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OnSH4_out.txt
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OnSH4_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= JN697604.1 Oryza nivara voucher IRRI:seed accession 106431
shattering 4 (sh4) gene, exon 1 and partial cds
Length=2450
Score E
Sequences producing significant alignments: (Bits) Value
Scaffold_453;HRSCAF=2583 736 0.0
Scaffold_18;HRSCAF=1069 671 0.0
> Scaffold_453;HRSCAF=2583
Length=4333358
Score = 736 bits (398), Expect = 0.0
Identities = 663/782 (85%), Gaps = 53/782 (7%)
Strand=Plus/Minus
Query 1588 ggcgacggggccggcgccgccgccgccgtcgccggcgtcggggtcggcgccgcgggACTA 1647
||||||||| || || ||||||||||||||||| | || ||||||||||||||||||
Sbjct 3281318 GGCGACGGGACCCGCTCCGCCGCCGCCGTCGCC-G-GT----GTCGGCGCCGCGGGACTA 3281265
Query 1648 CCGCAAGGGGAACTGGACGCTGCACGAGACGCTCATCCTCATCACCGCCAATCGTCTGGA 1707
||||||||| ||||||||||| ||||||||||||||||||||||||||||| || || ||
Sbjct 3281264 CCGCAAGGGCAACTGGACGCTCCACGAGACGCTCATCCTCATCACCGCCAAGCGCCTCGA 3281205
Query 1708 CGACGAccgccgcgccgg-cgt--t-g-gg-gg-cgcggcg--gctggt---ggc--ggc 1753
|||||||||||| || || || | | || || | || | |||||| ||| |||
Sbjct 3281204 CGACGACCGCCGTGCTGGTGGTGGTGGTGGTGGTGGTGGGGTTGCTGGTGCCGGCGTGGC 3281145
Query 1754 ggc-gccgggtcgccgccgacgccgAGGTCGGCGGAGCAGCGGTGGAAGTGGGTGGAGAA 1812
||| | |||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct 3281144 GGCGGTGGGGTCGCCGCCGACGCCGCGGTCGGCGGAGCAGCGGTGGAAGTGGGTGGAGAA 3281085
Query 1813 CTACTGCTGGAAGAACGGCTGCCTCCGCAGCCAGAACCAGTGCAATGACAAGTGGGACAA 1872
||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct 3281084 CTACTGCTGGAAGAACGGCTGCCTCCGCAGCCAGAACCAGTGCAACGACAAGTGGGACAA 3281025
Query 1873 CCTCCTCCGCGACTACAAGAAGGTCCGCGACTACGAGTCccgcgtcgccgccgccgccgc 1932
|||||||||||||||||||||||||||||||||||||||||| |||||||||| |||||
Sbjct 3281024 CCTCCTCCGCGACTACAAGAAGGTCCGCGACTACGAGTCCCGTATCGCCGCCGCGGCCGC 3280965
Query 1933 caccggcggcgcggccgccgccaactccgcccccctcccgTCGTACTGGACGATGGAGCG 1992
|| || || ||||||| |||||| | ||| |||||||||| |||||||| |||||||
Sbjct 3280964 CAGCGCCGCCGCGGCC-CCGCCACAT--GCCGCCCTCCCGTCCTACTGGACATTGGAGCG 3280908
Query 1993 GCACGAGCGCAAGGACTGCAACCTCCCCACCAACCTGGCGCCGGAGGTCTACGACGCGCT 2052
|||||||||||||||| ||||||| ||||| ||||| ||||| |||||| ||||||||||
Sbjct 3280907 GCACGAGCGCAAGGACCGCAACCTACCCACAAACCTCGCGCCCGAGGTCCACGACGCGCT 3280848
Query 2053 CTCCGAGGTGCTCTcccgccgcgcggcgcgacgcggcggcgccacgatcgcgcccacccc 2112
||||||||| || ||||||||||| ||||| || || ||||||||||||||||||||| |
