Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008674.1 Hibiscus syriacus cultivar Beakdansim tig00111689_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 899125
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:841609 original size:427 final size:429
Alignment explanation
Indices: 840700--841751 Score: 1994
Period size: 428 Copynumber: 2.5 Consensus size: 429
840690 AGGTATATAC
840700 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
* *
840765 GTTACG--GTATA-TATTATTAAATTAAAAATTCTAAATAATATTTTAT-AAATATCAAAACAAT
66 GTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAAT
* *
840826 CAACTAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAAACACTG
131 CAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTG
840891 TTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
196 TTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
840956 ATGGACACTTTCAATATAATAGGTAAACATATGATTAATAGGTAGCCCTTATATAATGTAATAGG
261 ATGGACACTTTCAATATAATAGGTAAACATATGATTAATAGGTAGCCCTTATATAATGTAATAGG
841021 TATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTG
326 TATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTG
841086 TCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTT
391 TCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTT
841125 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
841189 GTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAAT
66 GTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAAT
841254 CAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTG
131 CAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTG
841319 TTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
196 TTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
841384 ATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAG
261 ATGGACACTTTCAATATAATAGGTAAACATATGAT-TAATAGGTAGCCCTTATATAATGTAATAG
841449 GTATCGTTTATATAATGTAATAGGTAGTGGTTATA-TGTAAAG-GTCTATCCTTTTTATAAAAGT
325 GTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGT
841512 GTCCATACTTTTTTCACTGTGG-AAACATTAATTTAAGGTT
390 GTCCATAC-TTTTTCACTGTGGAAAACATTAATTTAAGGTT
841552 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
841617 GTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAAT
66 GTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAAT
841682 CAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTG
131 CAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTG
841747 TTAAA
196 TTAAA
841752 GTATCGATCC
Statistics
Matches: 616, Mismatches: 4, Indels: 11
0.98 0.01 0.02
Matches are distributed among these distances:
424 13 0.02
425 57 0.09
426 4 0.01
427 138 0.22
428 340 0.55
429 64 0.10
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (429 bp):
ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
GTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAAT
CAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTG
TTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
ATGGACACTTTCAATATAATAGGTAAACATATGATTAATAGGTAGCCCTTATATAATGTAATAGG
TATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTG
TCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTT
Found at i:842217 original size:23 final size:23
Alignment explanation
Indices: 842182--842229 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
842172 ATCAAGTACA
*
842182 ATAATATATTAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* * *
842205 ATAATGTAATAGGTAGCGTTTAT
1 ATAATATAATAGGTAACGCTTAT
842228 AT
1 AT
842230 TGACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:842935 original size:182 final size:181
Alignment explanation
Indices: 842616--842994 Score: 618
Period size: 182 Copynumber: 2.1 Consensus size: 181
842606 ACTTTTATAC
* *
842616 TACCGGTTTTGTCATTTCGAGATCC-ATTTTGTCATATTTTTACCTATTATATTGTTATGGATCG
1 TACCGGTTTTGTCATTTCGAGA-CCGATTTTATCATATTTTTACCTGTTATATTGTTAT-GATCG
* * * *
842680 ATACATTTTTATAAAGTATCGACATTTTATTGATGCTATAACTTCTAT-TCTTTTAAATTTCAAA
64 ATACATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTCT-TCTCTTTTAAATTCCAAA
* *
842744 AGAGTCGATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCTCTT
128 AGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTT
*
842798 TACCGGTTTTGTCATTTTGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATAGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTAT-GATCGA
