Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003235.1 Hibiscus syriacus cultivar Beakdansim tig00006807_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: 105403
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:109 original size:14 final size:14
Alignment explanation
Indices: 92--149 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
82 TTTCATTTCG
92 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
106 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
122 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
138 CGTTGCGATTTT
1 CGTTGCGATTTT
150 CATTTCGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:120 original size:32 final size:33
Alignment explanation
Indices: 77--165 Score: 162
Period size: 32 Copynumber: 2.7 Consensus size: 33
67 CATCCATTTC
77 GCGATTTTCATTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTTTGTCGTT
110 GCGA-TTTCATTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTTTGTCGTT
*
142 GCGATTTTCATTTCGCTTTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
166 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
32 32 0.59
33 22 0.41
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTTTGTCGTT
Found at i:184 original size:20 final size:19
Alignment explanation
Indices: 150--204 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
140 TTGCGATTTT
*
150 CATTTCGCTTTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
169 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
189 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
205 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:714 original size:18 final size:17
Alignment explanation
Indices: 671--714 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
661 GTCGATCAGA
*
671 TGATGGCTCTAGGTGAG
1 TGATGGCTCTAGGCGAG
* *
688 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGA-G
706 TGATGGCTC
1 TGATGGCTC
715 CCGAAGTGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.16, C:0.16, G:0.41, T:0.27
Consensus pattern (17 bp):
TGATGGCTCTAGGCGAG
Found at i:2314 original size:22 final size:22
Alignment explanation
Indices: 2289--2332 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2279 GATTTAGATA
2289 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2311 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2333 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2606 original size:20 final size:20
Alignment explanation
Indices: 2500--2614 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
2490 CGCTTTGAAA
*
2500 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
2521 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
2541 ATCACGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
2561 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
2582 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2602 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2615 TTCCCAATTC
Statistics
Matches: 75, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.65
21 24 0.32
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2626 original size:20 final size:20
Alignment explanation
Indices: 2603--2694 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
2593 ATAGTCAGTA
*
2603 TCGCATTGCGATTTCCCAAT
1 TCGCATTGCGATTTACCAAT
* **
2623 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
2643 TCGCATTGCGAATTTTCCAAT
1 TCGCATTGCG-ATTTACCAAT
* **
2664 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
2684 TCACATTGCGA
1 TCGCATTGCGA
2695 ATTGGGAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 41 0.72
21 16 0.28
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:2674 original size:41 final size:41
Alignment explanation
Indices: 2603--2697 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
2593 ATAGTCAGTA
2603 TCGCATTGCG-ATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
*
2643 TCGCATTGCGAATTTTCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
*
2684 TCACATTGCGAATT
1 TCGCATTGCGAATT
2698 GGGAAAATCG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
40 10 0.19
41 42 0.81
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:8731 original size:13 final size:13
Alignment explanation
Indices: 8713--8761 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
8703 TTATTACTAA
*
8713 AATAATTTTATTT
1 AATAATTTTATAT
*
8726 AATAATTTTATAA
1 AATAATTTTATAT
*
8739 AATAATATTATAT
1 AATAATTTTATAT
8752 AAT-ATTTTAT
1 AATAATTTTAT
8762 TTTAGTATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