Sbjct 3280847 CTCCGAGGTTCTATCCCGCCGCGCCGCGCGGCGGGGAGGCGCCACGATCGCGCCCACCTC 3280788
Query 2113 gccgccaccaccgctcgcgctgccgctgccgccgccgccgccgcc-ctcgccgc-c-gAA 2169
|| | || ||||| |||||||||| ||||||||||||||||| ||| || | | |||
Sbjct 3280787 TCC-CG-CC-CCGCTGGCGCTGCCGCCACCGCCGCCGCCGCCGCCACTCTCCCCTCCGAA 3280731
Query 2170 GCCTCTCGTCGCGCAGCAGCAGCACCACCATCACGGCCATCACCACCACCCACCTCCTCC 2229
||||||| || ||||||| |||||||| ||||| | |||| ||||||| |||| |||
Sbjct 3280730 GCCTCTCATCACGCAGCACCAGCACCAGCATCAT--C-ATCATCACCACCATCCTCATCC 3280674
Query 2230 TCAGCCGCCGCCGTCGTCGCTGCAGCTCCCTCCGGCGGTCGTGGCTCCGCCGCCGGCGTC 2289
|| | ||||||| | |||| ||| ||||| ||||| ||||||||||||||||
Sbjct 3280673 TC--C-GCCGCCG-C--CGCT-----TCC-TCCGGTGGTCG---CTCCGCCGCCGGCGTC 3280629
Query 2290 CGTTTCCGGTAATGGTCGGTGCGCGCACCGTACACTTAATACTCATAGTAGCTGTTACAT 2349
||||||||||| ||||||||||||||| ||| ||| ||||| |||||||||| ||
Sbjct 3280628 CGTTTCCGGTA-TGGTCGGTGCGCGCAAA-TACTTTTATTACTC---GTAGCTGTTATAT 3280574
Query 2350 CC 2351
||
Sbjct 3280573 CC 3280572
Score = 732 bits (396), Expect = 0.0
Identities = 663/783 (85%), Gaps = 54/783 (7%)
Strand=Plus/Minus
Query 1588 ggcgacggggccggcgccgccgccgccgtcgccggcgtcggggtcggcgccgcgggACTA 1647
||||||||| || || ||||||||||||||||| | || ||||||||||||||||||
Sbjct 3349187 GGCGACGGGACCCGCTCCGCCGCCGCCGTCGCC-G-GT----GTCGGCGCCGCGGGACTA 3349134
Query 1648 CCGCAAGGGGAACTGGACGCTGCACGAGACGCTCATCCTCATCACCGCCAATCGTCTGGA 1707
||||||||| ||||||||||| ||||||||||||||||||||||||||||| || || ||
Sbjct 3349133 CCGCAAGGGCAACTGGACGCTCCACGAGACGCTCATCCTCATCACCGCCAAGCGCCTCGA 3349074
Query 1708 CGACGAccgccgcgccgg-cgt--t-g-gg-gg-cgcggcg--gctggt---ggc--ggc 1753
|||||||||||| || || || | | || || | || | |||||| ||| |||
Sbjct 3349073 CGACGACCGCCGTGCTGGTGGTGGTGGTGGTGGTGGTGGGGTTGCTGGTGCCGGCGTGGC 3349014
Query 1754 ggc-gccgggtcgccgccgacgccgAGGTCGGCGGAGCAGCGGTGGAAGTGGGTGGAGAA 1812
||| | |||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct 3349013 GGCGGTGGGGTCGCCGCCGACGCCGCGGTCGGCGGAGCAGCGGTGGAAGTGGGTGGAGAA 3348954
Query 1813 CTACTGCTGGAAGAACGGCTGCCTCCGCAGCCAGAACCAGTGCAATGACAAGTGGGACAA 1872
||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct 3348953 CTACTGCTGGAAGAACGGCTGCCTCCGCAGCCAGAACCAGTGCAACGACAAGTGGGACAA 3348894
Query 1873 CCTCCTCCGCGACTACAAGAAGGTCCGCGACTACGAGTCccgcgtcgccgccgccg-ccg 1931
|||||||||||||||||||||||||||||||||||||||||| |||||||||||| |||
Sbjct 3348893 CCTCCTCCGCGACTACAAGAAGGTCCGCGACTACGAGTCCCGTATCGCCGCCGCCGGCCG 3348834
Query 1932 ccaccggcggcgcggccgccgccaactccgcccccctcccgTCGTACTGGACGATGGAGC 1991
||| || || ||||||| |||||| | ||| |||||||||| |||||||| ||||||
