Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008957.1 Kokia drynarioides strain JFW-HI SEQ_123653, 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: 121438
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 63 characters in sequence are not A, C, G, or T
Found at i:6793 original size:2 final size:2
Alignment explanation
Indices: 6786--6811 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6776 AATTTCAAAC
6786 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
6812 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7683 original size:27 final size:27
Alignment explanation
Indices: 7639--7714 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
7629 TATTAAGACA
* * *
7639 CGCCACAAAGGCTATTCTTTCAGAGTT
1 CGCCACAAAGGTTATTCTTTCAAAGTC
*
7666 CGCCACAAAGGTTTTTCTTTCAAAGTC
1 CGCCACAAAGGTTATTCTTTCAAAGTC
*
7693 CGTCACAAAGGTTATTCTTTCA
1 CGCCACAAAGGTTATTCTTTCA
7715 TGATGTGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (27 bp):
CGCCACAAAGGTTATTCTTTCAAAGTC
Found at i:14284 original size:6 final size:6
Alignment explanation
Indices: 14240--14268 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
14230 TTCAACAGCT
14240 CTTCCC CTTCCC CTTCCC CTTCCC CTTCC
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCC
14269 ACCTACCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CTTCCC
Found at i:28390 original size:29 final size:28
Alignment explanation
Indices: 28358--28442 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 28
28348 AAATTAGCCT
28358 TATAAAAATATATAAAATATTATCAAAAA
1 TATAAAAATATATAAAATATTAT-AAAAA
*
28387 TATAAAAGT-TATAGGAAAT-TTATAAAAA
1 TATAAAAATATATA--AAATATTATAAAAA
* *
28415 TCTAAAATATATTTAAAA-ATTATAAAAA
1 TATAAAA-ATATATAAAATATTATAAAAA
28443 AAACCATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
28 27 0.57
29 13 0.28
30 7 0.15
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (28 bp):
TATAAAAATATATAAAATATTATAAAAA
Found at i:31116 original size:31 final size:31
Alignment explanation
Indices: 31050--31130 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
31040 TTTTTGGATC
*
31050 ATTTAAGTTACTGAACTATTCAAAAAATTTG
1 ATTTAAGTCACTGAACTATTCAAAAAATTTG
* * ** *
31081 ATTTAAGTCATTGAACTATTTAAAAGTTTTT
1 ATTTAAGTCACTGAACTATTCAAAAAATTTG
31112 ATTT-AGTCACT-AGACTATT
1 ATTTAAGTCACTGA-ACTATT
31131 AAGTTTTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 1 0.02
30 12 0.29
31 29 0.69
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (31 bp):
ATTTAAGTCACTGAACTATTCAAAAAATTTG
Found at i:34732 original size:16 final size:17
Alignment explanation
Indices: 34706--34737 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
34696 AGATCAGTAA
34706 TTAATTATTTTTTAAAT
1 TTAATTATTTTTTAAAT
34723 TTAATT-TTTTTTAAA
1 TTAATTATTTTTTAAA
34738 AATTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTATTTTTTAAAT
Found at i:34743 original size:17 final size:17
Alignment explanation
Indices: 34704--34743 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
34694 CTAGATCAGT
34704 AATTAATTATTTTTTAA
