Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000414.1 Hibiscus syriacus cultivar Beakdansim tig00000760_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: 65328
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2081 original size:24 final size:24
Alignment explanation
Indices: 2053--2101 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2043 AGAACCTTCA
2053 ATTTATTGCCTCAAACAAAAACCT
1 ATTTATTGCCTCAAACAAAAACCT
2077 ATTTATTGCCTCAAACAAAAACCT
1 ATTTATTGCCTCAAACAAAAACCT
2101 A
1 A
2102 GAGAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.29
Consensus pattern (24 bp):
ATTTATTGCCTCAAACAAAAACCT
Found at i:6257 original size:60 final size:59
Alignment explanation
Indices: 6155--6268 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 59
6145 TGTTACTTTA
* *** *
6155 AATATCTAAATAAAAATATATATTTTTTAAATAAATATTTTAATATAAA-AATTAGTTG
1 AATATCTAAATAAAAACATATATAACTTAAATAAATATTTTAAAATAAATAATTAGTTG
*
6213 AATATCTAAATAAAAAACATCATATAACTTAAATATATATTTTAAAATAAATAATT
1 AATATCTAAAT-AAAAACAT-ATATAACTTAAATAAATATTTTAAAATAAATAATT
6269 TTTTATTAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 11 0.23
59 7 0.15
60 25 0.53
61 4 0.09
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (59 bp):
AATATCTAAATAAAAACATATATAACTTAAATAAATATTTTAAAATAAATAATTAGTTG
Found at i:8641 original size:14 final size:14
Alignment explanation
Indices: 8622--8649 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8612 AAGTGAAAGA
8622 ATAGTTATATAATT
1 ATAGTTATATAATT
8636 ATAGTTATATAATT
1 ATAGTTATATAATT
8650 TTTTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:8869 original size:23 final size:21
Alignment explanation
Indices: 8842--8884 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
8832 ATATAAAAAA
8842 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
8863 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
8884 T
1 T
8885 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:9120 original size:2 final size:2
Alignment explanation
Indices: 9113--9184 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
9103 CTTAGACAAT
9113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9155 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9185 AAATACATAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13676 original size:64 final size:63
Alignment explanation
Indices: 13536--13696 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
13526 AATTGTTCAG
* *
13536 TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCTTAAAATGGAAACATCGAATGCAAGT
1 TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCTTAAAATGAAAACATCGAAGGCAAGT
* * * * *
13599 AGTGCATCAATGCATAAGG-AGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTAATT
1 TGTGTATCGATGCAT-AGGAAGTGCATCGATGCA-CCCCTTAAAATGAAAACATCGAAGGCAAGT
* * *
13663 TGTGTATCGATGCATGGGTAGTGCATCAATGCAC
1 TGTGTATCGATGCATAGGAAGTGCATCGATGCAC
13697 ATGTTAAAGA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 29 0.35
64 54 0.65
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (63 bp):
TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCTTAAAATGAAAACATCGAAGGCAAGT
Found at i:13729 original size:20 final size:20
Alignment explanation
Indices: 13704--13741 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
13694 CACATGTTAA
13704 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
13724 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
13742 TCAATGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:14724 original size:23 final size:23
Alignment explanation
Indices: 14690--14742 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
14680 CATCTTATAT
* *
14690 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTAGGTGCAATTCTACGC
*
14713 GGCACTTAGGTGCAATTCTACGT
1 GGCACTTAGGTGCAATTCTACGC
14736 GGCACTT
1 GGCACTT
14743 CAGTGTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
GGCACTTAGGTGCAATTCTACGC
Found at i:15706 original size:20 final size:22
Alignment explanation
Indices: 15661--15718 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
15651 TTTTAAGGGG
15661 TGCATCGATGCACATGCTAAAGAA
1 TGCATCGATGCAC-TGCT-AAGAA
15685 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGCTAAGAA
15705 TGCATCGATGCACT
1 TGCATCGATGCACT
15719 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (22 bp):
TGCATCGATGCACTGCTAAGAA
