Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010188.1 Corchorus capsularis cultivar CVL-1 contig10209, 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: 100097
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:524 original size:33 final size:32
Alignment explanation
Indices: 441--578 Score: 116
Period size: 33 Copynumber: 4.2 Consensus size: 32
431 AAAGGATCAT
* **
441 GTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCAA
1 GTGGCCGG-TGTGGCCGGGCATCGCC-ATGTCGC
* * *
474 GTGTCCGGGTGTAGCCGGGCATGGCCATGTCGC
1 GTGGCC-GGTGTGGCCGGGCATCGCCATGTCGC
* *
507 GTGGCCGGTGATGGCCGGGCATCTCCATGTTGC
1 GTGGCCGGTG-TGGCCGGGCATCGCCATGTCGC
* * * *
540 ATGGCCGGTGTTGCGCAGGCATCTCCATGTCGC
1 GTGGCCGGTGTGGC-CGGGCATCGCCATGTCGC
573 GTGGCC
1 GTGGCC
579 AGATCTCCAA
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
32 8 0.09
33 77 0.89
34 2 0.02
ACGTcount: A:0.10, C:0.28, G:0.41, T:0.22
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATCGCCATGTCGC
Found at i:586 original size:21 final size:21
Alignment explanation
Indices: 560--599 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
550 TTGCGCAGGC
* *
560 ATCTCCATGTCGCGTGGCCAG
1 ATCTCCAAGTCGCATGGCCAG
581 ATCTCCAAGTCGCATGGCC
1 ATCTCCAAGTCGCATGGCC
600 GGTCACTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.35, G:0.25, T:0.23
Consensus pattern (21 bp):
ATCTCCAAGTCGCATGGCCAG
Found at i:14004 original size:76 final size:76
Alignment explanation
Indices: 13876--14026 Score: 275
Period size: 76 Copynumber: 2.0 Consensus size: 76
13866 ACCAAATTAA
13876 TCTCCATATATAAAGTACTTGACTTTCCGTAGTAGTACTCTAGATGTCCATAATATTTTCCACAT
1 TCTCCATATATAAAGTACTTGACTTTCCGTAGTAGTACTCTAGATGTCCATAATATTTTCCACAT
13941 AAGAGACCTCT
66 AAGAGACCTCT
* *
13952 TCTCCATATATAAAGTACTTGACTTTCGGTAGTAGTACTCTAGATGTTCATAATATTTTCCACAT
1 TCTCCATATATAAAGTACTTGACTTTCCGTAGTAGTACTCTAGATGTCCATAATATTTTCCACAT
*
14017 AAGAGGCCTC
66 AAGAGACCTC
14027 ATATTGACGT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (76 bp):
TCTCCATATATAAAGTACTTGACTTTCCGTAGTAGTACTCTAGATGTCCATAATATTTTCCACAT
AAGAGACCTCT
Found at i:34946 original size:41 final size:41
Alignment explanation
Indices: 34899--35208 Score: 290
Period size: 41 Copynumber: 7.5 Consensus size: 41
34889 CTTGTGTTAC
* *
34899 ATGTGCTTAGGGACTTTGACATAGATGCCTCTGTGTTATAA
1 ATGTGCTTTGGGACTTTGAGATAGATGCCTCTGTGTTATAA
** * * *
34940 ATGTGCTTAAGGACTTTAGAGAGAGTTG-TTCCTGTGTTATAA
1 ATGTGCTTTGGGACTTT-GAGATAGATGCCT-CTGTGTTATAA
* * * *
34982 TTGTGTTTTGGGACTTTGATATAGATGTCTCTGTGTTATAA
1 ATGTGCTTTGGGACTTTGAGATAGATGCCTCTGTGTTATAA
* * * * *
35023 ATGTG-TTTGAGGACTTTGAGAGAGTTTCCCCTGCGTTATAA
1 ATGTGCTTTG-GGACTTTGAGATAGATGCCTCTGTGTTATAA
* * *
35064 TTGTG-TTTGGGGACTTTGATATAGATGTCTCTGTGTTATAA
1 ATGTGCTTT-GGGACTTTGAGATAGATGCCTCTGTGTTATAA
* * *
35105 ATGTGC-TTGAGGACTTTAGAGAGAGTTGCCCCTGTGTTATAA
1 ATGTGCTTTG-GGACTTT-GAGATAGATGCCTCTGTGTTATAA
* *
35147 TTGTG-TTTGGGGACTTTGATATAGATGCCTCTGTGTTATAA
1 ATGTGCTTT-GGGACTTTGAGATAGATGCCTCTGTGTTATAA
35188 ATGTG-TTTGAGGACTTTGAGA
1 ATGTGCTTTG-GGACTTTGAGA
35209 GAGAAAATTG
Statistics
Matches: 216, Mismatches: 42, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
40 6 0.03
41 144 0.67
42 65 0.30
43 1 0.00
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.40