1 AATTAATTATTTTTTAA
*
34721 ATTTAATT-TTTTTTAAA
1 AATTAATTATTTTTT-AA
34738 AATTAA
1 AATTAA
34744 AATTTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTAATTATTTTTTAA
Found at i:34781 original size:26 final size:25
Alignment explanation
Indices: 34733--34785 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
34723 TTAATTTTTT
* *
34733 TTAAAAATTAAAATTTATTAAAACTA
1 TTAAAAATAAAAATTTA-TAAAAATA
34759 TTAAAAATAAAAA-TTATAAAAAATA
1 TTAAAAATAAAAATTTAT-AAAAATA
34784 TT
1 TT
34786 TTTTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.04
25 11 0.46
26 12 0.50
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
TTAAAAATAAAAATTTATAAAAATA
Found at i:48750 original size:19 final size:19
Alignment explanation
Indices: 48726--48768 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
48716 AAACATAAAT
48726 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
48745 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
48764 TAAAT
1 TAAAT
48769 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:49147 original size:15 final size:16
Alignment explanation
Indices: 49117--49149 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
49107 CAAAGAGCAG
49117 AAAAATTTTGTGTGAA
1 AAAAATTTTGTGTGAA
49133 AAAAATTTTGT-TGAA
1 AAAAATTTTGTGTGAA
49148 AA
1 AA
49150 TACAACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (16 bp):
AAAAATTTTGTGTGAA
Found at i:50869 original size:31 final size:30
Alignment explanation
Indices: 50800--50869 Score: 72
Period size: 31 Copynumber: 2.2 Consensus size: 30
50790 AATAAAGTAT
*
50800 TATTTTGTTGATATTATGTAAAATATCATAA
1 TATTTTGGTGATATTA-GTAAAATATCATAA
50831 TACTTTTGGT-ATATTA-TAAAATATTCATATTA
1 TA-TTTTGGTGATATTAGTAAAATA-TCATA--A
50863 TATTTTG
1 TATTTTG
50870 TAATAGAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
29 7 0.21
30 5 0.15
31 13 0.38
32 9 0.26
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (30 bp):
TATTTTGGTGATATTAGTAAAATATCATAA
Found at i:51655 original size:30 final size:29
Alignment explanation
Indices: 51619--51685 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
51609 GTATGCTACT
* *
51619 TTTTTTATATGTAAAATTAATATATGATTC
1 TTTTTTATATGTAAAACTAATATATG-TTA
** *
51649 TTTTTTACGTGTAAAACTAATGTATGTTA
1 TTTTTTATATGTAAAACTAATATATGTTA
51678 TTTTTTAT
1 TTTTTTAT
51686 GTTTGGTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.55
Consensus pattern (29 bp):
TTTTTTATATGTAAAACTAATATATGTTA
Found at i:53099 original size:23 final size:23
Alignment explanation
Indices: 53056--53100 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
53046 TTTAATAAAA
*
53056 TTTATATATAATATTTTTTGCAC
1 TTTATATATAATATTTCTTGCAC
*
53079 TTTATCTATAATCA-TTCTTGCA
1 TTTATATATAAT-ATTTCTTGCA
53101 TAAATTTTAA
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:0.29, C:0.13, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTATATATAATATTTCTTGCAC
Found at i:58076 original size:14 final size:14
Alignment explanation
Indices: 58057--58117 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
58047 ATCCTATCAT
