Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009429.1 Hibiscus syriacus cultivar Beakdansim tig00113411_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: 66614
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:15437 original size:227 final size:225
Alignment explanation
Indices: 15001--15445 Score: 750
Period size: 227 Copynumber: 2.0 Consensus size: 225
14991 GTAAATTATC
* * *
15001 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATTTTATTATTATCTTTAGTT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATTTTATTATTATATTTAGTT
**
15066 AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTT
66 AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAATTT
*
15131 GTGTAAATGAAATTATTAAATTAAATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAA
131 GTGTAAATGAAATTATTAAATTAAATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAA
15196 ACATAAATTACATAACTTTCAAAAAAGTATA
196 ACATAAATTACATAACTTT-AAAAAAGTATA
*
15227 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACAT-TTTATTATTATATTTAG
*
15292 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA-AAT
64 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAAT
* *
15356 TTGTGTAAATTAAATTA-TAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
129 TTGTGTAAATGAAATTATTAAATTAA-ATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
15420 GAAACATAAATTACATAACTTTAAAA
193 GAAACATAAATTACATAACTTTAAAA
15446 GCAGTTTTAA
Statistics
Matches: 206, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
226 48 0.23
227 83 0.40
228 75 0.36
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (225 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATTTTATTATTATATTTAGTT
AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAATTT
GTGTAAATGAAATTATTAAATTAAATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAA
ACATAAATTACATAACTTTAAAAAAGTATA
Found at i:18053 original size:33 final size:33
Alignment explanation
Indices: 18011--18076 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
18001 AAATAGATGG
*
18011 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
18044 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
18077 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:19904 original size:19 final size:19
Alignment explanation
Indices: 19860--19903 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
19850 AATGTCGAGT
19860 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
19879 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
19898 T-ATTTT
1 TAATTTT
19904 TTTATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:20612 original size:198 final size:198
Alignment explanation
Indices: 19986--21396 Score: 2550
Period size: 198 Copynumber: 7.1 Consensus size: 198
19976 TTAAGGGTCA
*
19986 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
20051 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
20116 AATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
20180 ATG
196 ATG
20183 TGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTT-TTTTCCAGAATGAATTAAAAACAAGGTGCATC
20248 AATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
20311 TAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
20375 AATG
195 AATG
* * * *
20379 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCATAATGAATTAAAAAC-AGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
20443 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
20508 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
20573 AATG
195 AATG
20577 TGTCGACACTAATATAG-TTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
20641 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
20706 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
20771 ATG
196 ATG
20774 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
20839 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
20903 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
20968 ATG
196 ATG
* *
20971 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
*
21036 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
21101 TAATATGTAA-TTTTCAATCTAACCGGTACAATTGTACCGGTTTTATGAGAGAATATGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
21165 AATG
195 AATG
* *
21169 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCATC
* *
21234 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
21299 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
21364 AATG
195 AATG
*
21368 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
21397 CTAATTTAAA
Statistics
Matches: 1182, Mismatches: 21, Indels: 20
0.97 0.02 0.02