Consensus pattern (41 bp):
ATGTGCTTTGGGACTTTGAGATAGATGCCTCTGTGTTATAA
Found at i:34998 original size:83 final size:83
Alignment explanation
Indices: 34908--35212 Score: 488
Period size: 83 Copynumber: 3.7 Consensus size: 83
34898 CATGTGCTTA
* * *
34908 GGGACTTTGACATAGATGCCTCTGTGTTATAAATGTGCTTAAGGACTTTAGAGAGAGTTGTTCCT
1 GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGTCCCT
*
34973 GTGTTATAATTGTGTTTT
66 GTGTTATAATTGTGTTTG
* *
34991 GGGACTTTGATATAGATGTCTCTGTGTTATAAATGTGTTTGAGGACTTT-GAGAGAGTT-TCCCC
1 GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGT-CCC
*
35054 TGCGTTATAATTGTGTTTG
65 TGTGTTATAATTGTGTTTG
* *
35073 GGGACTTTGATATAGATGTCTCTGTGTTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGCCCCT
1 GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGTCCCT
35138 GTGTTATAATTGTGTTTG
66 GTGTTATAATTGTGTTTG
*
35156 GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGAGAGA
1 GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTT-AGAGAGA
35213 AAATTGGCTT
Statistics
Matches: 206, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
81 1 0.00
82 76 0.37
83 122 0.59
84 7 0.03
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (83 bp):
GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGTCCCT
GTGTTATAATTGTGTTTG
Found at i:35181 original size:165 final size:165
Alignment explanation
Indices: 34908--35211 Score: 545
Period size: 165 Copynumber: 1.8 Consensus size: 165
34898 CATGTGCTTA
**
34908 GGGACTTTGACATAGATGCCTCTGTGTTATAAATGTGCTTAAGGACTTTAGAGAGAGTTGTTCCT
1 GGGACTTTGACATAGATGCCTCTGTGTTATAAATGTGCTTAAGGACTTTAGAGAGAGTTGCCCCT
* *
34973 GTGTTATAATTGTGTTTTGGGACTTTGATATAGATGTCTCTGTGTTATAAATGTGTTTGAGGACT
66 GTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACT
35038 TTGAGAGAGTTTCCCCTGCGTTATAATTGTGTTTG
131 TTGAGAGAGTTTCCCCTGCGTTATAATTGTGTTTG
* * *
35073 GGGACTTTGATATAGATGTCTCTGTGTTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGCCCCT
1 GGGACTTTGACATAGATGCCTCTGTGTTATAAATGTGCTTAAGGACTTTAGAGAGAGTTGCCCCT
35138 GTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACT
66 GTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACT
35203 TTGAGAGAG
131 TTGAGAGAG
35212 AAAATTGGCT
Statistics
Matches: 132, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
165 132 1.00
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.40
Consensus pattern (165 bp):
GGGACTTTGACATAGATGCCTCTGTGTTATAAATGTGCTTAAGGACTTTAGAGAGAGTTGCCCCT
GTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACT
TTGAGAGAGTTTCCCCTGCGTTATAATTGTGTTTG
Found at i:35322 original size:30 final size:31
Alignment explanation
Indices: 35274--35345 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
35264 ACGAAAATGT
* *
35274 AATTCAGGATACATCGTTA-CG-GATTGTGTC
1 AATTAAGGATACAACGTTATCGTG-TTGTGTC
*
35304 AATTAAGGATATAACGTTATCGTGTTGTGTC
1 AATTAAGGATACAACGTTATCGTGTTGTGTC
*
35335 AAATAAGGATA
1 AATTAAGGATA
35346 AAATCAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 16 0.44
31 19 0.53
32 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (31 bp):
AATTAAGGATACAACGTTATCGTGTTGTGTC
Found at i:37633 original size:35 final size:35
Alignment explanation
Indices: 37540--37662 Score: 131
Period size: 35 Copynumber: 3.5 Consensus size: 35
37530 TGAAATTTTC
* * * * *
