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ObSH3_out.txt
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ObSH3_out.txt
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BLASTN 2.2.28+
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: zizania_palustris_13Nov2018_okGsv.fasta
2,183 sequences; 1,288,768,912 total letters
Query= MH159201.1 Oryza barthii seed shattering 3 (SH3) gene, complete cds
Length=9543
Score E
Sequences producing significant alignments: (Bits) Value
Scaffold_3;HRSCAF=502 296 6e-77
Scaffold_1064;HRSCAF=3428 230 7e-57
> Scaffold_3;HRSCAF=502
Length=58865324
Score = 296 bits (160), Expect = 6e-77
Identities = 617/814 (76%), Gaps = 125/814 (15%)
Strand=Plus/Plus
Query 3171 TTGTGCTTGAGAGTGAATTGGCTTCTGCATGAAGGGTCACTG------T-CT-CTA---- 3218
||| || ||| | || |||||||||||||||||||||||||| | || |||
Sbjct 53534525 TTGAGCATGA-ATTGCATTGGCTTCTGCATGAAGGGTCACTGTCTATCTGCTGCTAGCTT 53534583
Query 3219 GCTAGCACCTTTCTTTCCTGCACTGTTCATGC--AT-G-TAGCTGAAGGCTTTGTGA-TT 3273
||| ||||||||||||||| |||||||||||| || | ||| ||||| |||| ||| ||
Sbjct 53534584 GCTTGCACCTTTCTTTCCTACACTGTTCATGCAGATAGCTAGGTGAAGCCTTTATGATTT 53534643
Query 3274 TC----CTACTA--C--T-GCTACTACTAC-TCT-G-TGGAGAGGCCAGACAGAGAGGCA 3321
|| ||| || | | | | ||||| | | | |||||| ||||| || ||
Sbjct 53534644 TCTATACTAGTATTCTGTGGAGAAGACTACAGATAGATAGAGAGGGGAGACA-TGA--CA 53534700
Query 3322 TGACATGACATACCATGCAAATGCATGGCTTCTTCCTTTAAAAAA-GTCACCAATAGATA 3380
|||||||||||||||||||||||||||| |||||||||||||||| ||| |||| ||||
Sbjct 53534701 TGACATGACATACCATGCAAATGCATGGTTTCTTCCTTTAAAAAAAGTCCCCAA--GATA 53534758
Query 3381 TGT--TG-TGAGGTTGTTTGCTTCTGTCACAACCAACTACTAGCAGCTAGCCCTTTTG-T 3436
||| | || | ||||||||||||||||||| | | |||| |||||||||| |
Sbjct 53534759 TGTAATACTGCAGCTGTTTGCTTCTGTCACAAC-A--T-CTAG----TAGCCCTTTTCAT 53534810
Query 3437 --GCTAGAT--ATGTGT--GGAGTGAAGTGTGATTTGAGCTAACTCCCCTCATGGGAGCA 3490
|| |||| |||| | || | || | ||||||||||||||||||| |||||||||||
Sbjct 53534811 CAGCAAGATGCATGTATATGGGGAGA-GAGTGATTTGAGCTAACTCCC-TCATGGGAGCA 53534868
Query 3491 CACACAATCATT--CT----CATTCA-GTCACTTTGCTTAATTATTTCTTTCTTCTTTCT 3543
|||| | ||||| | |||||| |||||| | ||||||| | | ||| | |
Sbjct 53534869 CACA-A-TCATTTGCAAGGGCATTCAAGTCACTCTT-TTAATTAAAT-T--CTT-TGG-T 53534920
Query 3544 TATGGGAGTGAGTGCCCAAAAAGTGAGTGAATGTAGGGAATCAAACAAAGTAGAGGTACT 3603
|||||||||||||||||||||||||||| || ||| ||||||||||||||| | ||
Sbjct 53534921 -ATGGGAGTGAGTGCCCAAAAAGTGAGTG--TG-AGG-AATCAAACAAAGTAG-GCC-CT 53534973
