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OrSH4_out.txt
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OrSH4_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= EU999927.1 Oryza rufipogon IRGC seed accession VOC4b shattering 4
(sh4) gene, exon 1 and partial cds
Length=2454
Score E
Sequences producing significant alignments: (Bits) Value
Scaffold_453;HRSCAF=2583 741 0.0
Scaffold_18;HRSCAF=1069 671 0.0
> Scaffold_453;HRSCAF=2583
Length=4333358
Score = 741 bits (401), Expect = 0.0
Identities = 664/782 (85%), Gaps = 53/782 (7%)
Strand=Plus/Minus
Query 1591 ggcgacggggccggcgccgccgccgccgtcgccggcgtcggggtcggcgccgcgggACTA 1650
||||||||| || || ||||||||||||||||| | || ||||||||||||||||||
Sbjct 3281318 GGCGACGGGACCCGCTCCGCCGCCGCCGTCGCC-G-GT----GTCGGCGCCGCGGGACTA 3281265
Query 1651 CCGCAAGGGGAACTGGACGCTGCACGAGACGCTCATCCTCATCACCGCCAAGCGTCTGGA 1710
||||||||| ||||||||||| |||||||||||||||||||||||||||||||| || ||
Sbjct 3281264 CCGCAAGGGCAACTGGACGCTCCACGAGACGCTCATCCTCATCACCGCCAAGCGCCTCGA 3281205
Query 1711 CGACGAccgccgcgccgg-cgt--t-g-gg-gg-cgcggcg--gctggt---ggc--ggc 1756
|||||||||||| || || || | | || || | || | |||||| ||| |||
Sbjct 3281204 CGACGACCGCCGTGCTGGTGGTGGTGGTGGTGGTGGTGGGGTTGCTGGTGCCGGCGTGGC 3281145
Query 1757 ggc-gccgggtcgccgccgacgccgAGGTCGGCGGAGCAGCGGTGGAAGTGGGTGGAGAA 1815
||| | |||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct 3281144 GGCGGTGGGGTCGCCGCCGACGCCGCGGTCGGCGGAGCAGCGGTGGAAGTGGGTGGAGAA 3281085
Query 1816 CTACTGCTGGAAGAACGGCTGCCTCCGCAGCCAGAACCAGTGCAATGACAAGTGGGACAA 1875
||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct 3281084 CTACTGCTGGAAGAACGGCTGCCTCCGCAGCCAGAACCAGTGCAACGACAAGTGGGACAA 3281025
Query 1876 CCTCCTCCGCGACTACAAGAAGGTCCGCGACTACGAGTCccgcgtcgccgccgccgccgc 1935
|||||||||||||||||||||||||||||||||||||||||| |||||||||| |||||
Sbjct 3281024 CCTCCTCCGCGACTACAAGAAGGTCCGCGACTACGAGTCCCGTATCGCCGCCGCGGCCGC 3280965
Query 1936 caccggcggcgcggccgccgccaactccgcccccctcccgTCGTACTGGACGATGGAGCG 1995
|| || || ||||||| |||||| | ||| |||||||||| |||||||| |||||||
Sbjct 3280964 CAGCGCCGCCGCGGCC-CCGCCACAT--GCCGCCCTCCCGTCCTACTGGACATTGGAGCG 3280908
Query 1996 GCACGAGCGCAAGGACTGCAACCTCCCCACCAACCTGGCGCCGGAGGTCTACGACGCGCT 2055
|||||||||||||||| ||||||| ||||| ||||| ||||| |||||| ||||||||||
Sbjct 3280907 GCACGAGCGCAAGGACCGCAACCTACCCACAAACCTCGCGCCCGAGGTCCACGACGCGCT 3280848
Query 2056 CTCCGAGGTGCTCTcccgccgcgcggcgcgacgcggcggcgccacgatcgcgcccacccc 2115
||||||||| || ||||||||||| ||||| || || ||||||||||||||||||||| |
Sbjct 3280847 CTCCGAGGTTCTATCCCGCCGCGCCGCGCGGCGGGGAGGCGCCACGATCGCGCCCACCTC 3280788