37540 GTTGTTGAAG-CCCCAAATATTGAATGAAGAATGA
1 GTTGTTGGAGTCCCCAAGTATTGAATGATGAAGGG
* ** *
37574 GTTGCTGGAGTATCCAACTATTGAATGATGAAGGG
1 GTTGTTGGAGTCCCCAAGTATTGAATGATGAAGGG
* * *
37609 GTTGTTGGAGTCCCCAAGTGTTGAACGATTAAGGG
1 GTTGTTGGAGTCCCCAAGTATTGAATGATGAAGGG
37644 GTTGTTGGAGTCCCCAAGT
1 GTTGTTGGAGTCCCCAAGT
37663 GCTGAATCGG
Statistics
Matches: 73, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
34 8 0.11
35 65 0.89
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (35 bp):
GTTGTTGGAGTCCCCAAGTATTGAATGATGAAGGG
Found at i:48641 original size:26 final size:27
Alignment explanation
Indices: 48596--48657 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
48586 GATTCGTCTG
*
48596 GTCTTGCTGTTGTAGTGCAGCTGAGTT
1 GTCTTGCTGCTGTAGTGCAGCTGAGTT
*
48623 GTCTTGTTGCTGT-GTGCAGCTGAGTT
1 GTCTTGCTGCTGTAGTGCAGCTGAGTT
*
48649 TTCTTGCTG
1 GTCTTGCTG
48658 GAATATCGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.08, C:0.16, G:0.32, T:0.44
Consensus pattern (27 bp):
GTCTTGCTGCTGTAGTGCAGCTGAGTT
Found at i:51878 original size:33 final size:32
Alignment explanation
Indices: 51840--51911 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
51830 AATTGATGTA
*
51840 AAGTTAATAAAAAATTGGAAGGGTAAATTGGAG
1 AAGTTAAT-AAAAATTAGAAGGGTAAATTGGAG
* * *
51873 AAGTTAATAAAAGTTATAGGGGTAAATTGGAG
1 AAGTTAATAAAAATTAGAAGGGTAAATTGGAG
51905 AAGTTAA
1 AAGTTAA
51912 GTATGAGTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
32 27 0.77
33 8 0.23
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (32 bp):
AAGTTAATAAAAATTAGAAGGGTAAATTGGAG
Found at i:51986 original size:22 final size:21
Alignment explanation
Indices: 51946--51986 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
51936 AATTACTAAA
**
51946 TACCGCCCCCTTTTTACTAGG
1 TACCGCCCCCTTTGGACTAGG
51967 TACCGCCCCCCTTTGGACTA
1 TACCG-CCCCCTTTGGACTA
51987 TTTTGCCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.15, C:0.41, G:0.15, T:0.29
Consensus pattern (21 bp):
TACCGCCCCCTTTGGACTAGG
Found at i:68989 original size:13 final size:13
Alignment explanation
Indices: 68973--68997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68963 TCAATTAAAA
68973 ATATATAATTAAT
1 ATATATAATTAAT
68986 ATATATAATTAA
1 ATATATAATTAA
68998 CTTGTACAAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATATAATTAAT
Found at i:72000 original size:18 final size:19
Alignment explanation
Indices: 71977--72012 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
71967 TTCCACTCAT
71977 TCTCTCTCCTTT-CTCTTC
1 TCTCTCTCCTTTACTCTTC
71995 TCTCTCTCCTTTACTCTT
1 TCTCTCTCCTTTACTCTT
72013 TCTACAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.56
Consensus pattern (19 bp):
TCTCTCTCCTTTACTCTTC
Found at i:73943 original size:2 final size:2
Alignment explanation
Indices: 73936--73969 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
73926 AAAATCTGTA
*
73936 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73970 AAAGTGTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:75496 original size:27 final size:27
Alignment explanation
Indices: 75466--75539 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
75456 AGGGTCACAT
*
75466 AGGGGCATTTTGGTCATTTTCACGTTC
1 AGGGGCATTTTGGTCATTTTCACATTC
** *
75493 AGGGGCATTTTGGTCATTTTTGCATTT
1 AGGGGCATTTTGGTCATTTTCACATTC