Matches are distributed among these distances:
194 23 0.02
195 20 0.02
196 150 0.13
197 378 0.32
198 491 0.42
199 120 0.10
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (198 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATG
Found at i:20882 original size:394 final size:395
Alignment explanation
Indices: 19986--21396 Score: 2564
Period size: 394 Copynumber: 3.6 Consensus size: 395
19976 TTAAGGGTCA
* *
19986 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
20051 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
20116 AATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
20180 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAATTAAAAACAAGGTGC
196 ATGTGTCGACACTAATATAGTTTGTGTCGATATTT-TTTTCCAGAATGAATTAAAAACAAGGTGC
20245 ATCAATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
260 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
20308 ATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
325 ATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
20373 ATAATG
390 ATAATG
* * *
20379 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCATAATGAATTAAAAAC-AGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
20443 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
20508 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
20573 AATGTGTCGACACTAATATAG-TTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
195 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
20637 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
260 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
*
20702 ATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
325 ATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
20767 AATAATG
389 AATAATG
*
20774 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
20839 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
20903 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
*
20968 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATAAAAAACAAGGTGC
196 ATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGC
* *
21033 ACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
260 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
* *
21098 ATGTAATATGTAATTTTCAATCTAACCGGTACAATTGTACCGGTTTTATGAGAGAATATGTCTAA
325 ATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
21163 ATAATG
390 ATAATG
*
21169 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCACC
* *
21234 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
21299 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
21364 AATGTGTCGACACTAATATATTTTGTGTCGATA
195 AATGTGTCGACACTAATATAGTTTGTGTCGATA
21397 CTAATTTAAA
Statistics
Matches: 984, Mismatches: 24, Indels: 16
0.96 0.02 0.02
Matches are distributed among these distances:
392 77 0.08
393 118 0.12
394 244 0.25
395 227 0.23
396 198 0.20
397 120 0.12
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (395 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCA
TCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
TGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
TAATG
Found at i:22887 original size:3 final size:3
Alignment explanation
Indices: 22873--22953 Score: 81
Period size: 3 Copynumber: 27.0 Consensus size: 3
22863 GCTGACGATG
* * * * ** *
22873 GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
22921 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
22954 CCAAACAAGT
Statistics
Matches: 61, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:24615 original size:183 final size:183
Alignment explanation
Indices: 24307--24971 Score: 1246
Period size: 183 Copynumber: 3.7 Consensus size: 183
24297 CTTTCAACAT
**
24307 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
24372 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
24437 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
24490 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
24555 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
*
24620 ATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
24673 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
24738 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
24803 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
24856 A-TATAATGTAATAGATAATTTTGTAATATAACCGGTAT-AA-ATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
* *
24918 GGTCTACAACCTATATCGATACTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATA
24972 CCATTTAAAA
Statistics
Matches: 474, Mismatches: 8, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
180 72 0.15
181 2 0.00
182 37 0.08
183 363 0.77
