BLASTN 2.2.26+
Reference:
Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000),
"A greedy algorithm for aligning DNA sequences", J Comput Biol 2000;
7(1-2):203-14.
Database: TAIR10_cdna_20110103_representative_gene_model_updated
33,602 sequences; 51,074,197 total letters
Query= Ahg938680
Length=714
Score E
Sequences producing significant alignments: (Bits) Value
AT3G57080.1 | Symbols: RPB5B, NRPE5 | Eukaryotic rpb5 RNA polym... 1038 0.0
AT2G41340.1 | Symbols: RPB5D | RNA polymerase II fifth largest ... 361 6e-99
> AT3G57080.1 | Symbols: RPB5B, NRPE5 | Eukaryotic rpb5 RNA polymerase
subunit family protein | chr3:21125857-21127636 FORWARD
LENGTH=856
Length=856
Score = 1038 bits (562), Expect = 0.0
Identities = 666/716 (93%), Gaps = 7/716 (1%)
Strand=Plus/Plus
Query 1 AGATAAGGGAGACGACAAAAATGGAAGTGAAAGGGAAGGAGACAGCTCCGAG-TCTATGT 59
|||||| || || |||||||||||||||||||||||| ||||||||| || | ||| |||
Sbjct 5 AGATAA-GG-GA-GACAAAAATGGAAGTGAAAGGGAAAGAGACAGCTTCG-GTTCTGTGT 60
Query 60 CTGAGCAAATACGTGGATCCATCGAGTGAAGAGAGTCATAGATACTATCTTGCGCGGCAA 119
||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| |
Sbjct 61 CTGAGCAAATACGTGGATCTATCGAGTGAAGAGAGTCATAGATACTATCTTGCGCGGCGA 120
Query 120 AATGCCTTGCAGATGCTCCGAGACAGAGGCTACCAAGTCTCCGACGAAGATATCAATCTC 179
|||| |||||||||||||||||||||||||||| ||||||||||||||||||||||||||
Sbjct 121 AATGGCTTGCAGATGCTCCGAGACAGAGGCTACGAAGTCTCCGACGAAGATATCAATCTC 180
Query 180 TCCCTTCACGATTTTCGAGCTGTTTACGGCGAACGTCCCGATGTTGATCGTCTCCGCATC 239
|||||||||||||||||| |||||||||| ||||||||||||||||||||||| ||||||
Sbjct 181 TCCCTTCACGATTTTCGAACTGTTTACGGTGAACGTCCCGATGTTGATCGTCTTCGCATC 240
Query 240 TCCGCTCAGCATCGCTCCGATTCTTCTAAAAAGGTCAAGGTTGTCTTTTTTGGTACTGGT 299
||||||| |||||||||||||||| | |||||||| || ||||||||||||||||| ||
Sbjct 241 TCCGCTCTGCATCGCTCCGATTCTACCAAAAAGGTAAAAATTGTCTTTTTTGGTACTAGT 300
Query 300 ATGGTTAAAGTCAATGCAATCCGCAGTATAGCAGCGGATGTACTTAGCCAAGAAAC-AGT 358
|||||||||||||| |||||||||||| ||| ||||||| |||||||||||||||| | |
Sbjct 301 ATGGTTAAAGTCAACGCAATCCGCAGTGTAGTAGCGGATATACTTAGCCAAGAAACCA-T 359
Query 359 AACTGGGCTGATTTTGGTTCTGCAAAGCCAAGTAACCAAACAAGCCATGAAAGCCATTGA 418
|||||||||||| ||||||||||||| ||| |||||||| |||||| |||||||||||||
Sbjct 360 AACTGGGCTGATATTGGTTCTGCAAAACCATGTAACCAATCAAGCCTTGAAAGCCATTGA 419
Query 419 ACTCTTTTCTTTCAAGGTCGAGATATTCCAGATAACCGATCTACTAGTCAACATAACCAA 478
||| |||||||||||||||||||||||||||||||| ||||| |||||||||||||||||
Sbjct 420 ACTTTTTTCTTTCAAGGTCGAGATATTCCAGATAACGGATCTGCTAGTCAACATAACCAA 479
Query 479 ACATGCACTCAAGCCACAACATCGGGTTTTGAATGATAAAGAGAAGACAACACTTCTCAA 538
|||| |||| ||||||||||||| ||| ||||||||| ||||||||||||||||||||||
Sbjct 480 ACATTCACTGAAGCCACAACATCAGGTGTTGAATGATGAAGAGAAGACAACACTTCTCAA 539
Query 539 GAAGTTCAGTATTGAGGAAAAACAGCAACCTCGGATTTCAAAGAAAGATGCGATCGTCCG 598
||||||||| |||||||||||||||| ||||||||||||||||||||||| ||||||||
Sbjct 540 GAAGTTCAGCATTGAGGAAAAACAGCTTCCTCGGATTTCAAAGAAAGATGCTATCGTCCG 599
Query 599 CTACTACGGATTAGAGAAAGGGCAAGTTGTGAAGGTGAATTATAGAGGCGAACTCACGGA 658
