Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009560.1 Corchorus capsularis cultivar CVL-1 contig09581, 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: 54911
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:20294 original size:42 final size:43
Alignment explanation
Indices: 20235--20330 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 43
20225 AAATTTATTT
* * *
20235 CCGTCAGTATATGCCAAAAGGTATATTGCAACAGTCAC-AAAA
1 CCGTCAGTATATACCAAAAGGCATATTGCAACAATCACGAAAA
* *
20277 CCGTCAGTATATACCAAAAGGCGTATTGCAACAATCACGAAAT
1 CCGTCAGTATATACCAAAAGGCATATTGCAACAATCACGAAAA
20320 CCGTCAGTATA
1 CCGTCAGTATA
20331 GACCTATACC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 34 0.71
43 14 0.29
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.22
Consensus pattern (43 bp):
CCGTCAGTATATACCAAAAGGCATATTGCAACAATCACGAAAA
Found at i:21345 original size:18 final size:20
Alignment explanation
Indices: 21322--21361 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
21312 GGGTATTTTA
21322 TTGATT-CAT-AATATAAAT
1 TTGATTACATAAATATAAAT
*
21340 TTGATTATATAAATATAAAT
1 TTGATTACATAAATATAAAT
21360 TT
1 TT
21362 ATTTTTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
TTGATTACATAAATATAAAT
Found at i:22896 original size:2 final size:2
Alignment explanation
Indices: 22889--23047 Score: 279
Period size: 2 Copynumber: 80.0 Consensus size: 2
22879 ACATGATTGC
22889 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
22931 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TAG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG
22974 AG AG AG AG AG AG AG AG AG AG TAG AG A- AG A- AG A- AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG
23014 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
23048 TGTGTGAAAG
Statistics
Matches: 152, Mismatches: 0, Indels: 10
0.94 0.00 0.06
Matches are distributed among these distances:
1 3 0.02
2 145 0.95
3 4 0.03
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.01
Consensus pattern (2 bp):
AG
Found at i:24148 original size:1 final size:1
Alignment explanation
Indices: 24142--24168 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
24132 AATTGTGTGG
24142 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
24169 AAAGTTGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26667 original size:107 final size:107
Alignment explanation
Indices: 26481--26783 Score: 581
Period size: 107 Copynumber: 2.8 Consensus size: 107
26471 ACAATCGGAA
26481 TAAATCTCAATATGCCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTACCATAAATA
1 TAAATCTCAATATGCCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTACCATAAATA
26546 AACCATCTACCTACCAAATACACAAATAAATAAATTATAAAC
66 AACCATCTACCTACCAAATACACAAATAAATAAATTATAAAC
*
26588 TAAATCTCAATATGCCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTATCATAAATA
1 TAAATCTCAATATGCCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTACCATAAATA
26653 AACCATCTACCTACCAAATACACAAATAAATAAATTATAAAC
66 AACCATCTACCTACCAAATACACAAATAAATAAATTATAAAC
26695 TAAATCTCAATATGCCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTACCATAAAT-
1 TAAATCTCAATATGCCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTACCATAAATA
26759 AACTCATCTACCTACCAAATACACA
66 AAC-CATCTACCTACCAAATACACA
26784 TGCAAGTAAA
Statistics
Matches: 193, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
106 3 0.02
107 190 0.98
ACGTcount: A:0.51, C:0.23, G:0.04, T:0.22
Consensus pattern (107 bp):
TAAATCTCAATATGCCCAAACATCTAAATGAGAAATCAACTCAAACTAAGAAACTACCATAAATA
AACCATCTACCTACCAAATACACAAATAAATAAATTATAAAC
Found at i:27500 original size:19 final size:19
Alignment explanation
Indices: 27476--27531 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
27466 CTTAACAATA
* *
27476 TATATTTTTAATATATATT
1 TATATTATTAGTATATATT
*
27495 TATATTATTAGTAAATATT
1 TATATTATTAGTATATATT