Query 2116 gccgccaccaccgctcgcgctgccgctgccgccgccgccgccgcc-ctcgccgc-c-gAA 2172
|| | || ||||| |||||||||| ||||||||||||||||| ||| || | | |||
Sbjct 3280787 TCC-CG-CC-CCGCTGGCGCTGCCGCCACCGCCGCCGCCGCCGCCACTCTCCCCTCCGAA 3280731
Query 2173 GCCTCTCGTCGCGCAGCAGCAGCACCACCATCACGGCCATCACCACCACCCACCTCCTCC 2232
||||||| || ||||||| |||||||| ||||| | |||| ||||||| |||| |||
Sbjct 3280730 GCCTCTCATCACGCAGCACCAGCACCAGCATCAT--C-ATCATCACCACCATCCTCATCC 3280674
Query 2233 TCAGCCGCCGCCGTCGTCGCTGCAGCTCCCTCCGGCGGTCGTGGCTCCGCCGCCGGCGTC 2292
|| | ||||||| | |||| ||| ||||| ||||| ||||||||||||||||
Sbjct 3280673 TC--C-GCCGCCG-C--CGCT-----TCC-TCCGGTGGTCG---CTCCGCCGCCGGCGTC 3280629
Query 2293 CGTTTCCGGTAATGGTCGGTGCGCGCACCGTACACTTAATACTCGTAGTAGCTGTTACAT 2352
||||||||||| ||||||||||||||| ||| ||| ||||||||| |||||| ||
Sbjct 3280628 CGTTTCCGGTA-TGGTCGGTGCGCGCAAA-TACTTTTATTACTCGTAG---CTGTTATAT 3280574
Query 2353 CC 2354
||
Sbjct 3280573 CC 3280572
Score = 737 bits (399), Expect = 0.0
Identities = 664/783 (85%), Gaps = 54/783 (7%)
Strand=Plus/Minus
Query 1591 ggcgacggggccggcgccgccgccgccgtcgccggcgtcggggtcggcgccgcgggACTA 1650
||||||||| || || ||||||||||||||||| | || ||||||||||||||||||
Sbjct 3349187 GGCGACGGGACCCGCTCCGCCGCCGCCGTCGCC-G-GT----GTCGGCGCCGCGGGACTA 3349134
Query 1651 CCGCAAGGGGAACTGGACGCTGCACGAGACGCTCATCCTCATCACCGCCAAGCGTCTGGA 1710
||||||||| ||||||||||| |||||||||||||||||||||||||||||||| || ||
Sbjct 3349133 CCGCAAGGGCAACTGGACGCTCCACGAGACGCTCATCCTCATCACCGCCAAGCGCCTCGA 3349074
Query 1711 CGACGAccgccgcgccgg-cgt--t-g-gg-gg-cgcggcg--gctggt---ggc--ggc 1756
|||||||||||| || || || | | || || | || | |||||| ||| |||
Sbjct 3349073 CGACGACCGCCGTGCTGGTGGTGGTGGTGGTGGTGGTGGGGTTGCTGGTGCCGGCGTGGC 3349014
Query 1757 ggc-gccgggtcgccgccgacgccgAGGTCGGCGGAGCAGCGGTGGAAGTGGGTGGAGAA 1815
||| | |||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct 3349013 GGCGGTGGGGTCGCCGCCGACGCCGCGGTCGGCGGAGCAGCGGTGGAAGTGGGTGGAGAA 3348954
Query 1816 CTACTGCTGGAAGAACGGCTGCCTCCGCAGCCAGAACCAGTGCAATGACAAGTGGGACAA 1875
||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct 3348953 CTACTGCTGGAAGAACGGCTGCCTCCGCAGCCAGAACCAGTGCAACGACAAGTGGGACAA 3348894
Query 1876 CCTCCTCCGCGACTACAAGAAGGTCCGCGACTACGAGTCccgcgtcgccgccgccg-ccg 1934
|||||||||||||||||||||||||||||||||||||||||| |||||||||||| |||
Sbjct 3348893 CCTCCTCCGCGACTACAAGAAGGTCCGCGACTACGAGTCCCGTATCGCCGCCGCCGGCCG 3348834
Query 1935 ccaccggcggcgcggccgccgccaactccgcccccctcccgTCGTACTGGACGATGGAGC 1994
||| || || ||||||| |||||| | ||| |||||||||| |||||||| ||||||
Sbjct 3348833 CCAGCGCCGCCGCGGCC-CCGCCACAT--GCCGCCCTCCCGTCCTACTGGACATTGGAGC 3348777