12 6 0.19
13 25 0.81
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATAATTTTATAT
Found at i:8739 original size:26 final size:25
Alignment explanation
Indices: 8710--8761 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
8700 AAGTTATTAC
* *
8710 TAAAATAATTTTATTTAATAATTTTA
1 TAAAATAATATTATATAAT-ATTTTA
8736 TAAAATAATATTATATAATATTTTA
1 TAAAATAATATTATATAATATTTTA
8761 T
1 T
8762 TTTAGTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TAAAATAATATTATATAATATTTTA
Found at i:8789 original size:25 final size:23
Alignment explanation
Indices: 8744--8790 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
8734 TATAAAATAA
*
8744 TATTATATAATATTTTATTTTAG
1 TATTATATAAAATTTTATTTTAG
8767 TATTATAATAAAATTCTTATTTTA
1 TATTAT-ATAAAATT-TTATTTTA
8791 ATATAGACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TATTATATAAAATTTTATTTTAG
Found at i:12903 original size:2 final size:2
Alignment explanation
Indices: 12896--12926 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12886 ATCAATTTAA
12896 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
12927 ATTTTACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:15734 original size:2 final size:2
Alignment explanation
Indices: 15727--15762 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
15717 AGTCACCGAG
*
15727 TC TC TC TC TC TC TC TC TC TC TC TC AC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
15763 ACGAGAACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:34592 original size:31 final size:30
Alignment explanation
Indices: 34529--34593 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
34519 GATTTAATCG
** *
34529 TTTAATATTTTTTCTTTATAATTTTAGGTA
1 TTTAATATTTTTTAGTTATAATTTTAAGTA
*
34559 TTTAATATTCTTTTAGTTATAATTTTAATTA
1 TTTAATATT-TTTTAGTTATAATTTTAAGTA
34590 TTTA
1 TTTA
34594 TACTGTAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (30 bp):
TTTAATATTTTTTAGTTATAATTTTAAGTA
Found at i:43259 original size:25 final size:25
Alignment explanation
Indices: 43220--43278 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
43210 AAACAATTAT
* *
43220 AAAGGAAAAAGAAAGTAAGAG-ACAGG
1 AAAGG-AAAAGAAAGGAAG-GCAAAGG
43246 AAAGGAAAAGAAAGGAAGGCAAAGG
1 AAAGGAAAAGAAAGGAAGGCAAAGG
43271 AAAGGAAA
1 AAAGGAAA
43279 TGATATATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 1 0.03
25 24 0.80
26 5 0.17
ACGTcount: A:0.63, C:0.03, G:0.32, T:0.02
Consensus pattern (25 bp):
AAAGGAAAAGAAAGGAAGGCAAAGG
Found at i:47102 original size:15 final size:15
Alignment explanation
Indices: 47078--47107 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47068 CTATACAAAT
*
47078 TATATTAAAATATGA
1 TATATGAAAATATGA
47093 TATATGAAAATATGA
1 TATATGAAAATATGA
47108 GTAAGTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (15 bp):
TATATGAAAATATGA
Found at i:47825 original size:103 final size:103
Alignment explanation
Indices: 47600--47817 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
47590 GTCGAGGGTC
47600 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
47665 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
47703 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
47768 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
47806 TATGTGGTCCTT
1 TATGTGGTCCTT
47818 ATGGACATTA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:47875 original size:22 final size:23
Alignment explanation
Indices: 47834--47892 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
47824 ATTATTATAT
47834 GGCACTACGGTGCAACTCTACGC
1 GGCACTACGGTGCAACTCTACGC
* * *
47857 GGCACTAC-GTGCAATTCTATGT
1 GGCACTACGGTGCAACTCTACGC
*
47879 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
47893 TTTATGAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAACTCTACGC
Found at i:52703 original size:103 final size:103
Alignment explanation
Indices: 52478--52695 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
52468 GTCGAGGGTC
52478 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
52543 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
52581 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
52646 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
52684 TATGTGGTCCTT
1 TATGTGGTCCTT
52696 ATGGACATTA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:52768 original size:23 final size:23
Alignment explanation
Indices: 52707--52779 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
52697 TGGACATTAT
*
52707 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