27514 TAT-TTATTAGTATATATT
1 TATATTATTAGTATATATT
27532 ATTATTTCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
18 14 0.42
19 19 0.58
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (19 bp):
TATATTATTAGTATATATT
Found at i:28180 original size:25 final size:26
Alignment explanation
Indices: 28135--28185 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
28125 AACAAAAAAA
28135 TTTCTTATTTAAAAGGTATAATAATT
1 TTTCTTATTTAAAAGGTATAATAATT
28161 TTTCTTATTT-AAAGGTATAATAATT
1 TTTCTTATTTAAAAGGTATAATAATT
28186 GATACTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (26 bp):
TTTCTTATTTAAAAGGTATAATAATT
Found at i:40879 original size:30 final size:30
Alignment explanation
Indices: 40845--40948 Score: 111
Period size: 30 Copynumber: 3.5 Consensus size: 30
40835 CGTCACCTGA
40845 GGTGCCATCATCTTGGGTGCAGTTGATTTT
1 GGTGCCATCATCTTGGGTGCAGTTGATTTT
* * * *
40875 GGTGCCACCATTTTGGGTGCCGTTGATTTC
1 GGTGCCATCATCTTGGGTGCAGTTGATTTT
* * * * *
40905 AGTGCCATCTTCTTTGGTGCA-ATCATCTTT
1 GGTGCCATCATCTTGGGTGCAGTTGAT-TTT
40935 GGTGCCATCATCTT
1 GGTGCCATCATCTT
40949 CTTCCATGGC
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
29 3 0.05
30 55 0.95
ACGTcount: A:0.13, C:0.22, G:0.25, T:0.39
Consensus pattern (30 bp):
GGTGCCATCATCTTGGGTGCAGTTGATTTT
Found at i:40924 original size:15 final size:15
Alignment explanation
Indices: 40906--40948 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
40896 GTTGATTTCA
*
40906 GTGCCATCTTCTTTG
1 GTGCCATCATCTTTG
*
40921 GTGCAATCATCTTTG
1 GTGCCATCATCTTTG
40936 GTGCCATCATCTT
1 GTGCCATCATCTT
40949 CTTCCATGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.42
Consensus pattern (15 bp):
GTGCCATCATCTTTG
Found at i:42212 original size:36 final size:36
Alignment explanation
Indices: 42161--42231 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
42151 GTTGAACAAG
* *
42161 TGTGGCAACTTGGTGC-GATGCGGCCACTAGGTGCGT
1 TGTGGCAACTAGGTGCAG-TGCGACCACTAGGTGCGT
*
42197 TGTGGCAACTAGGTGCAGTGCGACCACTTGGTGCG
1 TGTGGCAACTAGGTGCAGTGCGACCACTAGGTGCG
42232 GTGCAACCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.24
Consensus pattern (36 bp):
TGTGGCAACTAGGTGCAGTGCGACCACTAGGTGCGT
Found at i:42235 original size:18 final size:18
Alignment explanation
Indices: 42168--42250 Score: 60
Period size: 18 Copynumber: 4.6 Consensus size: 18
42158 AAGTGTGGCA
* *
42168 ACTTGGTGCGATGCGGCC
1 ACTTGGTGCGGTGCGACC
* * * * *
42186 ACTAGGTGCGTTGTGGCA
1 ACTTGGTGCGGTGCGACC
* *
42204 ACTAGGTGCAGTGCGACC
1 ACTTGGTGCGGTGCGACC
*
42222 ACTTGGTGCGGTGCAACC
1 ACTTGGTGCGGTGCGACC
42240 A-TTGGGTGCGG
1 ACTT-GGTGCGG
42251 CGCCTGGTGC
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
17 2 0.04
18 50 0.96
ACGTcount: A:0.16, C:0.23, G:0.39, T:0.23
Consensus pattern (18 bp):
ACTTGGTGCGGTGCGACC
Found at i:45387 original size:35 final size:35
Alignment explanation
Indices: 45341--46044 Score: 1036
Period size: 35 Copynumber: 19.9 Consensus size: 35
45331 AGCCGCACTG
* *
45341 GATCAACTCTGATCATC-GAAAATTTCTTGAAATGA
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
*
45376 GATCAACTCTGACCTCTTAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
45411 GATCAACTCTGACCTCAGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
45446 GATCAACTCTGACCTCTGAAAACTTCTTTAAAATGA
1 GATCAACTCTGACCTCTGAAAACTTC-TTGAAATGA
* * *
45482 GATCAACTCTGATCGTTTG-AAACTTCTTGGAATGA
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
45517 GATCAACTCTGACCTCTGAAAACTTCTTAATATGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTC----T-TGAAATGA
* *
45557 GATCAACTCTAACCTCTGGAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* * *
45592 AATCAACTCTGACTTCTGAAAATTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
45627 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
45662 GATCAACTCTGACCTCTGAAAACTTCTTGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* * * *