842863 TACATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
65 TACATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
842928 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTT
130 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTT
*
842980 TACCGGTTTTATCAT
1 TACCGGTTTTGTCAT
842995 ATTTTTACCT
Statistics
Matches: 184, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
181 3 0.02
182 181 0.98
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.42
Consensus pattern (181 bp):
TACCGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGATCGAT
ACATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
GTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTT
Found at i:843091 original size:162 final size:162
Alignment explanation
Indices: 842819--843156 Score: 586
Period size: 162 Copynumber: 2.1 Consensus size: 162
842809 TCATTTTGAG
* * *
842819 ACCGATTTTATCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGA
1 ACCGGTTTTATCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAATATCAA
*
842884 CACTTTATTAACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGT
66 AACTTTATTAACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGT
*
842949 ATCGACACTATCAACATATCCGGTAGCTCTTT
131 ATCGACACTATCAAAATATCCGGTAGCTCTTT
*
842981 ACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCAA
1 ACCGGTTTTATCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAATATCAA
*
843046 AACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGT
66 AACTTTATTAACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGT
*
843111 ATCGACACTATCAAAATATCTGGTAGCTCTTT
131 ATCGACACTATCAAAATATCCGGTAGCTCTTT
* *
843143 ATCGGTTTTGTCAT
1 ACCGGTTTTATCAT
843157 TTCGAGACCG
Statistics
Matches: 166, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 166 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (162 bp):
ACCGGTTTTATCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAATATCAA
AACTTTATTAACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGT
ATCGACACTATCAAAATATCCGGTAGCTCTTT
Found at i:843274 original size:344 final size:344
Alignment explanation
Indices: 842642--843338 Score: 1166
Period size: 344 Copynumber: 2.0 Consensus size: 344
842632 TCGAGATCCA
* * * *
842642 TTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACATTT
1 TTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAATATCAAAACTT
* *
842707 TATTGATGCTATAACTTCTATTCTTTTAAATTTCAAAAGAGTCGATACTTATAATAAAATATCGA
66 TATTGACGCTATAACTTCTATTCTTTTAAATTCCAAAAGAGTCGATACTTATAATAAAATATCGA
* *
842772 CACTATCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATTTTGAGACCGATTTTATCATATTT
131 CACTATCAAAATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCGATTTTATCATATTT
842837 TTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTATTAACGCTATA
196 TTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTATTAACGCTATA
842902 ACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATA
261 ACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATA
*
842967 TCCGGTAGCTCTTTACCGG
326 TCCGGTAGCGCTTTACCGG
* *
842986 TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCAAAACTT
1 TTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAATATCAAAACTT
* *
843051 TATT-AGCGCTATAACTTCT-TCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTATC
66 TATTGA-CGCTATAACTTCTAT-TCTTTTAAATTCCAAAAGAGTCGATACTTATAATAAAATATC
* *
843114 GACACTATCAAAATATCTGGTAGCTCTTTATCGGTTTTGTCATTTCGAGACCGATTTTATCATAT
129 GACACTATCAAAATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCGATTTTATCATAT
*
843179 TTTTACCTGTTATATTGTTAT-GAATCGATACATTTTTATAAAGTATCGACACTTTATTAGCGCT
194 TTTTACCTGTTATATTGTTATAG-ATCGATACATTTTTATAAAGTATCGACACTTTATTAACGCT
* * * *
843243 ATAATTTCTTCTCTTTTAAATTCCAAAAGTGTCGATTCTTATAATAAAGTATTGACACTTTCAAC
258 ATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTATCGACACTATCAAC
843308 ATATCCGGTAGCGCTTTACCGG
323 ATATCCGGTAGCGCTTTACCGG
843330 TTTTGTCAT
1 TTTTGTCAT
843339 TTCGAGACTG
Statistics
Matches: 329, Mismatches: 21, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
343 3 0.01
344 326 0.99
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.42
Consensus pattern (344 bp):
TTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAATATCAAAACTT
TATTGACGCTATAACTTCTATTCTTTTAAATTCCAAAAGAGTCGATACTTATAATAAAATATCGA
CACTATCAAAATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCGATTTTATCATATTT
TTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTATTAACGCTATA
ACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATA
TCCGGTAGCGCTTTACCGG
Found at i:843293 original size:182 final size:182
Alignment explanation
Indices: 842981--843415 Score: 726
Period size: 182 Copynumber: 2.4 Consensus size: 182
842971 GTAGCTCTTT
* * *
842981 ACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCAA
1 ACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
*
843046 AACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGT
66 CACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGT
* * *
843111 ATCGACACTATCAAAATATCTGGTAGCTCTTTATCGGTTTTGTCATTTCGAG
131 ATCGACACTATCAAAATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAG
*
843163 ACCGATTTTATCATATTTTTACCTGTTATATTGTTATGAATCGATACATTTTTATAAAGTATCGA
1 ACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
* *
843228 CACTTTATTAGCGCTATAATTTCTTCTCTTTTAAATTCCAAAAGTGTCGATTCTTATAATAAAGT
66 CACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGT
* * *
843293 ATTGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAG
131 ATCGACACTATCAAAATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAG
* * *
843345 ACTGATTTTATCATATTTTTACCTGTTATATTATTATGGATCGATATATTTTTATAAAGTATCGA
1 ACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
843410 CACTTT
66 CACTTT
843416 CAATATATCT
Statistics
Matches: 236, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
182 236 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (182 bp):
ACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
CACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGT
ATCGACACTATCAAAATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAG
Found at i:843483 original size:112 final size:111
Alignment explanation
Indices: 843286--843638 Score: 544
Period size: 112 Copynumber: 3.2 Consensus size: 111
843276 GATTCTTATA
* * * ** *
843286 ATAAAGTATTGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACTGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* * * *
843351 TTTATCATATTTTTACCTGTTATATTATTATGGATCGATATATTTTT
66 TTTGTC-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
**
843398 ATAAAGTATCGACACTTTCAATATATCTTGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
*
843463 TTTGTCTTTTTTTTTCCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTC-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
843510 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATATACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
843575 TTTGTCATTTTTTACCTGTTATATTGTTATGGATAGATACATTTTT
66 TTTGTCTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
843621 ATAAAGTATCGACACTTT
1 ATAAAGTATCGACACTTT
843639 ACCTGTTTTA
Statistics
Matches: 221, Mismatches: 20, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
111 55 0.25
112 166 0.75
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (111 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
TTTGTCTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:843715 original size:91 final size:90
Alignment explanation
Indices: 843545--843726 Score: 285
Period size: 91 Copynumber: 2.0 Consensus size: 90
843535 TCCGGTAGCG
* *
843545 CTTTACCTGTTTTGTCATTTATATACCGATTTTGTCATTTTTTACCTGTTATATTGTTATGGATA
1 CTTTACCTGTTTTATCATTTATAAACCGATTTTGTCATTTTTTACCTGTTATATTGTTATGGATA
843610 GATACATTTTTATAAAGTATCGACA
66 GATACATTTTTATAAAGTATCGACA
* *
843635 CTTTACCTGTTTTATCATTTATAAACCGGTTTTGTCATTTTTTTACTTGTTATATTGTTATGGAT
1 CTTTACCTGTTTTATCATTTATAAACCGATTTTGTCA-TTTTTTACCTGTTATATTGTTATGGAT
* *
843700 CA-ATATATTTTTATAAAGTATGGACA
65 -AGATACATTTTTATAAAGTATCGACA
843726 C
1 C
843727 AAACCGACAA
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
90 34 0.40
91 49 0.58
92 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.49
Consensus pattern (90 bp):
CTTTACCTGTTTTATCATTTATAAACCGATTTTGTCATTTTTTACCTGTTATATTGTTATGGATA
GATACATTTTTATAAAGTATCGACA
Found at i:851517 original size:24 final size:26
Alignment explanation
Indices: 851463--851510 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
851453 TGAAGTCAAA
851463 AAAAATTTAGAAGCTCGATTGAAGCC
1 AAAAATTTAGAAGCTCGATTGAAGCC
* *
851489 TAAAATTT-G-AGCTTGATTGAAG
1 AAAAATTTAGAAGCTCGATTGAAG
851511 TGAAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 1 0.05