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:27536 original size:23 final size:23
Alignment explanation
Indices: 27510--27572 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
27500 AATAGGTAAC
*
27510 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* * **
27533 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
27556 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
27573 ATGGTTATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:27580 original size:23 final size:23
Alignment explanation
Indices: 27510--27582 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
27500 AATAGGTAAC
* * **
27510 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
* *
27533 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
27556 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
27579 ATAT
1 ATAT
27583 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 40 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:27972 original size:23 final size:23
Alignment explanation
Indices: 27941--28003 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
27931 ATAGGTAAAC
*
27941 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
27964 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
27987 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
28004 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:28011 original size:23 final size:23
Alignment explanation
Indices: 27941--28013 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
27931 ATAGGTAAAC
* * **
27941 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
27964 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
27987 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
28010 ATAT
1 ATAT
28014 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:28400 original size:23 final size:23
Alignment explanation
Indices: 28369--28431 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
28359 ATAGGTAAAC
*
28369 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
28392 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
28415 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
28432 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:28439 original size:23 final size:23
Alignment explanation
Indices: 28369--28441 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
28359 ATAGGTAAAC
* * **
28369 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
28392 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
28415 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
28438 ATAT
1 ATAT
28442 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:28555 original size:429 final size:431
Alignment explanation
Indices: 27416--28859 Score: 2757
Period size: 430 Copynumber: 3.4 Consensus size: 431
27406 AATTCGCAGT
*
27416 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTAT-AAAAAAGTATCGATCCTTTTTAT-
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
27479 AAAAGTATGGACACTTTC-A-ATAATAGGT-AACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
*
27541 TAATATGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
*
27606 AAAAGTGTCCATAGTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
27671 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
*
27736 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
27801 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
*
27842 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCATTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
27907 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
27972 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
28037 AAAAGTGTCCATAC-TTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
28101 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
28166 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAA-TTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
28230 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
28271 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTT-AAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
28335 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
28400 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
28465 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
28530 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
*
28595 ATTAAATTTAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
28660 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
28701 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
28766 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATG---TAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