* *
75520 AAGGGTATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
75540 AAGTTCACTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.16, C:0.12, G:0.26, T:0.46
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCACATTC
Found at i:75880 original size:14 final size:14
Alignment explanation
Indices: 75861--75888 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
75851 GCATATTAAT
75861 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
75875 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
75889 ATTACTATCA
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:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:76100 original size:19 final size:20
Alignment explanation
Indices: 76076--76113 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
76066 AAATACAAGG
76076 CATTTGA-TTACAAATTGGA
1 CATTTGATTTACAAATTGGA
*
76095 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
76114 TGCTCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:76989 original size:12 final size:12
Alignment explanation
Indices: 76974--77000 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
76964 TTGCATCATC
76974 CCATTCATCAAT
1 CCATTCATCAAT
76986 CCATTCATCAAT
1 CCATTCATCAAT
76998 CCA
1 CCA
77001 AAAAGGAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (12 bp):
CCATTCATCAAT
Found at i:79543 original size:22 final size:21
Alignment explanation
Indices: 79517--80162 Score: 266
Period size: 22 Copynumber: 29.9 Consensus size: 21
79507 AAAGGAGCCA
79517 AAAATAGTAATCAGTAAAAGGT
1 AAAATAGTAATCAGTAAAA-GT
*
79539 AAAATGGTAATCAGTAAAGAGT
1 AAAATAGTAATCAGTAAA-AGT
*
79561 AAAGT-GATAATCAGTAAAGAGT
1 AAAATAG-TAATCAGTAAA-AGT
79583 --AATAG-AAGTCAGTAAGAAG-
1 AAAATAGTAA-TCAGTAA-AAGT
* *
79602 -CAATGGTAATCAGTAAAAAGT
1 AAAATAGTAATCAGT-AAAAGT
*
79623 AAAA-AGGTAATTAGTAAAAAGT
1 AAAATA-GTAATCAGT-AAAAGT
* *
79645 AAAATAGTAATTAGAAAAGAGT
1 AAAATAGTAATCAGTAAA-AGT
* **
79667 AAAATGGTAAAGAGTAAAGAGT
1 AAAATAGTAATCAGTAAA-AGT
** **
79689 --AATCAGTAAAGACAAAAATGAT
1 AAAAT-AGTAATCAGTAAAA-G-T
* * *
79711 AAAGAAAGAGTGAT-AGTAAGAGT
1 --A-AAATAGTAATCAGTAAAAGT
*
79734 AAAA-AGGTAAAAT-GGTAAAAAGT
1 AAAATA-GT--AATCAGT-AAAAGT
* *
79757 AAAA-GGTAATCAGTAAAGGGT
1 AAAATAGTAATCAGTAAA-AGT
* *
79778 AAAATGGTAATTAGTAAAAAGT
1 AAAATAGTAATCAGT-AAAAGT
* *
79800 AAAATGGTAATCAGTAAAAATT
1 AAAATAGTAATCAGT-AAAAGT
*
79822 AAAAGAGTAATCAGTAGAAAGT
1 AAAATAGTAATCAGTA-AAAGT
79844 --AATAGTAATCAGTAAGAAG-
1 AAAATAGTAATCAGTAA-AAGT
* *
79863 -CAATAGTAGTCAGTAAAAAGT
1 AAAATAGTAATCAGT-AAAAGT
*
79884 -AAATAGTAATCAGTAAGAGT
1 AAAATAGTAATCAGTAAAAGT
* * *
79904 AAAAAAGTAATAAGTTAGAAGT
1 AAAATAGTAATCAG-TAAAAGT
* * *
79926 AAAA-GGAAATCAGTAAGAGT
1 AAAATAGTAATCAGTAAAAGT
*
79946 AAAA-AGGTGATCAGTAAAGAGT
1 AAAATA-GTAATCAGTAAA-AGT
*
79968 AAAA-AGCTAATCAGCAAGAAGT
1 AAAATAG-TAATCAGTAA-AAGT
*
79990 AAAA-AGGTAATCAGTAAAAAGC
1 AAAATA-GTAATCAGT-AAAAGT
* *
80012 AAAA-GGCAATCAGTAAAAAGT
1 AAAATAGTAATCAGT-AAAAGT
* *
80033 AAAAGAGTAATCAGTAAAAAAGGAGCAG
1 AAAATAGTAATCAGT---AAA--AG--T
*
80061 AAAATAGTAATCAGT-AGAGT
1 AAAATAGTAATCAGTAAAAGT
*
80081 AAAATGGTAATCAGTAAAAAGT
1 AAAATAGTAATCAGT-AAAAGT
* ** *
80103 AAGAA-GGTAATCAACAAGAGT
1 AA-AATAGTAATCAGTAAAAGT
80124 AAAATAGTAATCAGTACAAAGT
1 AAAATAGTAATCAGTA-AAAGT