*
58057 TCCTTTTTCTTTTC
1 TCCTTTTCCTTTTC
58071 TCCTTTTCCTTTTC
1 TCCTTTTCCTTTTC
* *
58085 -CCTTTCCCCTTTC
1 TCCTTTTCCTTTTC
* * *
58098 CCCTTTCCCCTTTC
1 TCCTTTTCCTTTTC
*
58112 CCCTTT
1 TCCTTT
58118 CCTGAGTCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
13 11 0.26
14 32 0.74
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (14 bp):
TCCTTTTCCTTTTC
Found at i:58094 original size:7 final size:7
Alignment explanation
Indices: 58078--58119 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
58068 TTCTCCTTTT
*
58078 CCTTTTC
1 CCTTTCC
58085 CCTTTCC
1 CCTTTCC
58092 CCTTTCC
1 CCTTTCC
58099 CCTTTCC
1 CCTTTCC
58106 CCTTTCC
1 CCTTTCC
58113 CCTTTCC
1 CCTTTCC
58120 TGAGTCTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (7 bp):
CCTTTCC
Found at i:59599 original size:15 final size:16
Alignment explanation
Indices: 59570--59610 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
59560 CAAAATGAAC
*
59570 ATTATTTTTTAAATTA
1 ATTAATTTTTAAATTA
59586 ATTAATTTTT-AATTA
1 ATTAATTTTTAAATTA
*
59601 AATAATTTTT
1 ATTAATTTTT
59611 TCAACACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTAATTTTTAAATTA
Found at i:59611 original size:16 final size:17
Alignment explanation
Indices: 59573--59611 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
59563 AATGAACATT
*
59573 ATTTTTTAAATTAATTA
1 ATTTTTTAAATTAAATA
59590 A-TTTTT-AATTAAATA
1 ATTTTTTAAATTAAATA
59605 ATTTTTT
1 ATTTTTT
59612 CAACACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 9 0.45
16 10 0.50
17 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTTTAAATTAAATA
Found at i:66032 original size:14 final size:14
Alignment explanation
Indices: 66013--66040 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
66003 ACTTTGAGCA
66013 CTCACAGCTGTTCC
1 CTCACAGCTGTTCC
66027 CTCACAGCTGTTCC
1 CTCACAGCTGTTCC
66041 TTGAACCACT
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:0.14, C:0.43, G:0.14, T:0.29
Consensus pattern (14 bp):
CTCACAGCTGTTCC
Found at i:75642 original size:53 final size:53
Alignment explanation
Indices: 75552--75652 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
75542 TACCAATTGA
75552 TACCAAAAAAATAATTTTAAAATATATTTTAAATTTAACTTTATTATTTATTTG
1 TACCAAAAAAATAATTTTAAAATATATTTTAAATTTAA-TTTATTATTTATTTG
* * *
75606 TACC-AAAAAATATTTTTTAAAA-ATATTTTAACTTTAATTTTTTATTT
1 TACCAAAAAAATA-ATTTTAAAATATATTTTAAATTTAATTTATTATTT
75653 TTACTAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
52 9 0.21
53 22 0.51
54 12 0.28
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (53 bp):
TACCAAAAAAATAATTTTAAAATATATTTTAAATTTAATTTATTATTTATTTG
Found at i:76295 original size:18 final size:18
Alignment explanation
Indices: 76258--76313 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
76248 TAAAATACAC
*
76258 TTTATTT-AATAATA-TT
1 TTTATTTCAAAAATATTT
76274 TTTATTTCAAAAATATTT
1 TTTATTTCAAAAATATTT
*
76292 TTTATCTCAAAAATATTT
1 TTTATTTCAAAAATATTT
76310 TTTA
1 TTTA
76314 AAAATAATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.19
17 6 0.17
18 23 0.64