26 7 0.35
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (26 bp):
AAAAATTTAGAAGCTCGATTGAAGCC
Found at i:852722 original size:2 final size:2
Alignment explanation
Indices: 852715--852754 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
852705 ACGATGTTAA
852715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
852755 CCATCGTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:856657 original size:13 final size:14
Alignment explanation
Indices: 856634--856677 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
856624 TAATATTATA
856634 TAAAAATTATATTT
1 TAAAAATTATATTT
856648 TAAAAA-TATATTT
1 TAAAAATTATATTT
* *
856661 TAATTAATTTTATTT
1 TAA-AAATTATATTT
856676 TA
1 TA
856678 TTTACAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 10 0.38
14 8 0.31
15 8 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAAAATTATATTT
Found at i:862481 original size:23 final size:23
Alignment explanation
Indices: 862442--862510 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
862432 ACCAAACAAT
862442 GAAAAATATGTCA-AAAGACAGA
1 GAAAAATATGTCATAAAGACAGA
*
862464 GAAAAATATATCATAAAGACAGA
1 GAAAAATATGTCATAAAGACAGA
* ** *
862487 GGAAAACGTGCCATAAAGACAGA
1 GAAAAATATGTCATAAAGACAGA
862510 G
1 G
862511 TTATTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 12 0.30
23 28 0.70
ACGTcount: A:0.55, C:0.12, G:0.20, T:0.13
Consensus pattern (23 bp):
GAAAAATATGTCATAAAGACAGA
Found at i:862699 original size:22 final size:24
Alignment explanation
Indices: 862674--862726 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
862664 CCTTTATATA
*
862674 TATTTATGTGTTA-A-ACATGTAT
1 TATTTATATGTTACATACATGTAT
*
862696 TATTTTTATGTTACATACATGTAT
1 TATTTATATGTTACATACATGTAT
*
862720 TTTTTAT
1 TATTTAT
862727 TTTCTCGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 11 0.44
23 1 0.04
24 13 0.52
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (24 bp):
TATTTATATGTTACATACATGTAT
Found at i:878918 original size:20 final size:20
Alignment explanation
Indices: 878895--878966 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
878885 TGCGATTTTC
878895 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACACAAAAGT
* * *
878915 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACACAAAAGT
878935 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACACAAAAGT
878955 CAAATTCGCAAC
1 CAAATTCGCAAC
878967 TGAATTTCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.17
Consensus pattern (20 bp):
CAAATTCGCAACACAAAAGT
Found at i:878978 original size:19 final size:19
Alignment explanation
Indices: 878954--879081 Score: 168
Period size: 19 Copynumber: 6.7 Consensus size: 19
878944 AACACAAAAG
878954 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
878973 TCAAATTCACAACTGAATT
1 TCAAATTCGCAACTGAATT
*
878992 TCAAATTCGTAACTGAATT
1 TCAAATTCGCAACTGAATT
*
879011 TCAAATTCGTAACTGAATT
1 TCAAATTCGCAACTGAATT
*
879030 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
879050 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
879070 T-AATTTCGCAAC
1 TCAAATTCGCAAC
879082 AGGTTTTAAT
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
19 76 0.78
20 21 0.22
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:879089 original size:18 final size:18
Alignment explanation
Indices: 879068--879118 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
879058 GCAACACGAA
879068 TTTAATTTCGCAACAGGT
1 TTTAATTTCGCAACAGGT
879086 TTTAATTTCGCAACAGGT
1 TTTAATTTCGCAACAGGT
*
879104 TTTAGTTTCGCAACA
1 TTTAATTTCGCAACA
879119 CAAATGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (18 bp):
TTTAATTTCGCAACAGGT
Found at i:879181 original size:27 final size:27
Alignment explanation
Indices: 879151--879213 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
879141 CGCAGCAGCA
879151 GCAACTCATAACCTAAATCCCTAAATC
1 GCAACTCATAACCTAAATCCCTAAATC
879178 GCAACTCATAACCTAAATCCCTAAATC
1 GCAACTCATAACCTAAATCCCTAAATC
879205 GCAACTCAT
1 GCAACTCAT
879214 TCCATCTCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.22
Consensus pattern (27 bp):
GCAACTCATAACCTAAATCCCTAAATC
Found at i:879935 original size:12 final size:12
Alignment explanation
Indices: 879914--879947 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
879904 ACCACATTTC
*
879914 CAATACCAAACA
1 CAATATCAAACA
879926 CAATATCAAACA
1 CAATATCAAACA
*