*** *
52730 TACGCGGTACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
52753 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
52774 TATATG
1 TATATG
52780 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 6 0.15
22 3 0.08
23 31 0.77
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:55554 original size:35 final size:35
Alignment explanation
Indices: 55506--55583 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
55496 CAACACAATC
*
55506 TTCAATTTCATTTTAAAACTCAAATTCCAAAATAA
1 TTCAATTTCATTTTAAAACCCAAATTCCAAAATAA
* * *
55541 TTCAATTAT-ATTTTAAACCCCAAATTCTAAAATAC
1 TTCAATT-TCATTTTAAAACCCAAATTCCAAAATAA
55576 TTCAATTT
1 TTCAATTT
55584 AGGGTTTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 1 0.03
35 36 0.95
36 1 0.03
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (35 bp):
TTCAATTTCATTTTAAAACCCAAATTCCAAAATAA
Found at i:55625 original size:35 final size:35
Alignment explanation
Indices: 55579--55653 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
55569 AAAATACTTC
*
55579 AATTTAGGGTTTTGAATATAATTGAAGTATTTTGG
1 AATTTAGGGTTTAGAATATAATTGAAGTATTTTGG
* * *
55614 AATTTGGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAGAATATAATTGAAGTATTTTGG
55649 AATTT
1 AATTT
55654 TGAACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.45
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATATAATTGAAGTATTTTGG
Found at i:55917 original size:20 final size:20
Alignment explanation
Indices: 55892--55929 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55882 TTTGGTTCAC
55892 GGAATGGAAGATTACCAGTG
1 GGAATGGAAGATTACCAGTG
*
55912 GGAATGTAAGATTACCAG
1 GGAATGGAAGATTACCAG
55930 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.32, T:0.21
Consensus pattern (20 bp):
GGAATGGAAGATTACCAGTG
Found at i:56734 original size:19 final size:20
Alignment explanation
Indices: 56702--56739 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
56692 TCCTCTCATC
56702 TCTTCTTCCTTCTT-TCTTA
1 TCTTCTTCCTTCTTCTCTTA
56721 TCTTCTTCAC-TCTTCTCTT
1 TCTTCTTC-CTTCTTCTCTT
56740 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCCTTCTTCTCTTA
Found at i:57242 original size:21 final size:21
Alignment explanation
Indices: 57200--57242 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
57190 TTTCTGGGCT
* *
57200 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
57221 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
57242 A
1 A
57243 CGTATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:57294 original size:20 final size:20
Alignment explanation
Indices: 57269--57306 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57259 GAATGCTAGA
*
57269 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
57289 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
57307 TATAAAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:57631 original size:14 final size:15
Alignment explanation
Indices: 57596--57635 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
57586 ATTATGAGAC
57596 ATGACATGAATTCAT
1 ATGACATGAATTCAT
* *
57611 ATAACATGCATT-AT
1 ATGACATGAATTCAT
57625 ATGACATGAAT
1 ATGACATGAAT
57636 ATGCAGGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (15 bp):
ATGACATGAATTCAT
Found at i:57972 original size:23 final size:23
Alignment explanation
Indices: 57928--57972 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
57918 ATTATTATAT
*
57928 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
57951 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
57973 AGCTGTGGTG
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:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:63551 original size:19 final size:20
Alignment explanation
Indices: 63512--63556 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
63502 TCCAGATTCC
*
63512 TCTCATATCTTCTTCCTTCT
1 TCTCTTATCTTCTTCCTTCT
63532 T-TCTTATCTTCTTCAC-TCT
1 TCTCTTATCTTCTTC-CTTCT
63551 TCTCTT
1 TCTCTT
63557 CTTCCAAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (20 bp):
TCTCTTATCTTCTTCCTTCT
Found at i:64049 original size:21 final size:21
Alignment explanation
Indices: 64007--64049 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
63997 TTTCTGGGCT
* *
64007 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
64028 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
64049 A
1 A
64050 CGTATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:64101 original size:20 final size:20
Alignment explanation