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTATTTCAAAAATATTT
Found at i:78075 original size:58 final size:58
Alignment explanation
Indices: 77982--78193 Score: 243
Period size: 58 Copynumber: 3.6 Consensus size: 58
77972 AAAAATTTTT
* * * * **
77982 AAAAATG-CAATTTTTTTTCGAGAAAAGGAGGTGTCGGCCATGCAATGGCTTACACCC
1 AAAAATGTAAATTTTTTTTCGAGAAAAGGGGGTGTCGACCATGCAATGACCAACACCC
* *
78039 AAAAATGTAAATTTTTTTTCGAGAAAAGGGGATGTCGACCAGTTG--ATGACCAACACCA
1 AAAAATGTAAATTTTTTTTCGAGAAAAGGGGGTGTCGACCA--TGCAATGACCAACACCC
* *
78097 AAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGGGTGTCGATCATGCAATGACCAACACCC
1 AAAAA-TGT-AAATTTTTTT-TCGAGAAAAGGGGGTGTCGACCATGCAATGACCAACACCC
* *
78158 AAAAATGT-AATTTTTTTTCAAGCAAAGGGGGTGTCG
1 AAAAATGTAAATTTTTTTTCGAGAAAAGGGGGTGTCG
78194 GTCATTTGAT
Statistics
Matches: 132, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
57 24 0.18
58 52 0.39
59 4 0.03
60 14 0.11
61 38 0.29
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (58 bp):
AAAAATGTAAATTTTTTTTCGAGAAAAGGGGGTGTCGACCATGCAATGACCAACACCC
Found at i:78136 original size:61 final size:58
Alignment explanation
Indices: 77990--78221 Score: 204
Period size: 58 Copynumber: 3.9 Consensus size: 58
77980 TTAAAAATGC
* ** * ** * *
77990 AATTTTTTTTCGAGAAAAGGAGGTGTCGGCCA-TGCAATGGCTTACACCCAAAAATGT-A
1 AATTTTTTTTCGAGAAAAGGGGGTGTCGATCATTG--ATGACCAACACCAAAAAATTTGA
* *
78048 AATTTTTTTTCGAGAAAAGGGGATGTCGACCAGTTGATGACCAACACCAAAAAATTTTGA
1 AATTTTTTTTCGAGAAAAGGGGGTGTCGATCA-TTGATGACCAACACCAAAAAA-TTTGA
* *
78108 AATTTTTTTCTCGAGAAAAGGGGGTGTCGATCA-TGCAATGACCAACACCCAAAAA--TGT
1 AATTTTTTT-TCGAGAAAAGGGGGTGTCGATCATTG--ATGACCAACACCAAAAAATTTGA
* * * * *
78166 AATTTTTTTTCAAGCAAAGGGGGTGTCGGTCATTTGATGGCCAACACAAAAAAATT
1 AATTTTTTTTCGAGAAAAGGGGGTGTCGATCA-TTGATGACCAACACCAAAAAATT
78222 ATATTTTTTA
Statistics
Matches: 145, Mismatches: 18, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
57 35 0.24
58 54 0.37
59 6 0.04
60 12 0.08
61 38 0.26
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (58 bp):
AATTTTTTTTCGAGAAAAGGGGGTGTCGATCATTGATGACCAACACCAAAAAATTTGA
Found at i:78218 original size:118 final size:118
Alignment explanation
Indices: 77990--78221 Score: 322
Period size: 118 Copynumber: 2.0 Consensus size: 118
77980 TTAAAAATGC
* * **
77990 AATTTTTTTTCGAGAAAAGGAGGTGTCGGCCATGCAATGGCTTACACCCAAAAATGTAAATTTTT
1 AATTTTTTTTCGAGAAAAGGAGGTGTCGACCATGCAATGACCAACACCCAAAAATGTAAATTTTT
* *
78055 TTTCGAGAAAAGGGGATGTCGACCAGTTGATGACCAACACCAAAAAATTTTGA
66 TTTCAAGAAAAGGGGATGTCGACCAGTTGATGACCAACACAAAAAAATTTTGA
* *
78108 AATTTTTTTCTCGAGAAAAGGGGGTGTCGATCATGCAATGACCAACACCCAAAAATGT-AATTTT
1 AATTTTTTT-TCGAGAAAAGGAGGTGTCGACCATGCAATGACCAACACCCAAAAATGTAAATTTT
* * ** * *
78172 TTTTCAAGCAAAGGGGGTGTCGGTCATTTGATGGCCAACACAAAAAAATT
65 TTTTCAAGAAAAGGGGATGTCGACCAGTTGATGACCAACACAAAAAAATT
78222 ATATTTTTTA
Statistics
Matches: 99, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
118 57 0.58
119 42 0.42
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (118 bp):