879938 CAATCTCAAA
1 CAATATCAAA
879948 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:880100 original size:24 final size:24
Alignment explanation
Indices: 880073--880126 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
880063 GTATTCGAAA
880073 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
880097 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
880121 TTTGAT
1 TTTGAT
880127 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:882670 original size:25 final size:23
Alignment explanation
Indices: 882636--882683 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 23
882626 AAATCAATTA
882636 AACATTGTTATGGGTACGTTATTTG
1 AACATTGTTATGGGTA--TTATTTG
882661 AACATTGTTATGGGTATTATTTG
1 AACATTGTTATGGGTATTATTTG
882684 GAAAATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.30
25 16 0.70
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (23 bp):
AACATTGTTATGGGTATTATTTG
Found at i:883090 original size:18 final size:18
Alignment explanation
Indices: 883069--883105 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
883059 GTAATTAGAG
883069 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
*
883087 TTTGAGTTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
883105 T
1 T
883106 ATAAATTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:883112 original size:24 final size:24
Alignment explanation
Indices: 883061--883113 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
883051 TTTCATATGT
* * * *
883061 AATTAGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTAAATTTAAATATA
*
883085 AATTTGAGTTTAAATTTCAATATA
1 AATTTGAGTTTAAATTTAAATATA
883109 AATTT
1 AATTT
883114 CGGCTCCACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTAAATTTAAATATA
Found at i:885248 original size:21 final size:21
Alignment explanation
Indices: 885208--885248 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
885198 ACGGGCGGGA
*
885208 CCTTTTGAATGATGACAGGGG
1 CCTTTTGAACGATGACAGGGG
* *
885229 CCTTTTGAACGGTGAGAGGG
1 CCTTTTGAACGATGACAGGG
885249 CTTCTTCGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.15, G:0.37, T:0.27
Consensus pattern (21 bp):
CCTTTTGAACGATGACAGGGG
Found at i:885479 original size:4 final size:4
Alignment explanation
Indices: 885449--885490 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
885439 GGGCCGCTGA
* * *
885449 AAAT AAAT TAAT ACAT AAAT CAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
885491 TGTCAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:886915 original size:34 final size:33
Alignment explanation
Indices: 886874--886980 Score: 149
Period size: 34 Copynumber: 3.5 Consensus size: 33
886864 TCCCCGTTAC
886874 TTTAACACTTCTCCCATTTATCATTTAAAAACA
1 TTTAACACTTCTCCCATTTATCATTTAAAAACA
886907 CTTTAACACTTCTCCCATTTATCATTT-AAAACA
1 -TTTAACACTTCTCCCATTTATCATTTAAAAACA
886940 -TT-----TTCTCCCA-TTATCATTTAAAAACA
1 TTTAACACTTCTCCCATTTATCATTTAAAAACA
886966 TTTAACACTTCTCCC
1 TTTAACACTTCTCCC
886981 CCTTTTTGTT
Statistics
Matches: 66, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
25 9 0.14
26 14 0.21
27 2 0.03
31 2 0.03
32 7 0.11
33 6 0.09
34 26 0.39
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (33 bp):
TTTAACACTTCTCCCATTTATCATTTAAAAACA
Found at i:886953 original size:25 final size:27
Alignment explanation
Indices: 886916--886968 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
886906 ACTTTAACAC
886916 TTCTCCCATTTATCATTT-AAAACATT
1 TTCTCCCATTTATCATTTAAAAACATT
886942 TTCTCCCA-TTATCATTTAAAAACATT
1 TTCTCCCATTTATCATTTAAAAACATT
886968 T
1 T
886969 AACACTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (27 bp):
TTCTCCCATTTATCATTTAAAAACATT
Found at i:888646 original size:20 final size:22
Alignment explanation
Indices: 888600--888655 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
888590 TTCCCCTGTG
888600 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGGTTCCCCTTCAA
* *
888622 AGGGGAATTGGTT-CCC-TCAA
1 GGGGGAATCGGTTCCCCTTCAA
*
888642 GGGGG-ATCGATTCC
1 GGGGGAATCGGTTCC
888656 TCTGCACCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 5 0.18
20 9 0.32
21 3 0.11
22 11 0.39
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCTTCAA
Found at i:896096 original size:20 final size:20
Alignment explanation
Indices: 896071--896133 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
896061 AACTAAAATT