Query 1995 GGCACGAGCGCAAGGACTGCAACCTCCCCACCAACCTGGCGCCGGAGGTCTACGACGCGC 2054
||||||||||||||||| ||||||| ||||| ||||| ||||| |||||| |||||||||
Sbjct 3348776 GGCACGAGCGCAAGGACCGCAACCTACCCACAAACCTCGCGCCCGAGGTCCACGACGCGC 3348717
Query 2055 TCTCCGAGGTGCTCTcccgccgcgcggcgcgacgcggcggcgccacgatcgcgcccaccc 2114
|||||||||| || ||||||||||| ||||| || || |||||||||||||||||||||
Sbjct 3348716 TCTCCGAGGTTCTATCCCGCCGCGCCGCGCGGCGGGGAGGCGCCACGATCGCGCCCACCT 3348657
Query 2115 cgccgccaccaccgctcgcgctgccgctgccgccgccgccgccgcc-ctcgccgc-c-gA 2171
| || | || ||||| |||||||||| ||||||||||||||||| ||| || | | ||
Sbjct 3348656 CTCC-CG-CC-CCGCTGGCGCTGCCGCCACCGCCGCCGCCGCCGCCACTCTCCCCTCCGA 3348600
Query 2172 AGCCTCTCGTCGCGCAGCAGCAGCACCACCATCACGGCCATCACCACCACCCACCTCCTC 2231
|||||||| || ||||||| |||||||| ||||| | |||| || |||| |||| ||
Sbjct 3348599 AGCCTCTCATCACGCAGCACCAGCACCAGCATCAT--C-ATCATCATCACCATCCTCATC 3348543
Query 2232 CTCAGCCGCCGCCGTCGTCGCTGCAGCTCCCTCCGGCGGTCGTGGCTCCGCCGCCGGCGT 2291
||| | ||||||| | |||| ||| ||||| ||||| |||||||||||||||
Sbjct 3348542 CTC--C-GCCGCCG-C--CGCT-----TCC-TCCGGTGGTCG---CTCCGCCGCCGGCGT 3348498
Query 2292 CCGTTTCCGGTAATGGTCGGTGCGCGCACCGTACACTTAATACTCGTAGTAGCTGTTACA 2351
|||||||||||| ||||||||||||||| ||| ||| ||||||||| |||||| |
Sbjct 3348497 CCGTTTCCGGTA-TGGTCGGTGCGCGCAAA-TACTTTTATTACTCGTAG---CTGTTATA 3348443
Query 2352 TCC 2354
|||
Sbjct 3348442 TCC 3348440
> Scaffold_18;HRSCAF=1069
Length=98769966
Score = 671 bits (363), Expect = 0.0
Identities = 770/953 (81%), Gaps = 81/953 (8%)
Strand=Plus/Minus
Query 1278 GGaaaaaaaacgagggaaaaaacgggtgg-aaacacacgcaaaaacacaacgCCGTGCGG 1336
|||||||||||| | |||||| ||||| ||| ||||| || ||||||||||||
Sbjct 97798131 GGAAAAAAAACGTTCGCAAAAAC-GGTGGAAAAAACACG-GGGGAC-GAACGCCGTGCGG 97798075
Query 1337 CCTTGTAAATACGGGCGACGCCGACGCGCATCGCTCCCCGAACACC-AAACGCC-TCAGC 1394
|| ||||||||| || | | | | ||| | || ||| | || || ||||||| | |||
Sbjct 97798074 CCATGTAAATAC-GG-G-C-TC-AGGCG-A-CG--CCCAG-ACGCCAAAACGCCTTAAGC 97798025
Query 1395 TTGCCTTGGCTCTCGC--GAGTCGCTAC-GCCCGCGACGACACGACcgcgccgcgcgcgc 1451
|| || |||| | || || | | || || || || | | | ||| |||| | ||||
Sbjct 97798024 TTAGCTCGGCTTTAGCTACAG-CAC-ACGGCGCGTGA-G-GAGGCCCG-GCCG-G-GCGC 97797972
Query 1452 gcgAGCGAGCGAGCATGTCGGGCTCCTCTGCCGACCCCTCGCCATCCGCCTCGACCGCGG 1511
||| || ||| ||||||||| || | || ||||||||||||||| || || || |
Sbjct 97797971 GCG-CCGCGCG-GCATGTCGGCCT-C-CT-CCGACCCCTCGCCAT-CG--TCCTCCTC-- 97797922
Query 1512 GGGCGGCGGTCTCGCCGCTCGCGCTGCTCCGCGCGCACGGCCACGGCCACGGGCACCTG- 1570
||||||| ||||||||| ||||| ||||||||||| | | |||| ||||| |
Sbjct 97797921 -TGCGGCGGCCTCGCCGCTGGCGCTCATCCGCGCGCAC--ACTC-ACCACCCGCACCCGC 97797866