||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Sbjct 600 GTACTACGGATTAGAGAAAGGGCAAGTTGTGAAGGTGAATTACAGAGGCGAACTCACGGA 659
Query 659 ATCGCATGTTGCCTACCGATGTGTGGGGTGAAGAAACCAATAAAAAACCATCTTGT 714
|||||||||||||| |||||||||| ||||||||||||||| ||||||||||||||
Sbjct 660 ATCGCATGTTGCCTTCCGATGTGTGTGGTGAAGAAACCAATTAAAAACCATCTTGT 715
> AT2G41340.1 | Symbols: RPB5D | RNA polymerase II fifth largest
subunit, D | chr2:17229008-17230482 FORWARD LENGTH=715
Length=715
Score = 361 bits (195), Expect = 6e-99
Identities = 481/616 (78%), Gaps = 32/616 (5%)
Strand=Plus/Plus
Query 80 ATCGAGTGAAGAGAGTCATAGATACTATCTTGCGCGGCAAAATGCCTTGCAGATGCTCCG 139
||| |||| |||| |||| | ||| || || || || | || || || ||||||||||
Sbjct 66 ATCAAGTGTAGAGTGTCACAAATATTACCTGGCACGTCGAACCACCATGGAGATGCTCCG 125
Query 140 AGACAGAGGCTACCAAGTCTCCGACGAAGATATCAATCTCTCCCTTCACG-ATTTTCGAG 198
||||||||| ||| | ||||||||||||||||| || |||||||| || | | |||||||
Sbjct 126 AGACAGAGGATACGATGTCTCCGACGAAGATATTAACCTCTCCCTCCA-GCAATTTCGAG 184
Query 199 CTG-TTTACGGCGAACGTCCCGATGTTGATCGT-CTCCGCATCTCCGCTC-AGCATCGCT 255
| | | || || |||| ||| || || |||| | || || ||||| || | | |||||||
Sbjct 185 C-GCTCTATGGGGAACATCCTGACGTAGATC-TACTTCGTATCTCAGC-CAAACATCGCT 241
Query 256 CCGATTCTTCTAAAAAGGTCAAGGTTGTCTTTTTTGGTACTGGTATGGTTAAAGTCAATG 315
|||||||| |||||| || ||| || |||| ||| |||||||| |||||||||||||
Sbjct 242 TTGATTCTTCGAAAAAGATCTCGGTAGTGTTTTGTGGAACTGGTATAGTTAAAGTCAATG 301
Query 316 CAATCCGCAGT-ATAGCAGCGGATGTACTTAGCCAAG-AAACAGTAACTGGGCTGATTTT 373
| || ||| || || ||||| ||||| ||||||| || ||| | |||| || ||||| |
Sbjct 302 CGATGCGC-GTCATTGCAGCAGATGTGCTTAGCCGAGAAAATA-TAACCGGACTGATACT 359
Query 374 GGTTCTGCAAAGCCA-AGTAACCAAACAAGC-CATGAAAGCCATTGAACTCTTT-T-CTT 429
|||| ||||||| || | |||| || ||||| | | |||||| ||||||| ||| | |||
Sbjct 360 GGTTTTGCAAAGTCATA-TAACGAACCAAGCTC-TTAAAGCCGTTGAACT-TTTCTCCTT 416
Query 430 TCAAGGTCGAGATATTCCAGATAACCGATCTACTAGTCAACATAACCAAACATGCAC-TC 488
| ||||||||| ||||| |||| |||||| | | || ||| ||| |||||||| | |
Sbjct 417 T-AAGGTCGAGTTATTCGAGATTACCGATTTGTTGGTTAACGTAAGCAAACATG-TCTTG 474
Query 489 AAGCCACAACATCGGGTTTTGAATGATAAAGAGAA-GACAACACTTCTCAAGAAGTTCAG 547
| |||| |||||| |||| |||| ||||||||||| || | |||||||||||||||||||
Sbjct 475 AGGCCAAAACATCAGGTTCTGAACGATAAAGAGAAGGA-ATCACTTCTCAAGAAGTTCAG 533
Query 548 TATTGAGGAAAAACAGCAACCTCGGATT-TCAAAG-AAAGATGCGATCGTCCGCTACTAC 605
||||||||| ||||| | |||||| || || | | ||||| |||| || || |||||
Sbjct 534 TATTGAGGAGAAACAACTTCCTCGG-TTATCGA-GCAAAGACCCGATTGTGCGATACTAT 591
Query 606 GGATTAGAGAAAGGGCAAGTTGTGAAGGTGA-ATTATAGAGGCGAACTCACG-GAATCGC 663
||| |||||| ||||||||| ||||||| | || | | || ||| |||| | || ||||
Sbjct 592 GGACTAGAGACAGGGCAAGTCATGAAGGTCACAT-ACAAAGACGAGCTCA-GTGAGTCGC 649
Query 664 ATGTTGCCTACCGATG 679
||||| | ||||||||
Sbjct 650 ATGTTACATACCGATG 665
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 34611327283
Database: TAIR10_cdna_20110103_representative_gene_model_updated
Posted date: Sep 25, 2014 6:13 PM
Number of letters in database: 51,074,197
Number of sequences in database: 33,602
Matrix: blastn matrix 1 -2
Gap Penalties: Existence: 0, Extension: 2.5