AATTTTTTTTCGAGAAAAGGAGGTGTCGACCATGCAATGACCAACACCCAAAAATGTAAATTTTT
TTTCAAGAAAAGGGGATGTCGACCAGTTGATGACCAACACAAAAAAATTTTGA
Found at i:78219 original size:57 final size:57
Alignment explanation
Indices: 77982--78230 Score: 207
Period size: 57 Copynumber: 4.3 Consensus size: 57
77972 AAAAATTTTT
* * * * ** **
77982 AAAAATGCAATTTTTTTTCGAGAAAAGGAGGTGTCGGCCATGCAATGGCTTACACCC
1 AAAAATGTAATTTTTTTTCGAGAAAAGGGGGTGTCGACCATGCAATGACCAACACAA
*
78039 AAAAATGTAAATTTTTTTTCGAGAAAAGGGGATGTCGACCAGTTG--ATGACCAACACCAA
1 AAAAATGT-AATTTTTTTTCGAGAAAAGGGGGTGTCGACCA--TGCAATGACCAACA-CAA
* * * **
78098 AAAATTTTGAAATTTTTTTCTCGAGAAAAGGGGGTGTCGATCATGCAATGACCAACACCC
1 AAAA--ATGTAATTTTTTT-TCGAGAAAAGGGGGTGTCGACCATGCAATGACCAACACAA
* * ** *** *
78158 AAAAATGTAATTTTTTTTCAAGCAAAGGGGGTGTCGGTCATTTGATGGCCAACACAA
1 AAAAATGTAATTTTTTTTCGAGAAAAGGGGGTGTCGACCATGCAATGACCAACACAA
78215 AAAAAT-TATATTTTTT
1 AAAAATGTA-ATTTTTT
78231 ATCTGACAAA
Statistics
Matches: 156, Mismatches: 26, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
56 2 0.01
57 51 0.33
58 47 0.30
59 7 0.04
60 16 0.10
61 33 0.21
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (57 bp):
AAAAATGTAATTTTTTTTCGAGAAAAGGGGGTGTCGACCATGCAATGACCAACACAA
Found at i:86367 original size:5 final size:5
Alignment explanation
Indices: 86359--86383 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
86349 AAAAAAAACC
86359 GAAAT GAAAT GAAAT GAAAT GAAAT
1 GAAAT GAAAT GAAAT GAAAT GAAAT
86384 TCCAACAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (5 bp):
GAAAT
Found at i:88077 original size:13 final size:13
Alignment explanation
Indices: 88061--88085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88051 TTTTTTGTTT
88061 AATTTGATACTTA
1 AATTTGATACTTA
88074 AATTTGATACTT
1 AATTTGATACTT
88086 TTTCCTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
AATTTGATACTTA
Found at i:88095 original size:31 final size:31
Alignment explanation
Indices: 88060--88119 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
88050 TTTTTTTGTT
* *
88060 TAATTTGATACTTAAATTTGATACTTTTTCC
1 TAATTTGATACTTAAACTTGACACTTTTTCC
* *
88091 TAATTTGCTTCTTAAACTTGACACTTTTT
1 TAATTTGATACTTAAACTTGACACTTTTT
88120 TAAGTTTGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.52
Consensus pattern (31 bp):
TAATTTGATACTTAAACTTGACACTTTTTCC
Found at i:89486 original size:12 final size:13
Alignment explanation
Indices: 89455--89495 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
89445 TATTTAATTT
*
89455 ATAAAATTATAAA
1 ATAAATTTATAAA
89468 A-AAATTTA-AAA
1 ATAAATTTATAAA
*
89479 ATAAATTTATTAA
1 ATAAATTTATAAA
89492 ATAA
1 ATAA
89496 TAAATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 4 0.17
12 13 0.54
13 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAAATTTATAAA
Found at i:91390 original size:29 final size:29
Alignment explanation
Indices: 91358--91453 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 29
91348 TAAAAAACGG
91358 AATTTTTGGACATCCAGGGGTAAAATGGT
1 AATTTTTGGACATCCAGGGGTAAAATGGT
* * ****
91387 AATTTTTAGGAAAATCAAGATCAAAAATGG-
1 AATTTTT-GG-ACATCCAGGGGTAAAATGGT