45697 AATCAACTCTGATCGT-TGGAAACTTCTTGGAATGA
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
*
45732 GATCAACTCTGACCTCTGAAAACTTCTTGATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
45767 GATCAACTCTGACCTCTTAAAACTTCTTGATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
45802 GATCAACTCTGACCTCTTAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
45837 GATCAACTCTGACCTCTAAAAACTTCTTCAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
45872 GATCAACTCTGACCTCTAAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
45907 GATCAACTCTGACCTTTGGAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
45942 GATCAACTCTGACCTCTGAAAACTTCTTGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
45977 GATCAACTCTGACCTCTGAAAACTTCTTCAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
46012 GATCAACTCTGACCTCTGAAAACTTCTATGAAA
1 GATCAACTCTGACCTCTGAAAACTTCT-TGAAA
46045 GACCGCACAT
Statistics
Matches: 610, Mismatches: 47, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
34 9 0.01
35 531 0.87
36 34 0.06
37 4 0.01
39 1 0.00
40 31 0.05
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (35 bp):
GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
Found at i:46182 original size:22 final size:22
Alignment explanation
Indices: 46154--46201 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
46144 AACACCTGTA
*
46154 CTTGAC-TCTTCATCTACCCTTT
1 CTTGACTTCTTC-TCTACCCATT
*
46176 CTTGACTTCTTCTTTACCCATT
1 CTTGACTTCTTCTCTACCCATT
46198 CTTG
1 CTTG
46202 GCTACTGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.12, C:0.33, G:0.06, T:0.48
Consensus pattern (22 bp):
CTTGACTTCTTCTCTACCCATT
Found at i:47248 original size:36 final size:37
Alignment explanation
Indices: 47199--47277 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
47189 TGTCTTAAAA
* **
47199 ACTTTTTGAAAAACA-TTTTTCTTTTGAAAAGATTGC
1 ACTTTGTGAAAAACATTTTTTCTTTTGAAAAGATCAC
*
47235 ACTTTGTGGAAAACATTTTTTCTTTTGAAAAGATCAC
1 ACTTTGTGAAAAACATTTTTTCTTTTGAAAAGATCAC
47272 ACTTTG
1 ACTTTG
47278 AAGAAAATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
36 13 0.34
37 25 0.66
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (37 bp):
ACTTTGTGAAAAACATTTTTTCTTTTGAAAAGATCAC
Found at i:47501 original size:26 final size:26
Alignment explanation
Indices: 47467--47516 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
47457 TTCCTCCATC
47467 CTTTGCTTTTTCAACTTCTT-TCTTTT
1 CTTTGCTTTTTCAA-TTCTTATCTTTT
*
47493 CTTTTCTTTTTCAATTCTTATCTT
1 CTTTGCTTTTTCAATTCTTATCTT
47517 CATTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.10, C:0.22, G:0.02, T:0.66
Consensus pattern (26 bp):
CTTTGCTTTTTCAATTCTTATCTTTT
Found at i:47523 original size:26 final size:26
Alignment explanation
Indices: 47467--47527 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
47457 TTCCTCCATC
* *
47467 CTTTGCTTTTTCAACTTCTTTCTTTT
1 CTTTTCTTTTTCAACTTCTTTCTTAT
47493 CTTTTCTTTTTCAA-TTCTTATCTTCAT
1 CTTTTCTTTTTCAACTTCTT-TCTT-AT
*
47520 TTTTTCTT
1 CTTTTCTT
47528 CTCATACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 5 0.17
26 17 0.57
27 8 0.27
ACGTcount: A:0.10, C:0.21, G:0.02, T:0.67
Consensus pattern (26 bp):
CTTTTCTTTTTCAACTTCTTTCTTAT
Found at i:48006 original size:13 final size:14
Alignment explanation
Indices: 47988--48017 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
47978 TTCTTTCACA
47988 TTTTTTCTTTTT-T
1 TTTTTTCTTTTTCT
48001 TTTTTTCTTTTTCT
1 TTTTTTCTTTTTCT
48015 TTT
1 TTT
48018 GCTGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTCTTTTTCT
Found at i:53776 original size:6 final size:6
Alignment explanation
Indices: 53765--53790 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
53755 TAAATATTGA
53765 TTCTTT TTCTTT TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TT
53791 TTTACATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTCTTT
Done.