28828 TAATAGGTATCGTTTATATAATGTAATAGGTA
131 TAATAGGTATCGTTTATATAATGTAATAGGTA
28860 TCTATCTCGC
Statistics
Matches: 1003, Mismatches: 7, Indels: 14
0.98 0.01 0.01
Matches are distributed among these distances:
426 39 0.04
427 22 0.02
428 237 0.24
429 260 0.26
430 268 0.27
431 177 0.18
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (431 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:28844 original size:23 final size:23
Alignment explanation
Indices: 28818--28861 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
28808 TAGGTAGCCC
28818 TTATATAATGTAATAGGTATCGT
1 TTATATAATGTAATAGGTATCGT
28841 TTATATAATGTAATAGGTATC
1 TTATATAATGTAATAGGTATC
28862 TATCTCGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (23 bp):
TTATATAATGTAATAGGTATCGT
Found at i:29085 original size:18 final size:18
Alignment explanation
Indices: 29064--29100 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29054 GTAATTGGAG
29064 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
29082 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
29100 T
1 T
29101 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:29108 original size:24 final size:24
Alignment explanation
Indices: 29056--29102 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
29046 ATTCATATGT
* *
29056 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
29080 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
29103 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:34248 original size:15 final size:15
Alignment explanation
Indices: 34228--34271 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
34218 GGTATATTTG
34228 TTTTTATAATTTATT
1 TTTTTATAATTTATT
* *
34243 TTTTTACTCATTAATT
1 TTTTTA-TAATTTATT
*
34259 TTTTTATTATTTA
1 TTTTTATAATTTA
34272 AGCAATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTATAATTTATT
Found at i:35503 original size:83 final size:83
Alignment explanation
Indices: 35353--36070 Score: 738
Period size: 83 Copynumber: 8.7 Consensus size: 83
35343 TATGTTTTCA
* * * * * *
35353 ATTATTCAGAGAATCTCTACCATGTCATAGTGTTCCATCTCATCCGAAATCAAAGACGCATTTCA
1 ATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGCGCATTCCA
* *
35418 GGGGAAACATTTTCCATT
66 GGGGAAGCGTTTTCCATT
* * * * ** ** ** * *
35436 ATTATTTAAAGAATCTCTGCCATATTATAGTGTGGCATCTTATCTTAAATGAAAGGCGCGTTACA
1 ATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGCGCATTCCA
*
35501 GGGGAAGTGTTTTCCATT
66 GGGGAAGCGTTTTCCATT
* * ** * ***
35519 ATTATTCAGAGAATCTCTGTCATATCATAGTGTTTCATCCCATATGAAATGAAATGCTTGTTCCT
1 ATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGCGCATTCC-
*
35584 A-GGGAAACGTTTTCCATT
65 AGGGGAAGCGTTTTCCATT
* * * ** **
35602 ATTATTCAAAGAATCTCTGTCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGTGTGTTTTA
1 ATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGCGCATTCCA
** *
35667 GGGTTAGCATTTTCCATT
66 GGGGAAGCGTTTTCCATT
* * * ** * * *
35685 ATTATTTAGAGAACCTCTGCCATGTCATAGTGTTCCATCATATCCGAAATGAAAGGCACTTTCTA
1 ATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGCGCATTCCA
* *
35750 TGAGAAGCGTTTTCCATT
66 GGGGAAGCGTTTTCCATT
* * * *** **
35768 ATTATTCAAAGAATCTCTGTCATGTCATAGTATTTCATCCCATCCGAAATGAAAGAAACATTATA
1 ATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGCGCATTCCA
** *
35833 TAGGAAGCATTTTCCATT
66 GGGGAAGCGTTTTCCATT
* * *
35851 ATTATTCAAAGAATATCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGTGCATTCCA
1 ATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGCGCATTCCA
* *
35916 TGGGAAGCGTTTTCCAGT
66 GGGGAAGCGTTTTCCATT
* *
35934 ATTATTCAGAGAATCTTTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGCTCATTCCA
1 ATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGCGCATTCCA
*
35999 GGGGAAGTG-TTTCCATT
66 GGGGAAGCGTTTTCCATT
* * * * * *
36016 ATTATTGAGAGAATCTCTTCCATGTCATAATATTCCATCCCATCTGAAATGAAAG
1 ATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAG
36071 ACGCGTGTTT
Statistics
Matches: 529, Mismatches: 104, Indels: 5
0.83 0.16 0.01
Matches are distributed among these distances:
82 56 0.11
83 472 0.89
84 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (83 bp):
ATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGCGCATTCCA
GGGGAAGCGTTTTCCATT
Found at i:35798 original size:249 final size:245
Alignment explanation
Indices: 35353--36072 Score: 845
Period size: 249 Copynumber: 2.9 Consensus size: 245
35343 TATGTTTTCA
* * * * * **
35353 ATTATTCAGAGAATCTCTACCATGTCATAGTGTTCCATCTCATCCGAAATCAAAGACGCATTTCA
1 ATTATTCAAAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGTGCATTTCA
* * * * ** * **