896071 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGATTTTCATTTTC
* *
896091 GTGTTGCG------GTTTTG
1 GTGTTGCGATTTTCATTTTC
896105 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGATTTTCATTTTC
896125 GTGTTGCGA
1 GTGTTGCGA
896134 ATTTAAGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
14 12 0.36
20 21 0.64
ACGTcount: A:0.08, C:0.13, G:0.29, T:0.51
Consensus pattern (20 bp):
GTGTTGCGATTTTCATTTTC
Found at i:896108 original size:14 final size:14
Alignment explanation
Indices: 896085--896118 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
896075 TGCGATTTTC
896085 ATTTTCGTGTTGCG
1 ATTTTCGTGTTGCG
* *
896099 GTTTTGGTGTTGCG
1 ATTTTCGTGTTGCG
896113 ATTTTC
1 ATTTTC
896119 ATTTTCGTGT
Statistics
Matches: 16, Mismatches: 4, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.29, T:0.53
Consensus pattern (14 bp):
ATTTTCGTGTTGCG
Found at i:896144 original size:20 final size:20
Alignment explanation
Indices: 896105--896144 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
896095 TGCGGTTTTG
* * *
896105 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
896125 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
896145 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:896507 original size:22 final size:22
Alignment explanation
Indices: 896480--896531 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
896470 GAGATAGACA
896480 GATTTCGCCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACG
896502 GATTTCGCCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACG
*
896524 GATGTCGC
1 GATTTCGC
896532 TGTAGAGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.44, T:0.19
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACG
Found at i:896706 original size:20 final size:20
Alignment explanation
Indices: 896681--896743 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
896671 AATTCGCAAC
896681 TTGACTATCGCGTTGCGAAT
1 TTGACTATCGCGTTGCGAAT
* *
896701 TTGACT-TTGTGTTGCGAAT
1 TTGACTATCGCGTTGCGAAT
896720 TTGACTATCGCGTTGCGAAT
1 TTGACTATCGCGTTGCGAAT
896740 TTGA
1 TTGA
896744 TTCTGTGTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (20 bp):
TTGACTATCGCGTTGCGAAT
Found at i:896716 original size:19 final size:19
Alignment explanation
Indices: 896692--896756 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
896682 TGACTATCGC
896692 GTTGCGAATTTGACTTTGT
1 GTTGCGAATTTGACTTTGT
* *
896711 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TTGT
896731 GTTGCGAATTTGA-TTCTGT
1 GTTGCGAATTTGACTT-TGT
896750 GTTGCGA
1 GTTGCGA
896757 TTACAAATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 24 0.60
20 15 0.38
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.42
Consensus pattern (19 bp):
GTTGCGAATTTGACTTTGT
Found at i:896735 original size:39 final size:39
Alignment explanation
Indices: 896681--896756 Score: 136
Period size: 39 Copynumber: 1.9 Consensus size: 39
896671 AATTCGCAAC
896681 TTGACTATCGCGTTGCGAATTTGACTT-TGTGTTGCGAAT
1 TTGACTATCGCGTTGCGAATTTGA-TTCTGTGTTGCGAAT
896720 TTGACTATCGCGTTGCGAATTTGATTCTGTGTTGCGA
1 TTGACTATCGCGTTGCGAATTTGATTCTGTGTTGCGA
896757 TTACAAATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 2 0.06
39 34 0.94
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41
Consensus pattern (39 bp):
TTGACTATCGCGTTGCGAATTTGATTCTGTGTTGCGAAT
Found at i:896835 original size:20 final size:20
Alignment explanation
Indices: 896750--896836 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
896740 TTGATTCTGT
*
896750 GTTGCGA-TTACAAATTCGA
1 GTTGCGATTTACAAATTCGC
*
896769 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
** *
896789 GTTGCGAATTTGGAAAATCGC
1 GTTGCG-ATTTACAAATTCGC
** * *
896810 AATGCGATTTATATATTCGC
1 GTTGCGATTTACAAATTCGC
896830 GTTGCGA
1 GTTGCGA
896837 AATTGAAAAC
Statistics
Matches: 52, Mismatches: 14, Indels: 3
0.75 0.20 0.04
Matches are distributed among these distances:
19 7 0.13
20 31 0.60
21 14 0.27
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:898372 original size:15 final size:16
Alignment explanation
Indices: 898338--898376 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
898328 TTATTAAAAA
*
898338 ATATAAATAAATAAAT
1 ATATAAATAAATAAAG
*
898354 ATATAAA-AATTAAAG
1 ATATAAATAAATAAAG
898369 ATATAAAT
1 ATATAAAT
898377 TGTATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
ATATAAATAAATAAAG
Done.