* *
91417 AATTTTTGGACATTCGGGGGTAAAATGGT
1 AATTTTTGGACATCCAGGGGTAAAATGGT
91446 AATTTTTG
1 AATTTTTG
91454 AAAGTTTTAG
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
28 11 0.22
29 17 0.34
30 9 0.18
31 13 0.26
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.33
Consensus pattern (29 bp):
AATTTTTGGACATCCAGGGGTAAAATGGT
Found at i:91401 original size:59 final size:59
Alignment explanation
Indices: 91290--91452 Score: 202
Period size: 59 Copynumber: 2.7 Consensus size: 59
91280 AGTTAGGGTT
* * * * *
91290 AAAAATGGAATTTTTAGACA-CGTAGGGGTGAAAACGGTAACTTTTAAAAAAATCGAGATA
1 AAAAATGGAATTTTTGGACATC-CAGGGGT-AAAATGGTAATTTTTAAAAAAATCAAGATA
* ** *
91350 AAAAACGGAATTTTTGGACATCCAGGGGTAAAATGGTAATTTTTAGGAAAATCAAGATC
1 AAAAATGGAATTTTTGGACATCCAGGGGTAAAATGGTAATTTTTAAAAAAATCAAGATA
* *
91409 AAAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTT
1 AAAAATGGAATTTTTGGACATCCAGGGGTAAAATGGTAATTTTT
91453 GAAAGTTTTA
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
59 65 0.72
60 24 0.27
61 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGACATCCAGGGGTAAAATGGTAATTTTTAAAAAAATCAAGATA
Found at i:91466 original size:29 final size:29
Alignment explanation
Indices: 91434--91720 Score: 185
Period size: 30 Copynumber: 9.7 Consensus size: 29
91424 GGACATTCGG
91434 GGGT-AAAATGGTAATTTTTGAAAGTTTTA
1 GGGTAAAAATGG-AATTTTTGAAAGTTTTA
* * *
91463 GGGTCAAAAATAGAATTTTTG-GAGGTTTA
1 GGGT-AAAAATGGAATTTTTGAAAGTTTTA
*
91492 GGGGTAAAAATGGAATTTTTGGAAGTTTTA
1 -GGGTAAAAATGGAATTTTTGAAAGTTTTA
*
91522 GGGTTAAAAATGGAATTTTTGGAAG-TTTA
1 GGG-TAAAAATGGAATTTTTGAAAGTTTTA
* * *
91551 GGGGTAAAAATGTAAATTTT-AGAAGTTTCA
1 -GGGTAAAAATGGAATTTTTGA-AAGTTTTA
* ***
91581 AGGTAAAAAATGGAATTTTTGAAAGTTCGGG
1 GGGT-AAAAATGGAATTTTTGAAAGTT-TTA
** *
91612 GGGTAAAAATATAATTTTTGAAAG-TTTC
1 GGGTAAAAATGGAATTTTTGAAAGTTTTA
* *
91640 GAGATCAAAAATGAAATTTTT-AGAAG-TTTA
1 G-GGT-AAAAATGGAATTTTTGA-AAGTTTTA
** *
91670 GGGGTAAAAATATAATTTTT-AGAAGTTTCAA
1 -GGGTAAAAATGGAATTTTTGA-AAGTTT-TA
* * *
91701 GGTTAAAATTTGAATTTTTG
1 GGGTAAAAATGGAATTTTTG
91721 GATAGTTTAG
Statistics
Matches: 206, Mismatches: 34, Indels: 34
0.75 0.12 0.12
Matches are distributed among these distances:
28 1 0.00
29 74 0.36
30 119 0.58
31 12 0.06
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGAAAGTTTTA
Found at i:91470 original size:59 final size:60
Alignment explanation
Indices: 91350--91722 Score: 279
Period size: 59 Copynumber: 6.3 Consensus size: 60
91340 AATCGAGATA
* * * * * *
91350 AAAAACGGAATTTTTGGACATCCAGGGGT-AAAATGGTAATTTTTAGGAAA--ATCAAGATC
1 AAAAATGGAATTTTTGGACATTCAGGGGTAAAAATGGTAATTTTT--GAAAGTTTTAGGGTC
*
91409 AAAAATGGAATTTTTGGACATTCGGGGGT-AAAATGGTAATTTTTGAAAGTTTTAGGGTC
1 AAAAATGGAATTTTTGGACATTCAGGGGTAAAAATGGTAATTTTTGAAAGTTTTAGGGTC
* ** * * *
91468 AAAAATAGAATTTTTGGAGGTTTAGGGGTAAAAATGG-AATTTTTGGAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGGACATTCAGGGGTAAAAATGGTAATTTTTGAAAGTTTTAGGGTC
* * * * *
91527 AAAAATGGAATTTTTGGA-AGTTTAGGGGTAAAAAT-GTAAATTTT-AGAAGTTTCAAGGTA