Sbjct 3348833 CCAGCGCCGCCGCGGCC-CCGCCACAT--GCCGCCCTCCCGTCCTACTGGACATTGGAGC 3348777
Query 1992 GGCACGAGCGCAAGGACTGCAACCTCCCCACCAACCTGGCGCCGGAGGTCTACGACGCGC 2051
||||||||||||||||| ||||||| ||||| ||||| ||||| |||||| |||||||||
Sbjct 3348776 GGCACGAGCGCAAGGACCGCAACCTACCCACAAACCTCGCGCCCGAGGTCCACGACGCGC 3348717
Query 2052 TCTCCGAGGTGCTCTcccgccgcgcggcgcgacgcggcggcgccacgatcgcgcccaccc 2111
|||||||||| || ||||||||||| ||||| || || |||||||||||||||||||||
Sbjct 3348716 TCTCCGAGGTTCTATCCCGCCGCGCCGCGCGGCGGGGAGGCGCCACGATCGCGCCCACCT 3348657
Query 2112 cgccgccaccaccgctcgcgctgccgctgccgccgccgccgccgcc-ctcgccgc-c-gA 2168
| || | || ||||| |||||||||| ||||||||||||||||| ||| || | | ||
Sbjct 3348656 CTCC-CG-CC-CCGCTGGCGCTGCCGCCACCGCCGCCGCCGCCGCCACTCTCCCCTCCGA 3348600
Query 2169 AGCCTCTCGTCGCGCAGCAGCAGCACCACCATCACGGCCATCACCACCACCCACCTCCTC 2228
|||||||| || ||||||| |||||||| ||||| | |||| || |||| |||| ||
Sbjct 3348599 AGCCTCTCATCACGCAGCACCAGCACCAGCATCAT--C-ATCATCATCACCATCCTCATC 3348543
Query 2229 CTCAGCCGCCGCCGTCGTCGCTGCAGCTCCCTCCGGCGGTCGTGGCTCCGCCGCCGGCGT 2288
||| | ||||||| | |||| ||| ||||| ||||| |||||||||||||||
Sbjct 3348542 CTC--C-GCCGCCG-C--CGCT-----TCC-TCCGGTGGTCG---CTCCGCCGCCGGCGT 3348498
Query 2289 CCGTTTCCGGTAATGGTCGGTGCGCGCACCGTACACTTAATACTCATAGTAGCTGTTACA 2348
|||||||||||| ||||||||||||||| ||| ||| ||||| |||||||||| |
Sbjct 3348497 CCGTTTCCGGTA-TGGTCGGTGCGCGCAAA-TACTTTTATTACTC---GTAGCTGTTATA 3348443
Query 2349 TCC 2351
|||
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 1275 GGaaaaaaaacgagggaaaaaacgggtgg-aaacacacgcaaaaacacaacgCCGTGCGG 1333
|||||||||||| | |||||| ||||| ||| ||||| || ||||||||||||
Sbjct 97798131 GGAAAAAAAACGTTCGCAAAAAC-GGTGGAAAAAACACG-GGGGAC-GAACGCCGTGCGG 97798075
Query 1334 CCTTGTAAATACGGGCGACGCCGACGCGCATCGCTCCCCGAACACC-AAACGCC-TCAGC 1391
|| ||||||||| || | | | | ||| | || ||| | || || ||||||| | |||
Sbjct 97798074 CCATGTAAATAC-GG-G-C-TC-AGGCG-A-CG--CCCAG-ACGCCAAAACGCCTTAAGC 97798025
Query 1392 TTGCCTTGGCTCTCGC--CAGTCGCTAC-GCCCGCGACGACACGACcgcgccgcgcgcgc 1448
|| || |||| | || ||| | | || || || || | | | ||| |||| | ||||
Sbjct 97798024 TTAGCTCGGCTTTAGCTACAG-CAC-ACGGCGCGTGA-G-GAGGCCCG-GCCG-G-GCGC 97797972
Query 1449 gcgAGCGAGCGAGCATGTCGGGCTCCTCTGCCGACCCCTCGCCATCCGCCTCGACCGCGG 1508
||| || ||| ||||||||| || | || ||||||||||||||| || || || |
Sbjct 97797971 GCG-CCGCGCG-GCATGTCGGCCT-C-CT-CCGACCCCTCGCCAT-CG--TCCTCCTC-- 97797922
Query 1509 GGGCGGCGGTCTCGCCGCTCGCGCTGCTCCGCGCGCACGGCCACGGCCACGGGCACCTG- 1567
||||||| ||||||||| ||||| ||||||||||| | | |||| ||||| |