Query 3604 GTGCTCTTCAGGTTTGGGAAGAAAAAT-GGGA-AC---GG------CAAGGGACCAATGT 3652
| ||||||||||| |||||||||| | |||| | || |||||| |||||||
Sbjct 53534974 G-GCTCTTCAGGTCTGGGAAGAAATCTAGGGAGAAAATGGAATTGGCAAGGGGCCAATGT 53535032
Query 3653 GTGCAGGCATTGGAAAA-GGGTGC---CCCAATTCTGATCTGATCAGATATATATTCAGA 3708
| |||||||||||||| ||||| ||||| |||||||||||||||| ||
Sbjct 53535033 G--CAGGCATTGGAAAAAGGGTGGGTACCCAACTCTGATCTGATCAGATG--------GA 53535082
Query 3709 TCAGCAGAGCCCCTGATAAAAGTCATGGAGGAACAGTTATCCACATCTAAAGCTATAGC- 3767
|||||||||||||||||||| ||||||||| ||||||| ||| | |||||||||||||
Sbjct 53535083 TCAGCAGAGCCCCTGATAAAGGTCATGGAGCAACAGTTTCCCAGAGCTAAAGCTATAGCA 53535142
Query 3768 --TGTGTATTAATGTGTATCTGCAGTCTACACCAGCCTTA--T-GAAACATGCATGCATG 3822
|||||||| ||||||||||||| ||||||||||||||| | ||||||||||| ||
Sbjct 53535143 GCTGTGTATTTATGTGTATCTGCACTCTACACCAGCCTTAGCTTTGAACATGCATGCCTG 53535202
Query 3823 CATGCAT-GCCTTTGAGATTTGATTTTTTACTTCTCAGATTCTTTTGTACAAATGCAAAA 3881
| | | | ||| ||||||||||||| || | | ||||||||| || |||||||
Sbjct 53535203 CCTCCCTTTGCTT-GAGATTTGATTTTG--CTGCGT-G-TTCTTTTGTG-AA-TGCAAAA 53535255
Query 3882 AGA-AAA--TGA--TC-C-TTTGGAATCTAGCAT 3908
| | ||| | | || | |||||||||||||||
Sbjct 53535256 AAATAAAAATAAAATCTCCTTTGGAATCTAGCAT 53535289
Score = 174 bits (94), Expect = 3e-40
Identities = 155/184 (84%), Gaps = 5/184 (3%)
Strand=Plus/Plus
Query 4133 ATCAATCTACAGGTCAGTGTTCCAAGCAATAGCATGCTAAACATCGTGACCGTCCGTTGT 4192
|||||| | ||||||||||||||||||||||||||||| |||||||||||||||||||||
Sbjct 53535518 ATCAATGTGCAGGTCAGTGTTCCAAGCAATAGCATGCTGAACATCGTGACCGTCCGTTGT 53535577
Query 4193 GGCCATTGCACTAGCCTGTTGTCAGTGAACTTGCGAGGATTGGTCCAAGCATTCCCAGCA 4252
|| |||||||||||||| ||||||||||||||| |||||||| | ||| || |||| |
Sbjct 53535578 GGGCATTGCACTAGCCTCTTGTCAGTGAACTTGAGAGGATTGCTGCAATCACTCCCTGTT 53535637
Query 4253 GAAGATCATTTACAGGTTGACACAT--CAATATATACTACTCTT--T-CATGCATGAAAT 4307
||||||||| | |||||| ||| || |||| || ||| | || | || ||||||||
Sbjct 53535638 GAAGATCATCTCCAGGTTCACATATATCAATGCATGCTATTTTTCGTTCAAACATGAAAT 53535697
Query 4308 TATG 4311
||||
Sbjct 53535698 TATG 53535701
Score = 135 bits (73), Expect = 1e-28
Identities = 83/88 (94%), Gaps = 0/88 (0%)
Strand=Plus/Plus
Query 322 AGGAATGTCGGCACAGATCGTGCCGGCGCCGGAGCATGTGTGCTACGTGCACTGCAACTT 381
||||||||| |||||||||| |||||| |||||||||||||||||||||||||||||||
Sbjct 53532214 AGGAATGTCAGCACAGATCGCACCGGCGGCGGAGCATGTGTGCTACGTGCACTGCAACTT 53532273
Query 382 CTGCAACACAATTCTCGCGGTAATTTGT 409
||||||||| ||||||||||||||||||
Sbjct 53532274 CTGCAACACGATTCTCGCGGTAATTTGT 53532301