80146 AAAGA-A-TAATCAGTAAA
1 AAA-ATAGTAATCAGTAAA
80163 GTAGTGATGG
Statistics
Matches: 495, Mismatches: 74, Indels: 112
0.73 0.11 0.16
Matches are distributed among these distances:
19 4 0.01
20 101 0.20
21 114 0.23
22 222 0.45
23 22 0.04
24 6 0.01
25 4 0.01
26 6 0.01
27 2 0.00
28 14 0.03
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.20
Consensus pattern (21 bp):
AAAATAGTAATCAGTAAAAGT
Found at i:79632 original size:8 final size:7
Alignment explanation
Indices: 79613--79690 Score: 50
Period size: 7 Copynumber: 10.7 Consensus size: 7
79603 AATGGTAATC
79613 AGTAAAA
1 AGTAAAA
79620 AGTAAAA
1 AGTAAAA
**
79627 AGGTAATT
1 A-GTAAAA
79635 AGTAAAA
1 AGTAAAA
79642 AGTAAAA
1 AGTAAAA
**
79649 TAGTAATT
1 -AGTAAAA
79657 AG-AAAA
1 AGTAAAA
79663 GAGTAAAA
1 -AGTAAAA
* *
79671 TGGTAAAG
1 -AGTAAAA
*
79679 AGTAAAG
1 AGTAAAA
79686 AGTAA
1 AGTAA
79691 TCAGTAAAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
6 2 0.04
7 34 0.62
8 19 0.35
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (7 bp):
AGTAAAA
Found at i:79652 original size:15 final size:15
Alignment explanation
Indices: 79613--79654 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
79603 AATGGTAATC
79613 AGTAAAA-AGTAAAA
1 AGTAAAATAGTAAAA
*
79627 AGGT-AATTAGTAAAA
1 A-GTAAAATAGTAAAA
79642 AGTAAAATAGTAA
1 AGTAAAATAGTAA
79655 TTAGAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (15 bp):
AGTAAAATAGTAAAA
Found at i:79700 original size:36 final size:36
Alignment explanation
Indices: 79636--79801 Score: 115
Period size: 36 Copynumber: 4.5 Consensus size: 36
79626 AAGGTAATTA
* * *
79636 GTAAAAAGTAAAATAGTAATTAGAAAAGAGTAAAATG
1 GTAAAAAGT-AAAGAGTAATCAGTAAAGAGTAAAATG
* **
79673 GTAAAGAGTAAAGAGTAATCAGTAAAGACAAAAAT-
1 GTAAAAAGTAAAGAGTAATCAGTAAAGAGTAAAATG
* * *
79708 G-ATAAAG-AAAGAGTGATAGTAAGAGTAAAAAGGTAAAATG
1 GTAAAAAGTAAAGAGT-A-A-T--CAGTAAAGA-GTAAAATG
*
79748 GTAAAAAGTAAA-AGGTAATCAGTAAAGGGTAAAATG
1 GTAAAAAGTAAAGA-GTAATCAGTAAAGAGTAAAATG
** *
79784 GTAATTAGTAAAAAGTAA
1 GTAAAAAGTAAAGAGTAA
79802 AATGGTAATC
Statistics
Matches: 100, Mismatches: 18, Indels: 23
0.71 0.13 0.16
Matches are distributed among these distances:
33 7 0.07
34 5 0.05
35 2 0.02
36 44 0.44
37 15 0.15
38 7 0.07
39 6 0.06
40 2 0.02
41 7 0.07
42 5 0.05
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (36 bp):
GTAAAAAGTAAAGAGTAATCAGTAAAGAGTAAAATG
Found at i:79771 original size:14 final size:14
Alignment explanation
Indices: 79732--79809 Score: 59
Period size: 14 Copynumber: 5.3 Consensus size: 14
79722 GATAGTAAGA
79732 GTAAAAAGGTAAAATG
1 GTAAAAA-GTAAAA-G
79748 GTAAAAAGTAAAAG
1 GTAAAAAGTAAAAG
** *
79762 GTAATCAGTAAAGG
1 GTAAAAAGTAAAAG
* *
79776 GTAAAATGGTAATTA-
1 GTAAAA-AGTAA-AAG
79791 GTAAAAAGTAAAATG
1 GTAAAAAGTAAAA-G
79806 GTAA
1 GTAA
79810 TCAGTAAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
13 1 0.02
14 20 0.42
15 20 0.42
16 7 0.15
ACGTcount: A:0.54, C:0.01, G:0.23, T:0.22
Consensus pattern (14 bp):
GTAAAAAGTAAAAG
Found at i:79852 original size:20 final size:19
Alignment explanation
Indices: 79827--80051 Score: 99
Period size: 21 Copynumber: 10.7 Consensus size: 19
79817 AAATTAAAAG
79827 AGTAATCAGTAGAAAGTAAT
1 AGTAATCAGTA-AAAGTAAT
*
79847 AGTAATCAGTAAGAAGCAAT
1 AGTAATCAGTAA-AAGTAAT
*