Sbjct 97797921 -TGCGGCGGCCTCGCCGCTGGCGCTCATCCGCGCGCAC--ACTC-ACCACCCGCACCCGC 97797866
Query 1568 ACTGCTAcgccgccgtcgggggcgacggggccggcgccgccgccgccgtcgccggcgtcg 1627
|| | ||||| | |||| | |||||||||| |||||||||||||||||||| | ||
Sbjct 97797865 AC-GTCACGCCTCTGTCGCCGTCGACGGGGCCCGCGCCGCCGCCGCCGTCGCC-G-GT-- 97797811
Query 1628 gggtcggcgccgcgggACTACCGCAAGGGGAACTGGACGCTGCACGAGACGCTCATCCTC 1687
||||||||||||||||||||||||||| ||||||||||| |||||||||||| |||||
Sbjct 97797810 --GTCGGCGCCGCGGGACTACCGCAAGGGCAACTGGACGCTCCACGAGACGCTCGTCCTC 97797753
Query 1688 ATCACCGCCAATCGTCTGGACGACGAccgccgcgccggcgttgggggcgc-ggcggctgg 1746
||||||||||| || || |||||||||||||| || || | || || || ||| || ||
Sbjct 97797752 ATCACCGCCAAGCGCCTCGACGACGACCGCCGTGCTGGTGGTGCTGGTGCTGGC-GCCGG 97797694
Query 1747 tggcggcggc-gccgggt---cgccgccgacgccgAGGTCGGCGGAGCAGCGGTGGAAGT 1802
||||| || || |||| |||||||||||||| ||||||||||||||||||||||||
Sbjct 97797693 -CGCGGCAGCGGCGGGGTCGCCGCCGCCGACGCCGCGGTCGGCGGAGCAGCGGTGGAAGT 97797635
Query 1803 GGGTGGAGAACTACTGCTGGAAGAACGGCTGCCTCCGCAGCCAGAACCAGTGCAATGACA 1862
||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Sbjct 97797634 GGGTGGAGAACTACTGCTGGAAGAACGGCTGCCTCCGCAGCCAGAACCAGTGCAACGACA 97797575
Query 1863 AGTGGGACAACCTCCTCCGCGACTACAAGAAGGTCCGCGACTACGAGTCccgcgtcgccg 1922
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 97797574 AGTGGGACAACCTCCTCCGCGACTACAAGAAGGTCCGCGACTACGAGTCCCGCGTCGCCG 97797515
Query 1923 ccgccgccgccac--cggc----ggcgcg-gc-c-g-c-c-gcca-actccgcc-c---- 1964
|| | |||| | | |||| ||||| || | | | | |||| |||| ||| |
Sbjct 97797514 CCACGGCCGGCGCGGCGGCCTCTGGCGCCAGCACCGGCGCCGCCACACTC-GCCGCAGTA 97797456
Query 1965 c-cctcccgTCGTACTGGACGATGGAGCGGCACGAGCGCAAGGACTGCAACCTCCCCACC 2023
| ||||||||| |||||||| || ||||||||||| ||||||||| ||||||||||||||
Sbjct 97797455 CTCCTCCCGTCCTACTGGACCATCGAGCGGCACGACCGCAAGGACCGCAACCTCCCCACC 97797396
Query 2024 AACCTGGCGCCGGAGGTCTACGACGCGCTCTCCGAGGTGCTCTcccgccgcgcggcgcga 2083
||||| |||||||||||||||||||||||||| ||||| |||||||||||||| ||||||
Sbjct 97797395 AACCTCGCGCCGGAGGTCTACGACGCGCTCTCGGAGGTCCTCTCCCGCCGCGCCGCGCGA 97797336
Query 2084 cgcggcggcgccacgatcgcgcccaccccgccgccaccaccgctcgcgctgccgctgccg 2143
|| ||||||| ||||||||| |||||||| || || || | |||||| ||||||| |||
Sbjct 97797335 CGGGGCGGCGTCACGATCGCACCCACCCCTCCACC-CC-C-GCTCGCTCTGCCGCCGCCA 97797279
Query 2144 ccgccgccgccgcc-c--tcgccgccgAAGCCTCTCGTCGCGCAGCAGCAGCA 2193
|| || || || || | || || |||||||||||| || | |||||||||||
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: 3118662281240
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