Score = 128 bits (69), Expect = 2e-26
Identities = 105/122 (86%), Gaps = 4/122 (3%)
Strand=Plus/Plus
Query 8458 AGTGTTTGATTTTGACACCCACTAA-TATATCACTACAGGGAAGAGATCCGGAGGATAAA 8516
||||| |||||||| | || ||| ||| || | ||||||||| ||||||||||||||
Sbjct 53539153 AGTGTGTGATTTTG--ATGCATTAACAATA-CAATGCAGGGAAGAAATCCGGAGGATAAA 53539209
Query 8517 AGCAAACAATCCTGACATAAGCCACAGAGAAGCCTTCAGTACTGCAGCAAAGAATGTGAG 8576
|||||||| || ||||||||||||||||||||||||||||| |||||||||||||| ||
Sbjct 53539210 GGCAAACAACCCCGACATAAGCCACAGAGAAGCCTTCAGTACAGCAGCAAAGAATGTTAG 53539269
Query 8577 TA 8578
||
Sbjct 53539270 TA 53539271
Score = 122 bits (66), Expect = 1e-24
Identities = 80/87 (92%), Gaps = 0/87 (0%)
Strand=Plus/Plus
Query 9122 ttttttGCAGTGGGCGCATTTCCCGAACATCCATTTCGGGTTAGGCTCCCATGAGAGCAG 9181
||| ||||||||||| ||||| |||||||| |||||||| ||||||||| ||||||||||
Sbjct 53541378 TTTATTGCAGTGGGCACATTTTCCGAACATTCATTTCGGATTAGGCTCCAATGAGAGCAG 53541437
Query 9182 CAAGAAGCTCGATGAGGCCATTGGAGC 9208
||||||||||||||||||||| |||||
Sbjct 53541438 CAAGAAGCTCGATGAGGCCATCGGAGC 53541464
Score = 106 bits (57), Expect = 1e-19
Identities = 65/69 (94%), Gaps = 0/69 (0%)
Strand=Plus/Plus
Query 8273 ATACAACTTGCAGCTCCAGAGAAGAGGCAGCGGGTTCCTTCAGCTTATAACAGATTTATC 8332
|||||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||
Sbjct 53539032 ATACAACTCGCAGCACCAGAGAAGAGGCAGCGGGTTCCTTCAGCTTATAACAGATTTATT 53539091
Query 8333 AAGTGAGTT 8341
|||| ||||
Sbjct 53539092 AAGTAAGTT 53539100
> Scaffold_1064;HRSCAF=3428
Length=111260184
Score = 230 bits (124), Expect = 7e-57
Identities = 366/471 (78%), Gaps = 63/471 (13%)
Strand=Plus/Plus
Query 3536 TTCTTTCTTATGGGAGTGAGTGCCCAAAAAGTGAGTGAATGTAGGGAATCAAACAAAGTA 3595
|||||||| ||||||||||||||||||||||||| || || | |||||||||||||| |
Sbjct 61605689 TTCTTTCTCATGGGAGTGAGTGCCCAAAAAGTGAATG--TG-A-GGAATCAAACAAAG-A 61605743
Query 3596 GAGGTACTGTGCTCTTCAGG-TTTG-GG--A---A--GA-AAAA--T--G-GG-AACGGC 3639
||| ||| |||||||||| || | || | | || |||| | | || || |||
Sbjct 61605744 -AGGCCCTG-GCTCTTCAGGCTTGGAGGAAATCTAGGGAGAAAATGTAAGTGGCAAGGGC 61605801
Query 3640 AAGGGACCAA--TG----TGTGCAGGCATTGGAAAAGG--GTG-CCCCAATTCTGATCTG 3690
| ||||||| | |||||| ||||||||||||| | | ||| |||||||||||
Sbjct 61605802 CAAGGACCAAGGGGCCAATGTGCATGCATTGGAAAAGGCTGGGTACCCTATTCTGATCTG 61605861
Query 3691 ATCAGATATATATTCA--GATCAGCAGAGCCCCTGATAAAAGTCATGGAGGAACAGTTAT 3748
|||| ||| || || |||||||||||||||||||||||||||||||| ||||||| |
Sbjct 61605862 GTCAG--ATAGATGCATGGATCAGCAGAGCCCCTGATAAAAGTCATGGAGCAACAGTTTT 61605919
