPY 63
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: 25,594,358
Number of extensions: 557129
Number of successful extensions: 3127
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 3123
Number of HSP's successfully gapped: 2
Length of query: 293
Length of database: 18,297,164
Length adjustment: 102
Effective length of query: 191
Effective length of database: 14,934,836
Effective search space: 2852553676
Effective search space used: 2852553676
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-013862
(881 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_Chr11 521 e-145
Sscrofa_Chr09 137 1e-29
gb|GL892329.2| Sus scrofa unplaced genomic scaffold ChrUScaf216 131 7e-28
>Sscrofa_Chr11
|| Length = 87690581
Score = 521 bits (263), Expect = e-145
Identities = 315/338 (93%), Gaps = 8/338 (2%)
Strand = Plus / Plus
Query: 451 aagcggggccaggagaagccgcagccgcgctcccacacgcggtgaggcggggcgagggct 510
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4724351 aagcggggccaggagaagccgcagccgcgctcccacacgcggtgaggcggggcgagggct 4724410
Query: 511 cgggcgtccccgcccccggcccggggatgcggagacccggcgaggacctnnnnnnnnnnn 570
|||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4724411 cgggcgtccccgcccccggcccggggatgcggagacccggcgaggacctgcccgcggccg 4724470
Query: 571 nnnnnnnnnnnatgcgggacgtcccggctgcagcagcgcgtcgccgaggctcgtgctctg 630
|||| ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4724471 ccc--------atgcaggacgtcccggctgcagcagcgcgtcgccgaggctcgtgctctg 4724522
Query: 631 caggtgccccggcagcgagttcaggctgcctcgcggggcaatagccctgggtattgtttc 690
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4724523 caggtgccccggcagcgagttcaggctgcctcgcggggcaatagccctgggtattgtttc 4724582
Query: 691 cattctactttgggagctggcttcaaaataaagctagaacttaaacgttttcagagattg 750
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4724583 cattctactttgggagctggcttcaaaataaagctagaacttaaacgttttcagagattg 4724642
Query: 751 ctaaaactagttccacttttctgtttgtttggtttttt 788
||||||||||||||||||||||||||||||||||||||
Sbjct: 4724643 ctaaaactagttccacttttctgtttgtttggtttttt 4724680
Score = 347 bits (175), Expect = 6e-93
Identities = 175/175 (100%)
Strand = Plus / Plus
Query: 233 ggatgaagtgtcctcttgctggtaccaataagagatttctcattaacacaattaagaaca 292
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4724133 ggatgaagtgtcctcttgctggtaccaataagagatttctcattaacacaattaagaaca 4724192
Query: 293 ctctgccgtcccacaaggagcaagaccatgaacccaaagaggccagtgcggagcctgcga 352
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4724193 ctctgccgtcccacaaggagcaagaccatgaacccaaagaggccagtgcggagcctgcga 4724252
Query: 353 aaagccagagccagaaggaggaaggccggcagaagcacagaccgcatccgtacaa 407
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4724253 aaagccagagccagaaggaggaaggccggcagaagcacagaccgcatccgtacaa 4724307
Score = 214 bits (108), Expect = 6e-53
Identities = 108/108 (100%)
Strand = Plus / Plus
Query: 52 ctgcgcccgcacgcttcgcggtatggggcagagccttcggcgggccggcaccacctgagg 111
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4679172 ctgcgcccgcacgcttcgcggtatggggcagagccttcggcgggccggcaccacctgagg 4679231
Query: 112 atcccggaagccgcccccgcgatggaagaggaccaggagctggagagg 159
||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4679232 atcccggaagccgcccccgcgatggaagaggaccaggagctggagagg 4679279
Score = 155 bits (78), Expect = 5e-35
Identities = 78/78 (100%)
Strand = Plus / Plus
Query: 157 aggaaagcaatagaagaactacttaaagaggcaaaacgtggaaagacgagggcagaaaca 216
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 4705324 aggaaagcaatagaagaactacttaaagaggcaaaacgtggaaagacgagggcagaaaca 4705383
Query: 217 atgggacctatgggttgg 234
||||||||||||||||||
Sbjct: 4705384 atgggacctatgggttgg 4705401
Score = 101 bits (51), Expect = 6e-19
Identities = 63/66 (95%), Gaps = 2/66 (3%)
Strand = Plus / Plus
Query: 816 atgtgctgccacttgtggtcatttctcaatgtttctcgaaaaataaaaagagttataaaa 875
||||||||| |||||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct: 4724708 atgtgctgcaacttgtggtcatttctcaatgtttctcgaaaaat--aaagagttataaaa 4724765
Query: 876 tctata 881
||||||
Sbjct: 4724766 tctata 4724771
>Sscrofa_Chr09
|| Length = 153670197
Score = 137 bits (69), Expect = 1e-29
Identities = 84/89 (94%)
Strand = Plus / Plus
Query: 70 cggtatggggcagagccttcggcgggccggcaccacctgaggatcccggaagccgccccc 129
||||||||||||||||||||||| |||| || |||||||| |||||||||||||||||||
Sbjct: 27454262 cggtatggggcagagccttcggctggccagcgccacctgaagatcccggaagccgccccc 27454321
Query: 130 gcgatggaagaggaccaggagctggagag 158
||||||||||||||||||||||||||||
Sbjct: 27454322 acgatggaagaggaccaggagctggagag 27454350
>gb|GL892329.2| Sus scrofa unplaced genomic scaffold ChrUScaf216
Length = 166430
Score = 131 bits (66), Expect = 7e-28
Identities = 81/86 (94%)
Strand = Plus / Minus
Query: 73 tatggggcagagccttcggcgggccggcaccacctgaggatcccggaagccgcccccgcg 132
|||||||||||||||||||| |||| || |||||||| ||||||||||||||||||| ||
Sbjct: 153656 tatggggcagagccttcggctggccagcgccacctgaagatcccggaagccgcccccacg 153597
Query: 133 atggaagaggaccaggagctggagag 158
||||||||||||||||||||||||||
Sbjct: 153596 atggaagaggaccaggagctggagag 153571
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: 20,724,811
Number of extensions: 462
Number of successful extensions: 462
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 461
Number of HSP's successfully gapped: 8
Length of query: 881
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 860
Effective length of database: 2,808,413,156
Effective search space: 2415235314160
Effective search space used: 2415235314160
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)