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= Ahg496480
Length=477
Score E
Sequences producing significant alignments: (Bits) Value
AT3G28956.1 | Symbols: | RNA polymerase II, Rpb4, core protein... 608 1e-173
AT5G62950.1 | Symbols: | RNA polymerase II, Rpb4, core protein... 575 1e-163
> AT3G28956.1 | Symbols: | RNA polymerase II, Rpb4, core protein
| chr3:10980700-10982244 REVERSE LENGTH=657
Length=657
Score = 608 bits (329), Expect = 1e-173
Identities = 405/441 (92%), Gaps = 7/441 (2%)
Strand=Plus/Plus
Query 42 GAAAAAGCTTCTTTTTGTATGAAGGCAAACGCAGGAGCACTTACCAATTTCGAAG-TGCT 100
||||||||||||||||| ||||||||||| |||||||||||||||||||||| || ||||
Sbjct 137 GAAAAAGCTTCTTTTTGAATGAAGGCAAATGCAGGAGCACTTACCAATTTCG-AGTTGCT 195
Query 101 TGACTTCTTAAACTCAAGGGGTGCATCAAAAGATACTACAAGAGTTATTGCTCCAATTGC 160
|||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||
Sbjct 196 TGACTTCTTAAACTCAAGAGGTGCTTCAAAAGATACTACAAGAGTTATTGCTCCAATTGC 255
Query 161 TAGATCAGAATACAAGGTCTATGATTATTTGGTGGAGACTGCTGCTTCTACTCAAACACG 220
|||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Sbjct 256 TAGATCAGAATACAAGGTCTATGATTATTTGGTGGAGACTGCTGCTTCCACTCAAACACG 315
Query 221 AGAGAGCGTTACCAAATTCGCAGACAAGTGCAAAGATTTCAAAGTCGCCAAAGCTGAGAT 280
||||||||||| ||||| |||||||||||| |||||||||||| |||| |||||||||||
Sbjct 316 AGAGAGCGTTAACAAATCCGCAGACAAGTGTAAAGATTTCAAACTCGCTAAAGCTGAGAT 375
Query 281 TCTCAATATCATCAATCTCCGGCCTTCTTCTATTGTCGAATTGTTACCGATCATAGAGAC 340
||||||||||||||||||| ||||||||||||| |||||| ||||||||||||||||||
Sbjct 376 TCTCAATATCATCAATCTCTGGCCTTCTTCTATAGTCGAACTGTTACCGATCATAGAGA- 434
Query 341 ACCG-GATGATCGAAAAATCAACACAGATGGGATATTAGAGCTTGTGAAGGATTTGTTAC 399
||| ||||||||| ||||| ||||||||||||||||||||||||||||||||||| |||
Sbjct 435 ACCTTGATGATCGAGAAATCGACACAGATGGGATATTAGAGCTTGTGAAGGATTTGCTAC 494
Query 400 CGCCTCTGCCAACAACTGAAACACATGAAGATAATGCCGAAGAAGAA-A--CAGACAACG 456
| |||||||| ||| |||||| | | ||||||||| ||||||||| | |||| || |
Sbjct 495 CTCCTCTGCCTACAGCTGAAAGTCCTAAAGATAATGATGAAGAAGAAGAAACAGAGAATG 554
Query 457 GTGAACAGTTGTGACTTGCAA 477
||||||||| |||||||||||
Sbjct 555 GTGAACAGTCGTGACTTGCAA 575
> AT5G62950.1 | Symbols: | RNA polymerase II, Rpb4, core protein
| chr5:25262225-25263867 REVERSE LENGTH=828
Length=828
Score = 575 bits (311), Expect = 1e-163
Identities = 381/415 (92%), Gaps = 4/415 (1%)
Strand=Plus/Plus
Query 63 AAGGCAAACGCAGGAGCACTTACCAATTTCGAAGTGCTTGAC-TTCTTAAACTCAAGGGG 121
|||||||| ||||||||||| ||||||||||||||||||||| ||||| ||||| || ||
Sbjct 291 AAGGCAAATGCAGGAGCACTGACCAATTTCGAAGTGCTTGACTTTCTT-AACTCGAGAGG 349
Query 122 TGCATCAAAAGATACTACAAGAGTTATTGCTCCAATTGCTAGATCAGAATACAAGGTCTA 181
||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||
Sbjct 350 TGCATCAAAAGATACTACAAGAGTTATAGCTCCAATTGCTAGATCAGAATACAAGGTCTA 409
Query 182 TGATTATTTGGTGGAGACTGCTGCTTCTACTCAAACACGAGAGAGCGTTACCAAATTCGC 241
||||||||||||||||||||||||||| |||||||||||||||||| ||| |||||||||
Sbjct 410 TGATTATTTGGTGGAGACTGCTGCTTCCACTCAAACACGAGAGAGCATTAACAAATTCGC 469
Query 242 AGACAAGTGCAAAGATTTCAAAGTCGCCAAAGCTGAGATTCTCAATATCATCAATCTCCG 301
||||||||| |||||||||||| |||| ||||||||||||||||||||||||||||||||
Sbjct 470 AGACAAGTGTAAAGATTTCAAACTCGCTAAAGCTGAGATTCTCAATATCATCAATCTCCG 529
Query 302 GCCTTCTTCTATTGTCGAATTGTTACCGATCATAGAGACACC-GGATGATCGAAAAATCA 360
|||||||||||| |||||| |||||||||||||||||| ||| |||||||||| |||||
Sbjct 530 GCCTTCTTCTATAGTCGAACTGTTACCGATCATAGAGA-ACCTGGATGATCGAGAAATCG 588
Query 361 ACACAGATGGGATATTAGAGCTTGTGAAGGATTTGTTACCGCCTCTGCCAACAACTGAAA 420
|||| ||||||||||||||||||||||||||||||||||| |||||||| ||||||| ||
Sbjct 589 ACACTGATGGGATATTAGAGCTTGTGAAGGATTTGTTACCTCCTCTGCCTACAACTGCAA 648
Query 421 CACATGAAGATAATGCCGAAGAAGAAACAGACAACGGTGAACAGTTGTGACTTGC 475
| | ||||| ||| |||||||||||||| || |||||||||| ||||| |||
Sbjct 649 GTCCTAAAGATGATGATGAAGAAGAAACAGAGAATGGTGAACAGTCGTGACGTGC 703
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 22705834444
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