Query 3749 CCACATCTAAAGCTATAGCTGTGTATTAATGTGTATCTGCAGTCTACACCAGCCTTATGA 3808
||| | ||||||||| |||||||||| ||||||||||||||||||| |||||||| |||
Sbjct 61605920 CCAGAGCTAAAGCTA--GCTGTGTATTTATGTGTATCTGCAGTCTACCCCAGCCTT-TGA 61605976
Query 3809 AACATGCATGCATGCATGCATGCCTTTGAGATTTGATTTTT-TACTT-CTCAGATTCTTT 3866
| |||| ||||||||| | | | ||||||||||||| | || || | ||||||
Sbjct 61605977 A-CATG--TGCATGCAT-C-T---T--GAGATTTGATTTTGCTGCTAGCTT-G-TTCTTT 61606024
Query 3867 TGTACAAATGCAAAAAGAAAATGA--TCCTTTGGAATCTAGCATTTGTTACATATTTACA 3924
|| |||||||||||| |||| | |||||||||||| ||||| || ||||| ||| ||
Sbjct 61606025 TG--CAAATGCAAAAAAAAAAAAAGCTCCTTTGGAATCAAGCATCTGCTACATGTTTGCA 61606082
Query 3925 ATATA-A-AGTGCTA-TACTTGTTTACTTTTCATTCTA--CTTGTTCCAGC 3970
|| || | || || |||| |||||||||||| || ||| |||||||
Sbjct 61606083 ATGTACACAGCACTGGTACTA-TTTACTTTTCATCCTGTTCTTATTCCAGC 61606132
Score = 152 bits (82), Expect = 1e-33
Identities = 93/98 (95%), Gaps = 2/98 (2%)
Strand=Plus/Plus
Query 313 CGGG-GCTAGAGGAATGTCGGCACAGATCGTGCCGGCGCCGGAGCATGTGTGCTACGTGC 371
|||| ||| |||||||||| ||||| |||| |||||||||||||||||||||||||||||
Sbjct 61603563 CGGGAGCT-GAGGAATGTCAGCACAAATCGCGCCGGCGCCGGAGCATGTGTGCTACGTGC 61603621
Query 372 ACTGCAACTTCTGCAACACAATTCTCGCGGTAATTTGT 409
||||||||||||||||||||||||||||||||||||||
Sbjct 61603622 ACTGCAACTTCTGCAACACAATTCTCGCGGTAATTTGT 61603659
Score = 141 bits (76), Expect = 3e-30
Identities = 84/88 (95%), Gaps = 0/88 (0%)
Strand=Plus/Plus
Query 8491 TACAGGGAAGAGATCCGGAGGATAAAAGCAAACAATCCTGACATAAGCCACAGAGAAGCC 8550
||||||||||| ||||||||||||||||||||||| |||||||||||||||| |||||||
Sbjct 61608082 TACAGGGAAGAAATCCGGAGGATAAAAGCAAACAACCCTGACATAAGCCACAAAGAAGCC 61608141
Query 8551 TTCAGTACTGCAGCAAAGAATGTGAGTA 8578
||||||||||||||||||||||| ||||
Sbjct 61608142 TTCAGTACTGCAGCAAAGAATGTTAGTA 61608169
Score = 97.1 bits (52), Expect = 7e-17
Identities = 64/69 (93%), Gaps = 3/69 (4%)
Strand=Plus/Plus
Query 8277 AACTTGCAGCTCCA---GAGAAGAGGCAGCGGGTTCCTTCAGCTTATAACAGATTTATCA 8333
|||||||||| ||| ||||||||||||||||||||||||||||||||||||||||| |
Sbjct 61607649 AACTTGCAGCACCAGCTGAGAAGAGGCAGCGGGTTCCTTCAGCTTATAACAGATTTATTA 61607708
Query 8334 AGTGAGTTT 8342
|||||||||
Sbjct 61607709 AGTGAGTTT 61607717
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 12256816721616
Database: zizania_palustris_13Nov2018_okGsv.fasta
Posted date: Jul 9, 2019 4:10 PM
Number of letters in database: 1,288,768,912
Number of sequences in database: 2,183
Matrix: blastn matrix 1 -2
Gap Penalties: Existence: 0, Extension: 2.5