Found at i:16727 original size:23 final size:23
Alignment explanation
Indices: 16686--16737 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
16676 CATCTTATAT
* *
16686 GGCACTTCGGTCCATTTCTACGC
1 GGCACTTAGGTCCAATTCTACGC
* *
16709 GGCACTTAGGTGCAATTCTACGT
1 GGCACTTAGGTCCAATTCTACGC
16732 GGCACT
1 GGCACT
16738 CGGTGCATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.29, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTAGGTCCAATTCTACGC
Found at i:18074 original size:7 final size:7
Alignment explanation
Indices: 18062--18113 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
18052 AAATCAATAA
18062 TTAGGGT
1 TTAGGGT
18069 TTAGGGT
1 TTAGGGT
*
18076 TTAGGAT
1 TTAGGGT
18083 TATA--GT
1 T-TAGGGT
18089 TTAAGGGT
1 TT-AGGGT
18097 TTAGGGT
1 TTAGGGT
*
18104 TTAAGGT
1 TTAGGGT
18111 TTA
1 TTA
18114 AGATTTTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 1 0.03
6 3 0.08
7 28 0.74
8 6 0.16
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:18608 original size:7 final size:7
Alignment explanation
Indices: 18596--18629 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
18586 GAATGGTTAG
18596 GGTTTAA
1 GGTTTAA
18603 GGTTTAA
1 GGTTTAA
* *
18610 GATTTAT
1 GGTTTAA
18617 GGTTTAA
1 GGTTTAA
18624 GGTTTA
1 GGTTTA
18630 GGATTTTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (7 bp):
GGTTTAA
Found at i:18622 original size:21 final size:21
Alignment explanation
Indices: 18596--18635 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
18586 GAATGGTTAG
18596 GGTTTAAGGTTTAAGATTTAT
1 GGTTTAAGGTTTAAGATTTAT
*
18617 GGTTTAAGGTTTAGGATTT
1 GGTTTAAGGTTTAAGATTT
18636 TCATCAATAA
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:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (21 bp):
GGTTTAAGGTTTAAGATTTAT
Found at i:18678 original size:14 final size:14
Alignment explanation
Indices: 18655--18684 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18645 ACCAAAATAT
*
18655 TTTAGGATTTAGGG
1 TTTAGAATTTAGGG
18669 TTTAGAATTTAGGG
1 TTTAGAATTTAGGG
18683 TT
1 TT
18685 CATAAAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (14 bp):
TTTAGAATTTAGGG
Found at i:23701 original size:33 final size:33
Alignment explanation
Indices: 23663--23733 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
23653 TATATTAAAT
*
23663 TAAATTAAAATATAACTGAGTTAATCAAATTTA
1 TAAATTAAAATATAACTGAGTTAATAAAATTTA
*
23696 TAAATTAAAATATAACTGAGTTATTAAAATTTA
1 TAAATTAAAATATAACTGAGTTAATAAAATTTA
23729 TAAAT
1 TAAAT
23734 AATAGAGATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (33 bp):
TAAATTAAAATATAACTGAGTTAATAAAATTTA
Found at i:23968 original size:8 final size:7
Alignment explanation
Indices: 23943--23972 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
23933 ATAGTTGATA
23943 TAAAATT
1 TAAAATT
23950 TAAAATT
1 TAAAATT
23957 TAAAAGTT
1 TAAAA-TT
23965 TAAAATT
1 TAAAATT
23972 T
1 T
23973 TCCATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (7 bp):
TAAAATT
Found at i:23968 original size:15 final size:14
Alignment explanation
Indices: 23943--23972 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
23933 ATAGTTGATA
23943 TAAAATTTAAAATT
1 TAAAATTTAAAATT
23957 TAAAAGTTTAAAATT
1 TAAAA-TTTAAAATT
23972 T
1 T
23973 TCCATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
TAAAATTTAAAATT
Found at i:34776 original size:23 final size:23
Alignment explanation
Indices: 34750--34794 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
34740 CACCACAGCT
*
34750 CGTATAAATGCACC-TAAGTGCCC
1 CGTAGAAATGCACCGT-AGTGCCC
*
34773 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGTAGTGCC
34795 ATATAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGTAGTGCCC
Found at i:35043 original size:149 final size:149
Alignment explanation
Indices: 34773--35076 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
34763 CTAAGTGCCC
*
34773 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
34838 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATA
34903 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
34922 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
34987 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATA
35052 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
35071 CGTAGA
1 CGTAGA
35077 CCCTCTACTC
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATA
CATATGTCCTAAAGAACCG
