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