79867 AGTAGTCAGTAAAAAGTAAAT
1 AGTAATCAGT-AAAAGT-AAT
* *
79888 AGTAATCAGTAAGAGTAAAAA
1 AGTAATCAGTAAAAGT--AAT
* * *
79909 AGTAATAAGTTAGAAGTAAA
1 AGTAATCAG-TAAAAGTAAT
* * *
79929 AGGAAATCAGTAAGAGTAAAA
1 A-GTAATCAGTAAAAGT-AAT
* *
79950 AGGTGATCAGTAAAGAGTAAAA
1 A-GTAATCAGTAAA-AGT-AAT
* *
79972 AGCTAATCAGCAAGAAGTAAAA
1 AG-TAATCAGTAA-AAGT-AAT
* *
79994 AGGTAATCAGTAAAAAGCAAA
1 A-GTAATCAGT-AAAAGTAAT
* *
80015 AGGCAATCAGTAAAAAGTAAAAG
1 A-GTAATCAGT-AAAAGT--AAT
80038 AGTAATCAGTAAAA
1 AGTAATCAGTAAAA
80052 AAGGAGCAGA
Statistics
Matches: 167, Mismatches: 24, Indels: 27
0.77 0.11 0.12
Matches are distributed among these distances:
19 1 0.01
20 43 0.26
21 69 0.41
22 47 0.28
23 7 0.04
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (19 bp):
AGTAATCAGTAAAAGTAAT
Found at i:80161 original size:91 final size:90
Alignment explanation
Indices: 79884--80139 Score: 224
Period size: 91 Copynumber: 2.9 Consensus size: 90
79874 AGTAAAAAGT
* * * * * * * *
79884 AAATAGTAATCAGTAAGAGTAAAAAAGTAATAAGTTAGAAGTAAAAGGAAATCAGTAAGAGTAAA
1 AAATAGTAATCAGT-AGAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAGAAAAAGTAAA
* *
79949 A-AGGTGATCAGT---AAA-GAG--TA
65 AGA-GTAATCAGTAAAAAAGGAGAAGA
*
79969 AAA-AGCTAATCAGCAAGAAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAGTAAAAAGT
1 AAATAG-TAATCAG-TAG-AGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAG-AAAAAGT
*
80033 AAAAGAGTAATCAGTAAAAAAGGAGCAGA
62 AAAAGAGTAATCAGTAAAAAAGGAGAAGA
* * * *
80062 AAATAGTAATCAGTAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCA-ACAAGAGTAA
1 AAATAGTAATCAGTAGAGTAAAAAGGTAATCAGTAAAAAGCAA-AAGGCAATCAGA-AAAAGTAA
*
80126 AATAGTAATCAGTA
64 AAGAGTAATCAGTA
80140 CAAAGTAAAG
Statistics
Matches: 140, Mismatches: 17, Indels: 22
0.78 0.09 0.12
Matches are distributed among these distances:
84 2 0.01
85 12 0.09
86 32 0.23
87 17 0.12
88 1 0.01
90 4 0.03
91 48 0.34
92 11 0.08
93 11 0.08
94 2 0.01
ACGTcount: A:0.55, C:0.07, G:0.21, T:0.18
Consensus pattern (90 bp):
AAATAGTAATCAGTAGAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAGAAAAAGTAAAA
GAGTAATCAGTAAAAAAGGAGAAGA
Found at i:80720 original size:16 final size:15
Alignment explanation
Indices: 80699--80738 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 15
80689 TGCTTTATTT
80699 TAATTGTTTTCCTTTA
1 TAATTGTTTT-CTTTA
80715 TAATTGCTTTTCTTTA
1 TAATTG-TTTTCTTTA
80731 TAATTGTT
1 TAATTGTT
80739 ATTTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 17 0.74
17 4 0.17
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.62
Consensus pattern (15 bp):
TAATTGTTTTCTTTA
Found at i:81028 original size:26 final size:26
Alignment explanation
Indices: 80999--81080 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 26
80989 TTTTTTCTAA
*
80999 AAAAAAAATCTTTTATTTTTGTGTTT
1 AAAAAAAATCTTTTATTTTTGTATTT
* * * *
81025 -AAAAAAATTTTCTTATTGTTGCATTA
1 AAAAAAAATCTT-TTATTTTTGTATTT
* *
81051 AAAAAAAATTCTCTTATTTTCTGTTTTT
1 AAAAAAAA-TCTTTTATTTT-TGTATTT
81079 AA
1 AA
81081 TTTTTATTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
25 10 0.24
26 10 0.24
27 13 0.32
28 8 0.20
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.50
Consensus pattern (26 bp):
AAAAAAAATCTTTTATTTTTGTATTT
Found at i:81760 original size:30 final size:30
Alignment explanation