Query 1571 ACTGCTAcgccgccgtcgggggcgacggggccggcgccgccgccgccgtcgccggcgtcg 1630
|| | ||||| | |||| | |||||||||| |||||||||||||||||||| | ||
Sbjct 97797865 AC-GTCACGCCTCTGTCGCCGTCGACGGGGCCCGCGCCGCCGCCGCCGTCGCC-G-GT-- 97797811
Query 1631 gggtcggcgccgcgggACTACCGCAAGGGGAACTGGACGCTGCACGAGACGCTCATCCTC 1690
||||||||||||||||||||||||||| ||||||||||| |||||||||||| |||||
Sbjct 97797810 --GTCGGCGCCGCGGGACTACCGCAAGGGCAACTGGACGCTCCACGAGACGCTCGTCCTC 97797753
Query 1691 ATCACCGCCAAGCGTCTGGACGACGAccgccgcgccggcgttgggggcgc-ggcggctgg 1749
|||||||||||||| || |||||||||||||| || || | || || || ||| || ||
Sbjct 97797752 ATCACCGCCAAGCGCCTCGACGACGACCGCCGTGCTGGTGGTGCTGGTGCTGGC-GCCGG 97797694
Query 1750 tggcggcggc-gccgggt---cgccgccgacgccgAGGTCGGCGGAGCAGCGGTGGAAGT 1805
||||| || || |||| |||||||||||||| ||||||||||||||||||||||||
Sbjct 97797693 -CGCGGCAGCGGCGGGGTCGCCGCCGCCGACGCCGCGGTCGGCGGAGCAGCGGTGGAAGT 97797635
Query 1806 GGGTGGAGAACTACTGCTGGAAGAACGGCTGCCTCCGCAGCCAGAACCAGTGCAATGACA 1865
||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Sbjct 97797634 GGGTGGAGAACTACTGCTGGAAGAACGGCTGCCTCCGCAGCCAGAACCAGTGCAACGACA 97797575
Query 1866 AGTGGGACAACCTCCTCCGCGACTACAAGAAGGTCCGCGACTACGAGTCccgcgtcgccg 1925
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 97797574 AGTGGGACAACCTCCTCCGCGACTACAAGAAGGTCCGCGACTACGAGTCCCGCGTCGCCG 97797515
Query 1926 ccgccgccgccac--cggc----ggcgcg-gc-c-g-c-c-gcca-actccgcc-c---- 1967
|| | |||| | | |||| ||||| || | | | | |||| |||| ||| |
Sbjct 97797514 CCACGGCCGGCGCGGCGGCCTCTGGCGCCAGCACCGGCGCCGCCACACTC-GCCGCAGTA 97797456
Query 1968 c-cctcccgTCGTACTGGACGATGGAGCGGCACGAGCGCAAGGACTGCAACCTCCCCACC 2026
| ||||||||| |||||||| || ||||||||||| ||||||||| ||||||||||||||
Sbjct 97797455 CTCCTCCCGTCCTACTGGACCATCGAGCGGCACGACCGCAAGGACCGCAACCTCCCCACC 97797396
Query 2027 AACCTGGCGCCGGAGGTCTACGACGCGCTCTCCGAGGTGCTCTcccgccgcgcggcgcga 2086
||||| |||||||||||||||||||||||||| ||||| |||||||||||||| ||||||
Sbjct 97797395 AACCTCGCGCCGGAGGTCTACGACGCGCTCTCGGAGGTCCTCTCCCGCCGCGCCGCGCGA 97797336
Query 2087 cgcggcggcgccacgatcgcgcccaccccgccgccaccaccgctcgcgctgccgctgccg 2146
|| ||||||| ||||||||| |||||||| || || || | |||||| ||||||| |||
Sbjct 97797335 CGGGGCGGCGTCACGATCGCACCCACCCCTCCACC-CC-C-GCTCGCTCTGCCGCCGCCA 97797279
Query 2147 ccgccgccgccgcc-c--tcgccgccgAAGCCTCTCGTCGCGCAGCAGCAGCA 2196
|| || || || || | || || |||||||||||| || | |||||||||||
Sbjct 97797278 CCACCCCCACCTCCACCCTCCCCTCCGAAGCCTCTCATCACCCAGCAGCAGCA 97797226
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 3123817094928
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