1 AAAAATGGAATTTTTGGACA-TTCAGGGGTAAAAATGGTAATTTTTGA-AAGTTTTAGGGTC
* * * * *
91586 AAAAATGGAATTTTT-GAAAGTTCGGGGGGTAAAAAT-ATAATTTTTGAAAG-TTTCGAGATC
1 AAAAATGGAATTTTTGGACA-TTC-AGGGGTAAAAATGGTAATTTTTGAAAGTTTTAG-GGTC
* * * * * * *
91646 AAAAATGAAATTTTTAGA-AGTTTAGGGGTAAAAAT-ATAATTTTT-AGAAGTTTCAAGGTT
1 AAAAATGGAATTTTTGGACA-TTCAGGGGTAAAAATGGTAATTTTTGA-AAGTTTTAGGGTC
* *
91705 AAAATTTGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
91723 TAGTTTAGGG
Statistics
Matches: 259, Mismatches: 42, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
57 4 0.02
58 4 0.02
59 198 0.76
60 50 0.19
61 3 0.01
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.35
Consensus pattern (60 bp):
AAAAATGGAATTTTTGGACATTCAGGGGTAAAAATGGTAATTTTTGAAAGTTTTAGGGTC
Found at i:107118 original size:29 final size:30
Alignment explanation
Indices: 107059--107124 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
107049 ATAGTTAGAC
*
107059 CTAAATTTTAAAATCTAAAAAATAAAAAAA
1 CTAAATTTTAAAATATAAAAAATAAAAAAA
*
107089 CTAAATTTTATAAA-AT-AAAAATATAAAAA
1 CTAAATTTTA-AAATATAAAAAATAAAAAAA
107118 CTAAATT
1 CTAAATT
107125 CCTGAGTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 19 0.58
30 11 0.33
31 3 0.09
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (30 bp):
CTAAATTTTAAAATATAAAAAATAAAAAAA
Found at i:109246 original size:19 final size:19
Alignment explanation
Indices: 109209--109247 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
109199 GAATTTTTTT
*
109209 TAAATATTTTTAATTTTTA
1 TAAATATTTTTAATATTTA
109228 TAAATA-TTTTAATGATTTA
1 TAAATATTTTTAAT-ATTTA
109247 T
1 T
109248 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TAAATATTTTTAATATTTA
Found at i:117839 original size:26 final size:26
Alignment explanation
Indices: 117801--117863 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
117791 AAGCAAACCA
* *
117801 AAACAAAACTGTAAAATCATGTGAAT
1 AAACAAAAGTGTAAAATCAGGTGAAT
117827 AAACAAAAGTGTAAAATCAGGTGAAT
1 AAACAAAAGTGTAAAATCAGGTGAAT
117853 AAACAAAAGTG
1 AAACAAAAGTG
117864 CTCACCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.56, C:0.10, G:0.16, T:0.19
Consensus pattern (26 bp):
AAACAAAAGTGTAAAATCAGGTGAAT
Found at i:120123 original size:2 final size:2
Alignment explanation
Indices: 120118--120153 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
120108 GAAAAAAATA
120118 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
120154 GTCAATCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:121072 original size:42 final size:43
Alignment explanation
Indices: 121024--121110 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
121014 TTATCAAGAG
**
121024 ATAAAAG-AAAAGGATTGTTCATATTTGAACCGGAAATATGAT
1 ATAAAAGAAAAAAAATTGTTCATATTTGAACCGGAAATATGAT
121066 ATAAAAGAAAAAAAATTGTTCATATTTGAACCGGAAATATGAT
1 ATAAAAGAAAAAAAATTGTTCATATTTGAACCGGAAATATGAT
121109 AT
1 AT
121111 CAACATAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
42 7 0.17
43 35 0.83
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (43 bp):
ATAAAAGAAAAAAAATTGTTCATATTTGAACCGGAAATATGAT
Done.