Indices: 81726--81798 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
81716 AGAAGATGGG
*
81726 ATCGCACCAAAGACATCAAAGGATGGAGGA
1 ATCGCACCAAAGACACCAAAGGATGGAGGA
** **
81756 ATCGCACCAAAGATGCCATTGGATGGAGGA
1 ATCGCACCAAAGACACCAAAGGATGGAGGA
81786 ATCGCACCAAAGA
1 ATCGCACCAAAGA
81799 TGCCATTTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (30 bp):
ATCGCACCAAAGACACCAAAGGATGGAGGA
Found at i:81799 original size:30 final size:30
Alignment explanation
Indices: 81746--81805 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
81736 AGACATCAAA
81746 GGATGGAGGAATCGCACCAAAGATGCCATT
1 GGATGGAGGAATCGCACCAAAGATGCCATT
81776 GGATGGAGGAATCGCACCAAAGATGCCATT
1 GGATGGAGGAATCGCACCAAAGATGCCATT
81806 TGATCCTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.30, T:0.17
Consensus pattern (30 bp):
GGATGGAGGAATCGCACCAAAGATGCCATT
Found at i:83577 original size:17 final size:17
Alignment explanation
Indices: 83550--83589 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
83540 GTTACTTACA
*
83550 TTTTAATTTTCTTTTTTG
1 TTTT-ATTTTCTTTTTCG
83568 TTTTATTTTCTTTTTCG
1 TTTTATTTTCTTTTTCG
83585 TTTTA
1 TTTTA
83590 GGAATTCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTTATTTTCTTTTTCG
Found at i:92170 original size:15 final size:15
Alignment explanation
Indices: 92150--92179 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
92140 AAATAGCCAC
92150 CTTTCTCTTTAGAAA
1 CTTTCTCTTTAGAAA
*
92165 CTTTCTCTTTTGAAA
1 CTTTCTCTTTAGAAA
92180 GGAGAGTTGG
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:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (15 bp):
CTTTCTCTTTAGAAA
Found at i:93804 original size:41 final size:41
Alignment explanation
Indices: 93755--93836 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
93745 TTTTGAAAAG
* * *
93755 CGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTAT
1 CGAATTTTGATATTGGACCCACAAATGAAATGCAATCTTAT
93796 CGAATTTTGATATTGGACCCACAAATGAAATGCAATCTTAT
1 CGAATTTTGATATTGGACCCACAAATGAAATGCAATCTTAT
93837 TATAAAACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (41 bp):
CGAATTTTGATATTGGACCCACAAATGAAATGCAATCTTAT
Found at i:94147 original size:20 final size:22
Alignment explanation
Indices: 94119--94159 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
94109 TTTTCCTCAG
*
94119 TTTC-TTTTTT-TTTCTTTTTC
1 TTTCATTTTTTCTCTCTTTTTC
94139 TTTCATTTTTTCTCTCTTTTT
1 TTTCATTTTTTCTCTCTTTTT
94160 TCTCTCTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTCATTTTTTCTCTCTTTTTC
Found at i:94160 original size:11 final size:11
Alignment explanation
Indices: 94121--94167 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
94111 TTCCTCAGTT
*
94121 TCTTTTTT-TT
1 TCTTTTTTCTC
*
94131 TC-TTTTTCTT
1 TCTTTTTTCTC
94141 TCATTTTTTCTC
1 TC-TTTTTTCTC
94153 TCTTTTTTCTC
1 TCTTTTTTCTC
94164 TCTT
1 TCTT
94168 GTAGGCGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
9 5 0.15
10 6 0.18
11 13 0.39
12 9 0.27
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (11 bp):
TCTTTTTTCTC
Found at i:95211 original size:41 final size:41
Alignment explanation
Indices: 95162--95243 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
95152 TTTTGAAAAG
* *
95162 CGAATTTTGATATTGGACTCACAAATGGAATGCAATCTTAT
1 CGAATTTTGATATTGGACCCACAAATGAAATGCAATCTTAT