Found at i:35668 original size:66 final size:66
Alignment explanation
Indices: 35551--35701 Score: 232
Period size: 67 Copynumber: 2.3 Consensus size: 66
35541 TTTTTTTCAT
* *
35551 GGGGGAATCGGTTCCCCCCCCTGGGGTATCGATTCCCCACTAGCATTCTGGAA-TTCATATTCGT
1 GGGGGTATCGGTT--CCCCCCTGGGGTATCGATTCCCCACTAGCATACTGGAAGTTCATATTCGT
35615 TGA
64 TGA
* *
35618 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATACTGGAAGTTCATATTCGTT
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCCACTAGCATACTGGAAGTTCATATTCGTT
35683 GA
65 GA
35685 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
35702 TTGAATGGGT
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
65 7 0.09
66 28 0.36
67 43 0.55
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.29
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCACTAGCATACTGGAAGTTCATATTCGTTG
A
Found at i:41769 original size:23 final size:23
Alignment explanation
Indices: 41743--41787 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41733 CACCACAGCT
*
41743 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
41766 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
41788 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:41959 original size:147 final size:148
Alignment explanation
Indices: 41766--42067 Score: 570
Period size: 147 Copynumber: 2.0 Consensus size: 148
41756 CGAAGTGCCC
*
41766 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCA-ATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
41831 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATA
65 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATA
41896 CATATGTCCTAAAGAACCG
130 CATATGTCCTAAAGAACCG
41915 CGTAGAATTGCACCGTAGTGCC-ATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
1 CGTAGAATTGCACCGTAGTGCCAATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
41979 ATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATAC
66 ATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATAC
42044 ATATGTCCTAAAGAACCG
131 ATATGTCCTAAAGAACCG
42062 CGTAGA
1 CGTAGA
42068 CCCTCTACTC
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
147 129 0.85
149 22 0.15
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (148 bp):
CGTAGAATTGCACCGTAGTGCCAATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
ATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATAC
ATATGTCCTAAAGAACCG
Found at i:42662 original size:66 final size:66
Alignment explanation
Indices: 42545--42695 Score: 232
Period size: 67 Copynumber: 2.3 Consensus size: 66
42535 TTTTTTTCAT
* *
42545 GGGGGAATCGGTTCCCCCCCCTGGGGTATCGATTCCCCACTAGCATTCTGGAA-TTCATATTCGT
1 GGGGGTATCGGTT--CCCCCCTGGGGTATCGATTCCCCACTAGCATACTGGAAGTTCATATTCGT
42609 TGA
64 TGA
* *
42612 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATACTGGAAGTTCATATTCGTT
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCCACTAGCATACTGGAAGTTCATATTCGTT
42677 GA
65 GA
42679 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
42696 TTGAATGGGT
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
65 7 0.09
66 28 0.36
67 43 0.55
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.29
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCACTAGCATACTGGAAGTTCATATTCGTTG
A
Found at i:51518 original size:17 final size:17
Alignment explanation
Indices: 51496--51533 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
51486 CAATCACACT
51496 AGTGAATGAATGTGGAA
1 AGTGAATGAATGTGGAA
51513 AGTGAATGAATGTGGAA
1 AGTGAATGAATGTGGAA
51530 AGTG
1 AGTG
51534 TATCACACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.37, T:0.24
Consensus pattern (17 bp):
AGTGAATGAATGTGGAA
Found at i:59071 original size:18 final size:18
Alignment explanation
Indices: 59048--59083 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
59038 GCAATAAGTC
*
59048 TAATATCAGTAGTAAAAA
1 TAATATAAGTAGTAAAAA
*
59066 TAATATAAGTCGTAAAAA
1 TAATATAAGTAGTAAAAA
59084 CAAGTATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (18 bp):
TAATATAAGTAGTAAAAA
Found at i:62842 original size:37 final size:36
Alignment explanation
Indices: 62767--62842 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
62757 TTTTTATATT
*
62767 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
62803 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
62840 TTT
1 TTT
62843 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Done.