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= Ahg906638
Length=486
Score E
Sequences producing significant alignments: (Bits) Value
AT3G28956.1 | Symbols: | RNA polymerase II, Rpb4, core protein... 599 8e-171
AT5G62950.1 | Symbols: | RNA polymerase II, Rpb4, core protein... 590 5e-168
> AT3G28956.1 | Symbols: | RNA polymerase II, Rpb4, core protein
| chr3:10980700-10982244 REVERSE LENGTH=657
Length=657
Score = 599 bits (324), Expect = 8e-171
Identities = 386/415 (93%), Gaps = 7/415 (2%)
Strand=Plus/Plus
Query 77 TGAAGGCAAATGCAGGAGCACTTACCAATTTCGAAG-TGCTTGACTTCTTAAACTCAAGA 135
||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||
Sbjct 156 TGAAGGCAAATGCAGGAGCACTTACCAATTTCG-AGTTGCTTGACTTCTTAAACTCAAGA 214
Query 136 GGTGCATCAAAAGATACTACAAGAGTTATTGCTCCAATTGCTAGATCAGAATACAAGGTT 195
||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 215 GGTGCTTCAAAAGATACTACAAGAGTTATTGCTCCAATTGCTAGATCAGAATACAAGGTC 274
Query 196 TATGATTATTTGGTGGAGACTGCTGCTTCCACTCAAACACGAGAGAGCGTTACCAAATTC 255
|||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |
Sbjct 275 TATGATTATTTGGTGGAGACTGCTGCTTCCACTCAAACACGAGAGAGCGTTAACAAATCC 334
Query 256 GCAGACAAGTGCAAAGATTTCAAAGTCGCCAAAGCTGAGATTCTCAATATCATCAATCTC 315
||||||||||| |||||||||||| |||| ||||||||||||||||||||||||||||||
Sbjct 335 GCAGACAAGTGTAAAGATTTCAAACTCGCTAAAGCTGAGATTCTCAATATCATCAATCTC 394
Query 316 CGGCCTTCCTCTATTGTCGAACTGTTACCGATCATAGAGACACC-GGATGATCGAGAAAT 374
||||||| ||||| ||||||||||||||||||||||||| ||| ||||||||||||||
Sbjct 395 TGGCCTTCTTCTATAGTCGAACTGTTACCGATCATAGAGA-ACCTTGATGATCGAGAAAT 453
Query 375 CGACACAGATGGGATATTAGAGCTTGTGAAGGATTTGCTACCGCTTCTGCCAACAACTGA 434
|||||||||||||||||||||||||||||||||||||||||| | |||||| ||| ||||
Sbjct 454 CGACACAGATGGGATATTAGAGCTTGTGAAGGATTTGCTACCTCCTCTGCCTACAGCTGA 513
Query 435 AACTCATAAAGATAATGAC-AA-A-GAAGAAACTGACAACGTTGAACAGTCGTGA 486
|| || |||||||||||| || | |||||||| || || | |||||||||||||
Sbjct 514 AAGTCCTAAAGATAATGATGAAGAAGAAGAAACAGAGAATGGTGAACAGTCGTGA 568
Score = 56.5 bits (30), Expect = 2e-07
Identities = 32/33 (97%), Gaps = 0/33 (0%)
Strand=Plus/Plus
Query 42 TTTCAGGAGCAAAAACTCTGATTTTGGAGCATC 74
||||||||||||||||||||||||||||| |||
Sbjct 53 TTTCAGGAGCAAAAACTCTGATTTTGGAGTATC 85
> AT5G62950.1 | Symbols: | RNA polymerase II, Rpb4, core protein
| chr5:25262225-25263867 REVERSE LENGTH=828
Length=828
Score = 590 bits (319), Expect = 5e-168
Identities = 383/414 (93%), Gaps = 4/414 (1%)
Strand=Plus/Plus
Query 75 AGTGAAGGCAAATGCAGGAGCACTTACCAATTTCGAAGTGCTTGAC-TTCTTAAACTCAA 133
||| |||||||||||||||||||| ||||||||||||||||||||| ||||| ||||| |
Sbjct 287 AGTCAAGGCAAATGCAGGAGCACTGACCAATTTCGAAGTGCTTGACTTTCTT-AACTCGA 345
Query 134 GAGGTGCATCAAAAGATACTACAAGAGTTATTGCTCCAATTGCTAGATCAGAATACAAGG 193
||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct 346 GAGGTGCATCAAAAGATACTACAAGAGTTATAGCTCCAATTGCTAGATCAGAATACAAGG 405
Query 194 TTTATGATTATTTGGTGGAGACTGCTGCTTCCACTCAAACACGAGAGAGCGTTACCAAAT 253
| |||||||||||||||||||||||||||||||||||||||||||||||| ||| |||||
Sbjct 406 TCTATGATTATTTGGTGGAGACTGCTGCTTCCACTCAAACACGAGAGAGCATTAACAAAT 465
Query 254 TCGCAGACAAGTGCAAAGATTTCAAAGTCGCCAAAGCTGAGATTCTCAATATCATCAATC 313
||||||||||||| |||||||||||| |||| ||||||||||||||||||||||||||||
Sbjct 466 TCGCAGACAAGTGTAAAGATTTCAAACTCGCTAAAGCTGAGATTCTCAATATCATCAATC 525
Query 314 TCCGGCCTTCCTCTATTGTCGAACTGTTACCGATCATAGAGACACC-GGATGATCGAGAA 372
|||||||||| ||||| ||||||||||||||||||||||||| ||| |||||||||||||
Sbjct 526 TCCGGCCTTCTTCTATAGTCGAACTGTTACCGATCATAGAGA-ACCTGGATGATCGAGAA 584
Query 373 ATCGACACAGATGGGATATTAGAGCTTGTGAAGGATTTGCTACCGCTTCTGCCAACAACT 432
|||||||| |||||||||||||||||||||||||||||| |||| | |||||| ||||||
Sbjct 585 ATCGACACTGATGGGATATTAGAGCTTGTGAAGGATTTGTTACCTCCTCTGCCTACAACT 644
Query 433 GAAACTCATAAAGATAATGACAAAGAAGAAACTGACAACGTTGAACAGTCGTGA 486
| || || ||||||| |||| |||||||||| || || | |||||||||||||
Sbjct 645 GCAAGTCCTAAAGATGATGATGAAGAAGAAACAGAGAATGGTGAACAGTCGTGA 698
Score = 54.7 bits (29), Expect = 8e-07
Identities = 29/29 (100%), Gaps = 0/29 (0%)
Strand=Plus/Plus
Query 46 AGGAGCAAAAACTCTGATTTTGGAGCATC 74
|||||||||||||||||||||||||||||
Sbjct 156 AGGAGCAAAAACTCTGATTTTGGAGCATC 184
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 23157941767
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