Indices: 64076--64113 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
64066 GAATGCTAGA
*
64076 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
64096 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
64114 TATAAAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:64440 original size:14 final size:15
Alignment explanation
Indices: 64405--64444 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
64395 ATTATGAGAC
64405 ATGACATGAATTCAT
1 ATGACATGAATTCAT
* *
64420 ATAACATGCATT-AT
1 ATGACATGAATTCAT
64434 ATGACATGAAT
1 ATGACATGAAT
64445 ATGCAGGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (15 bp):
ATGACATGAATTCAT
Found at i:67208 original size:15 final size:13
Alignment explanation
Indices: 67188--67225 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
67178 CTTTCCTAGC
67188 ATTATCATATATATT
1 ATTATCAT-TAT-TT
67203 ATTATCATTATTT
1 ATTATCATTATTT
67216 A-TATCATTAT
1 ATTATCATTAT
67226 CATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
14 3 0.13
15 8 0.35
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTATCATTATTT
Found at i:67369 original size:2 final size:2
Alignment explanation
Indices: 67362--67407 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
67352 CATATCCATC
67362 AT 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 AT
67404 AT AT
1 AT AT
67408 TGTATTTGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67535 original size:23 final size:23
Alignment explanation
Indices: 67507--67575 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
67497 CACCACAGCT
* * *
67507 CGTATAAATGCACCGAAGTGCCG
1 CGTATAATTGCACCGTAGTGCCA
67530 CGTATAATTGCACCGTAGTGCCA
1 CGTATAATTGCACCGTAGTGCCA
*
67553 CGTAGAATTGCACCGTAGTGCCA
1 CGTATAATTGCACCGTAGTGCCA
67576 TATAATAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTATAATTGCACCGTAGTGCCA
Found at i:69344 original size:29 final size:30
Alignment explanation
Indices: 69273--69332 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
69263 CAATTTAAGG
69273 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
69304 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
69333 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:69468 original size:36 final size:37
Alignment explanation
Indices: 69428--69499 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
69418 ATTGCCCAAG
* * *
69428 GGGTATAGATTCCC-CCCCAGGGGGTACAGATACCCT
1 GGGTACAGATACCCGCCCCAGGGGATACAGATACCCT
69464 GGGTACAGATACCCGCCCCAGGGGATACAGATACCC
1 GGGTACAGATACCCGCCCCAGGGGATACAGATACCC
69500 CCTGCAGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 12 0.38
37 20 0.62
ACGTcount: A:0.25, C:0.32, G:0.28, T:0.15
Consensus pattern (37 bp):
GGGTACAGATACCCGCCCCAGGGGATACAGATACCCT
Found at i:69469 original size:15 final size:15
Alignment explanation
Indices: 69449--69477 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
69439 CCCCCCCAGG
69449 GGGTACAGATACCCT
1 GGGTACAGATACCCT
69464 GGGTACAGATACCC
1 GGGTACAGATACCC
69478 GCCCCAGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (15 bp):
GGGTACAGATACCCT
Found at i:69618 original size:21 final size:21
Alignment explanation
Indices: 69592--69634 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
69582 ATTTGAATAT
*
69592 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
69613 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
69634 T
1 T
69635 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:69701 original size:20 final size:22
Alignment explanation
Indices: 69663--69702 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
69653 TTGGAGTATA
69663 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
69685 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
69703 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:72781 original size:29 final size:30
Alignment explanation
Indices: 72711--72769 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
72701 AATTTAAGAC
72711 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAA
72742 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
72770 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:72884 original size:21 final size:21
Alignment explanation
Indices: 72859--72902 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
72849 TTCAAGATTG
72859 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
*
72880 CCCAGGGGGTACATATACCCC
1 CCCAGGGGGTACAGATACCCC
72901 CC
1 CC
72903 TGCAGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.41, G:0.25, T:0.11