35418 GGGGAAACATTTTCCATTATTATTTAAAGAATCTCTGCCATATTATAGTGTGGCATCTTATCTTA
66 -GGGAAGCATTTTCCATTATTATTTAGAGAATCTCTGCCATGTCATAGTGTTCCATCATATCCGA
* * *
35483 AATGAAAGGCGCGTTACAGGGGAAGTGTTTTCCATTATTATTCAGAGAATCTCTGTCATATCATA
130 AATGAAAGGCAC-TTTCAGGGGAAGTGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCATA
* * * * *
35548 GTGTTTCATCCCATATGAAATGAAATG-C-TTGTTCCTAGGGAAACGTTTTCCATT
194 GTATTTCATCCCATCTGAAATGAAA-GACATT-AT-ATA-GGAAACATTTTCCATT
* ** *
35602 ATTATTCAAAGAATCTCTGTCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGTGTGTTTTA
1 ATTATTCAAAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGTGCATTTCA
* *
35667 GGGTTAGCATTTTCCATTATTATTTAGAGAACCTCTGCCATGTCATAGTGTTCCATCATATCCGA
66 GGG-AAGCATTTTCCATTATTATTTAGAGAATCTCTGCCATGTCATAGTGTTCCATCATATCCGA
* * * *
35732 AATGAAAGGCACTTTCTATGAGAAGCGTTTTCCATTATTATTCAAAGAATCTCTGTCATGTCATA
130 AATGAAAGGCACTTTC-AGGGGAAGTGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCATA
* *
35797 GTATTTCATCCCATCCGAAATGAAAGAAACATTATATAGGAAGCATTTTCCATT
194 GTATTTCATCCCATCTGAAATGAAAG--ACATTATATAGGAAACATTTTCCATT
* *
35851 ATTATTCAAAGAATATCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGTGCATTCCA
1 ATTATTCAAAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGTGCATTTCA
* * * * * **
35916 TGGGAAGCGTTTTCCAGTATTATTCAGAGAATCTTTGCCATGTCATAGTGTTTCATCCCATCCGA
66 -GGGAAGCATTTTCCATTATTATTTAGAGAATCTCTGCCATGTCATAGTGTTCCATCATATCCGA
* * *
35981 AATGAAAGGCTCATTCCAGGGGAAGTG-TTTCCATTATTATTGAGAGAATCTCT-TCCATGTCAT
130 AATGAAAGGCAC-TTTCAGGGGAAGTGTTTTCCATTATTATTCAGAGAATCTCTGT-CATGTCAT
* *
36044 AATATTCCATCCCATCTGAAATGAAAGAC
193 AGTATTTCATCCCATCTGAAATGAAAGAC
36073 GCGTGTTTAT
Statistics
Matches: 401, Mismatches: 61, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
246 2 0.00
247 1 0.00
248 63 0.16
249 323 0.81
250 8 0.02
251 2 0.00
252 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (245 bp):
ATTATTCAAAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGGTGCATTTCA
GGGAAGCATTTTCCATTATTATTTAGAGAATCTCTGCCATGTCATAGTGTTCCATCATATCCGAA
ATGAAAGGCACTTTCAGGGGAAGTGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCATAGT
ATTTCATCCCATCTGAAATGAAAGACATTATATAGGAAACATTTTCCATT
Found at i:36616 original size:65 final size:66
Alignment explanation
Indices: 36449--36639 Score: 251
Period size: 65 Copynumber: 2.9 Consensus size: 66
36439 GACTGATTGA
* * * *
36449 TGAATATTGTATAGATCACTCAATGAGACTCATATACCTTTATGGTGCATGAGGTGGAGTTATAA
1 TGAATATTGTATTGATCACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTCATAA
36514 T
66 T
* * * * * *
36515 TGAATACTGCACAT-ATCAGTCAATGAGACTCATGTACCTTTGTGGTGCTTGAGG-GGGGTCATA
1 TGAATATTGTA-TTGATCACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTCATA
36578 AT
65 AT
**
36580 TGAATATTGTATTGATCACTCAATGAGACTTGTGTACCTTTGTGGTGCATGAGGTGGAGT
1 TGAATATTGTATTGATCACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGT
36640 GACTATATGA
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
64 1 0.01
65 54 0.52
66 49 0.47
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (66 bp):
TGAATATTGTATTGATCACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTCATAA
T
Found at i:40100 original size:17 final size:17
Alignment explanation
Indices: 40057--40124 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
40047 AAGAGTTAGA
40057 TTAATAAATGAACTAGT
1 TTAATAAATGAACTAGT
* * *
40074 TTGATGAATGATCTAGT
1 TTAATAAATGAACTAGT
* *
40091 TTAATTAATGAACTAACT
1 TTAATAAATGAACT-AGT
* *
40109 TTATTCAATGAACTAG
1 TTAATAAATGAACTAG
40125 ATGCATGAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
17 26 0.65
18 14 0.35
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (17 bp):
TTAATAAATGAACTAGT
Found at i:42435 original size:77 final size:77
Alignment explanation
Indices: 42353--42495 Score: 205
Period size: 77 Copynumber: 1.9 Consensus size: 77
42343 TTATCGATCA
** * *
42353 ATTTTGTTTAATGCATATGTTACATTTTCGTATCAAAACCTTTGTGTACTTTCGGCACTATGTGT
1 ATTTTGTTTAATGCATACATTACATTTTCGTATCAAAACATTTGTGTACTTTCGACACTATGTGT
42418 GGTCATCGATTG
66 GGTCATCGATTG
* * ** *
42430 ATTTTGTTTAATGCATACATTGCATTTTCTTATCAGTACATTTGTGTTCTTTCGACACTATGTGT
1 ATTTTGTTTAATGCATACATTACATTTTCGTATCAAAACATTTGTGTACTTTCGACACTATGTGT
42495 G
66 G
42496 CATGCATGGT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
77 57 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (77 bp):
ATTTTGTTTAATGCATACATTACATTTTCGTATCAAAACATTTGTGTACTTTCGACACTATGTGT
GGTCATCGATTG
Found at i:55596 original size:20 final size:20
Alignment explanation
Indices: 55567--55605 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55557 AACGATTCCC
*
55567 GGAAACATAGAAAAAGAACA