95203 CGAATTTTGATATTGGACCCACAAATGAAATGCAATCTTAT
1 CGAATTTTGATATTGGACCCACAAATGAAATGCAATCTTAT
95244 TATAAAACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (41 bp):
CGAATTTTGATATTGGACCCACAAATGAAATGCAATCTTAT
Found at i:95541 original size:11 final size:10
Alignment explanation
Indices: 95525--95587 Score: 63
Period size: 10 Copynumber: 6.1 Consensus size: 10
95515 CTTTTCTTCA
95525 TTTTCTTTTCT
1 TTTTCTTTT-T
95536 TTTTCTTTTT
1 TTTTCTTTTT
* *
95546 CTTTCATTTT
1 TTTTCTTTTT
* *
95556 TTCTCTCTTT
1 TTTTCTTTTT
95566 TTTTCTTTTT
1 TTTTCTTTTT
*
95576 ATTTCATTTTT
1 TTTTC-TTTTT
95587 T
1 T
95588 ACATGCACTT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
10 27 0.66
11 14 0.34
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:96896 original size:17 final size:17
Alignment explanation
Indices: 96876--96945 Score: 60
Period size: 17 Copynumber: 4.3 Consensus size: 17
96866 CTTTTTCCTC
96876 TTTTTCTCTTTTTTCA-
1 TTTTTCTCTTTTTTCAT
* *
96892 -TTTT-TCATTTATC-T
1 TTTTTCTCTTTTTTCAT
*
96906 TTCTTTTTCTTTTTTCAT
1 TT-TTTCTCTTTTTTCAT
96924 TTTTTCAT-TTTTTTCAT
1 TTTTTC-TCTTTTTTCAT
96941 TTTTT
1 TTTTT
96946 TTTTGGGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
14 7 0.16
15 5 0.12
16 3 0.07
17 24 0.56
18 4 0.09
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTCTCTTTTTTCAT
Found at i:96912 original size:24 final size:24
Alignment explanation
Indices: 96884--96944 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
96874 TCTTTTTCTC
*
96884 TTTTTTCATTTTTCA-TTTATCTT
1 TTTTTTCATTTTTCATTTTATCAT
* *
96907 TCTTTTTCTTTTTTCATTTTTTCAT
1 T-TTTTTCATTTTTCATTTTATCAT
96932 TTTTTTCATTTTT
1 TTTTTTCATTTTT
96945 TTTTTGGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 1 0.03
24 24 0.75
25 7 0.22
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTTCATTTTTCATTTTATCAT
Found at i:96920 original size:31 final size:30
Alignment explanation
Indices: 96877--96949 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 30
96867 TTTTTCCTCT
96877 TTTTCTCTTTTTTCA-TTTTTCATTTATCTTTC
1 TTTT-TCTTTTTTCATTTTTTCATTT-T-TTTC
96909 TTTTTCTTTTTTCATTTTTTCATTTTTTTC
1 TTTTTCTTTTTTCATTTTTTCATTTTTTTC
*
96939 ATTTT-TTTTTT
1 TTTTTCTTTTTT
96950 GGGAAATTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 6 0.15
30 8 0.21
31 11 0.28
32 14 0.36
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (30 bp):
TTTTTCTTTTTTCATTTTTTCATTTTTTTC
Found at i:96935 original size:9 final size:9
Alignment explanation
Indices: 96915--96946 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
96905 TTTCTTTTTC
96915 TTTTTTCA-
1 TTTTTTCAT
96923 TTTTTTCAT
1 TTTTTTCAT
96932 TTTTTTCAT
1 TTTTTTCAT
96941 TTTTTT
1 TTTTTT
96947 TTTGGGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:99085 original size:10 final size:10
Alignment explanation
Indices: 99070--99123 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
99060 GCCTAATCGA
99070 TGGCCGGTTG
1 TGGCCGGTTG
99080 TGGCCGGTTGG
1 TGGCCGGTT-G
** *
99091 TGCGCCAATCG
1 TG-GCCGGTTG
99102 ATGGCCGGTTG
1 -TGGCCGGTTG
99113 TGGCCGGTTG
1 TGGCCGGTTG
99123 T
1 T
99124 CCCATGCGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
10 20 0.57
11 9 0.26
12 6 0.17
ACGTcount: A:0.06, C:0.22, G:0.44, T:0.28
Consensus pattern (10 bp):
TGGCCGGTTG
Done.