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:73040 original size:21 final size:21
Alignment explanation
Indices: 73014--73056 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
73004 ATTTGAATAT
*
73014 TATGAAAGGGTATCGATTCCC
1 TATGAAAGGGTACCGATTCCC
*
73035 TATGAAGGGGTACCGATTCCC
1 TATGAAAGGGTACCGATTCCC
73056 T
1 T
73057 CTATTATGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
TATGAAAGGGTACCGATTCCC
Found at i:73122 original size:20 final size:22
Alignment explanation
Indices: 73084--73123 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
73074 TTTGAGTATA
73084 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
73106 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
73124 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:73404 original size:32 final size:34
Alignment explanation
Indices: 73337--73406 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
73327 TTTTGTAAAG
*
73337 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCGTGTAAAAGCTA
* *
73371 GGGAAATGTTATAGTTTAGCCCG-G-AAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCGTGTAAAAGCTA
73403 GGGA
1 GGGA
73407 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 12 0.36
33 1 0.03
34 20 0.61
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.23
Consensus pattern (34 bp):
GGGAAAGGTTATAGCTTAGCCCGTGTAAAAGCTA
Found at i:76110 original size:2 final size:2
Alignment explanation
Indices: 76103--76137 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
76093 ATAATATTAG
76103 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
76138 TTTACATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:89339 original size:13 final size:14
Alignment explanation
Indices: 89321--89355 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
89311 ATAAATATAT
89321 ATTTTATAT-TTTA
1 ATTTTATATATTTA
89334 ATTTTATATATTTA
1 ATTTTATATATTTA
*
89348 ATTATATA
1 ATTTTATA
89356 ATATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTATATATTTA
Found at i:89588 original size:30 final size:30
Alignment explanation
Indices: 89554--89623 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
89544 TCGCGTTATG
89554 CAAAACGTGATTAAAAGATATCACTTTCTA
1 CAAAACGTGATTAAAAGATATCACTTTCTA
** * ** *
89584 CAAAATATGATTAAAATATATCGTTTTCTG
1 CAAAACGTGATTAAAAGATATCACTTTCTA
89614 CAAAACGTGA
1 CAAAACGTGA
89624 GATTCAATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.31
Consensus pattern (30 bp):
CAAAACGTGATTAAAAGATATCACTTTCTA
Found at i:96384 original size:19 final size:22
Alignment explanation
Indices: 96352--96408 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 22
96342 AATATTTAAA
* *
96352 ATATATTTATATATTTTT-TTT
1 ATATATTTAAATATTTTTATTC
96373 A-ATA-TTAAATATTTTTATTC
1 ATATATTTAAATATTTTTATTC
96393 ATATATTTAAATATTT
1 ATATATTTAAATATTT
96409 CTGTTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 11 0.35
20 6 0.19
21 4 0.13
22 10 0.32
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATATTTAAATATTTTTATTC
Found at i:96430 original size:41 final size:41
Alignment explanation
Indices: 96352--96430 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 41
96342 AATATTTAAA
* * *
96352 ATATATTTATATATTTTTTTTAATATTAAATATTTTTATTC
1 ATATATTTAAATATTTTGTTTAATATAAAATATTTTTATTC
96393 ATATATTTAAATATTTCTGTTTAA-A-AAAATATATTTTA
1 ATATATTTAAATATTT-TGTTTAATATAAAATAT-TTTTA
96431 AATATTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 6 0.18
41 21 0.64
42 6 0.18
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (41 bp):
ATATATTTAAATATTTTGTTTAATATAAAATATTTTTATTC
Found at i:104078 original size:2 final size:2
Alignment explanation
Indices: 104073--104101 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
104063 TATCTCTCTC
104073 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
104102 TCACTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:105339 original size:47 final size:46
Alignment explanation
Indices: 105270--105368 Score: 130
Period size: 49 Copynumber: 2.1 Consensus size: 46
105260 TCAATACTAA
105270 AAACATAGTTTAAATTTTTCAGTTT-AAAACACCTTCAGTTG-ACAT
1 AAACATAGTTTAAATTTTTCAGTTTGAAAACACCTT-AGTTGAACAT
* *
105315 AAACATAGTACTTAATTTTTTCAGTTTGGATAACACCTTAGTTGAACAT
1 AAACATAGT--TTAAATTTTTCAGTTT-GAAAACACCTTAGTTGAACAT
105364 AAACA
1 AAACA
105369 ATTTTATGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
45 9 0.19
47 15 0.32
48 5 0.11
49 18 0.38
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (46 bp):
AAACATAGTTTAAATTTTTCAGTTTGAAAACACCTTAGTTGAACAT
Done.