1 GGAAAAATAGAAAAAGAACA
*
55587 GGAAAAATAGAAAACGAAC
1 GGAAAAATAGAAAAAGAAC
55606 CGTAACAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.10, G:0.21, T:0.05
Consensus pattern (20 bp):
GGAAAAATAGAAAAAGAACA
Found at i:57373 original size:16 final size:16
Alignment explanation
Indices: 57349--57398 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
57339 CCGGTTTCGA
*
57349 TTTTAAAAAAATCGGT
1 TTTTAAAAAAACCGGT
*
57365 TTTTTAAAAAACCGG-
1 TTTTAAAAAAACCGGT
* *
57380 TTATAAAAAAACCGAT
1 TTTTAAAAAAACCGGT
57396 TTT
1 TTT
57399 AATATTCCAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (16 bp):
TTTTAAAAAAACCGGT
Found at i:57818 original size:13 final size:13
Alignment explanation
Indices: 57797--57826 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
57787 AAGTTCGATA
57797 AATTCAAATACTT
1 AATTCAAATACTT
*
57810 AATTGAAATACTT
1 AATTCAAATACTT
57823 AATT
1 AATT
57827 AACTCAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (13 bp):
AATTCAAATACTT
Found at i:57933 original size:32 final size:33
Alignment explanation
Indices: 57837--57935 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
57827 AACTCAACAT
* * *
57837 AATTAAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
57870 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
57903 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
57935 A
1 A
57936 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:57954 original size:21 final size:21
Alignment explanation
Indices: 57930--57969 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
57920 ACTTCAAGTT
57930 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
57951 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
57970 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:60388 original size:20 final size:20
Alignment explanation
Indices: 60360--60397 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
60350 TAAAATAACC
* *
60360 GGTTTAAAAAAATCCGATCA
1 GGTTAAAAAAAAACCGATCA
60380 GGTTAAAAAAAAACCGAT
1 GGTTAAAAAAAAACCGAT
60398 TTTTCCCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.21
Consensus pattern (20 bp):
GGTTAAAAAAAAACCGATCA
Found at i:61840 original size:20 final size:20
Alignment explanation
Indices: 61815--61853 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
61805 TAAATTAAAT
*
61815 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
61835 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
61854 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:61900 original size:20 final size:21
Alignment explanation
Indices: 61867--61906 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
61857 TCTATTAGTT
61867 ATTAGATATGATCA-TTTTTA
1 ATTAGATATGATCAGTTTTTA
61887 ATTAGATA-GAATCAGTTTTT
1 ATTAGATATG-ATCAGTTTTT
61907 TATTCTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 12 0.67
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (21 bp):
ATTAGATATGATCAGTTTTTA
Found at i:61933 original size:53 final size:52
Alignment explanation
Indices: 61814--61963 Score: 266
Period size: 53 Copynumber: 2.9 Consensus size: 52
61804 CTAAATTAAA
*
61814 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
*
61866 TATTAGATATGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
61919 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
61964 GTTGCTAATT
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 10 0.11
52 34 0.36
53 50 0.53
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.49
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:61945 original size:20 final size:20
Alignment explanation
Indices: 61920--61959 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
61910 TCTATTAGTT
*
61920 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
61940 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
61960 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:65577 original size:12 final size:12
Alignment explanation
Indices: 65560--65587 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
65550 ACATTGTTTG
65560 ACAGGAGATGAC
1 ACAGGAGATGAC
65572 ACAGGAGATGAC
1 ACAGGAGATGAC
65584 ACAG
1 ACAG
65588 TAGAGTTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.18, G:0.32, T:0.07
Consensus pattern (12 bp):
ACAGGAGATGAC
Found at i:66562 original size:20 final size:20
Alignment explanation
Indices: 66537--66575 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
66527 TAAATTAAAT
*
66537 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
66557 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
66576 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Done.