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= Ahg938369
Length=717
Score E
Sequences producing significant alignments: (Bits) Value
AT3G54490.1 | Symbols: RPB5E | RNA polymerase II fifth largest ... 1031 0.0
> AT3G54490.1 | Symbols: RPB5E | RNA polymerase II fifth largest
subunit, E | chr3:20173619-20175462 FORWARD LENGTH=921
Length=921
Score = 1031 bits (558), Expect = 0.0
Identities = 670/721 (93%), Gaps = 20/721 (3%)
Strand=Plus/Plus
Query 16 GGAGGTGAAAATGGCCGAAGAAGGGTGCTGTGAAAATGGTGAGTCGACGTTTAAAAATGG 75
||||| || ||||||||||||||||||||||||||||| ||||||||||||| | | ||
Sbjct 57 GGAGGAGACAATGGCCGAAGAAGGGTGCTGTGAAAATGTTGAGTCGACGTTTGACGACGG 116
Query 76 TAGCC-ACTGTATTTCGAAGACTGAGGACACCGGAGGAATCGACAGCAAGAGGTTTTACT 134
|| || ||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct 117 TA-CCAACTGTATTTCGAAGACTGAGGACACCGGAGGAATCGAAAGCAAGAGGTTTTACT 175
Query 135 TGGCTCGCACGACAGCTTTTGAGATGCTTCGCGACAGAGGCTACGAAGTTAATGAAGCTG 194
|||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Sbjct 176 TGGCTCGCACGACAGCTTTTGAGATGCTTCGCGATAGAGGCTACGAAGTTAATGAAGCTG 235
Query 195 AGCTCTCTCTCACTCTTTCTGATTTTCGTTCTGTTTTTGGTGAGAAGCCTGACCTTGAAC 254
|||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||
Sbjct 236 AGCTCTCTCTCACTCTTTCTGAGTTTCGTTCTGTTTTTGGTGAGAAGCCTGAGCTTGAAC 295
Query 255 GCCTCCGTATCTGCGTTCCTCTCCGCTCAGATCCCAAGAAAAAGATCCTTGTTGTGTTCA 314
|||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
Sbjct 296 GCCTCCGTATCTGCGTTCCTCTTCGCTCAGATCCCAAGAAAAAGATCCTTGTTGTGTTCA 355
Query 315 TGGGAACTGAACCAATCACCGTGAAATCAGTTCGTGCTATTCATAGTCAGATTTCCAACA 374
||||||||||||||||||||||||| |||||||||||| |||||| ||||||||||||||
Sbjct 356 TGGGAACTGAACCAATCACCGTGAAGTCAGTTCGTGCTCTTCATATTCAGATTTCCAACA 415
Query 375 ATGTAGGCGTGAATGCTATGATTCTGATATTACAGAGCAAAATGAACCACTTTGCCCACA 434
|||||||| || |||||||||||||| | ||||||||||||||||||||||||||||| |
Sbjct 416 ATGTAGGCTTGCATGCTATGATTCTGGTTTTACAGAGCAAAATGAACCACTTTGCCCAGA 475
Query 435 AGGAATTGACAACCTTCCCTTTTACAGTTGAAACTATCCCGATTGGAGATTTGTTGGTCA 494
||| |||||| |||||||||||||||||||||||| ||||||||| ||||||||||||||
Sbjct 476 AGGCATTGACTACCTTCCCTTTTACAGTTGAAACTTTCCCGATTGAAGATTTGTTGGTCA 535
Query 495 ACATCACAAAGCATATTCAGCAGCCAAAGATTGAGATTTTAAACAAAGAGGAGAAAGAAC 554
||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 536 ACATCACAAAGCACATTCAGCAGCCAAAGATTGAGATTTTAAACAAAGAGGAGAAAGAAC 595
Query 555 AATTGCTGAGGAAGCATGCCCTTGAGGACAAACAG-----------G-AGGA------CA 596
|| |||||||||||||||| ||||||||||||||| | |||| ||
Sbjct 596 AACTGCTGAGGAAGCATGCACTTGAGGACAAACAGCTTCCTTATTTGCAGGAGAAGGACA 655
Query 597 GCTTCGTCAGATACTATGGGTTAAAGAAAAAACAGGTGGTGAAGATTACATACAGTAAAG 656
|||| || || |||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 656 GCTTTGTGAGGTACTATGGGTTAAAGAAAAAACAGGTGGTGAAGATTACATACAGTAAAG 715
Query 657 AGCCTATTGGGGATTTTGTGACATACCGATGCATCATCTGAACTCTGAAGAAAGGCAAAT 716
||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 716 AGCCTGTTGGGGATTTTGTGACATACCGATGCATCATCTGAACTCTGAAGAAAGGCAAAT 775
Query 717 T 717
|
Sbjct 776 T 776
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 34762029724
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