Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012508.1 Corchorus capsularis cultivar CVL-1 contig12529, 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: 67550
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:186 original size:2 final size:2
Alignment explanation
Indices: 179--203 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
169 AAATCTAAAT
179 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 T
204 GGCACTCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19176 original size:23 final size:24
Alignment explanation
Indices: 19145--19189 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
19135 TAGGAGATCC
19145 TAAACATAAAAAAATAATTAAAAA
1 TAAACATAAAAAAATAATTAAAAA
* *
19169 TAAA-ATAACAAGATAATTAAA
1 TAAACATAAAAAAATAATTAAA
19190 GTGGGCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (24 bp):
TAAACATAAAAAAATAATTAAAAA
Found at i:30442 original size:31 final size:31
Alignment explanation
Indices: 30356--30448 Score: 114
Period size: 31 Copynumber: 3.0 Consensus size: 31
30346 CATTAGGGGC
* * *
30356 TGATTTGAGCCGATTTTGCAATGCTAGGGAC
1 TGATTTGAGCCGATTTTGCAACGTTAGGGAA
* * *
30387 TGATGTGAGCCAATTTTGCTACGTTAGGGAA
1 TGATTTGAGCCGATTTTGCAACGTTAGGGAA
*
30418 TGATTTCAGCCGATTTTGCAACGTTATGGGA
1 TGATTTGAGCCGATTTTGCAACGTTA-GGGA
30449 TTAATTAACC
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 47 0.92
32 4 0.08
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (31 bp):
TGATTTGAGCCGATTTTGCAACGTTAGGGAA
Found at i:34026 original size:29 final size:29
Alignment explanation
Indices: 33984--34047 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
33974 ATTTGTTAAA
33984 ATAATTTAACCAATTTTCATTCAAAAAGG
1 ATAATTTAACCAATTTTCATTCAAAAAGG
*
34013 ATAATTTAGCCAATTTTCATTCAAAAAGG
1 ATAATTTAACCAATTTTCATTCAAAAAGG
34042 ATAATT
1 ATAATT
34048 GGTATGGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (29 bp):
ATAATTTAACCAATTTTCATTCAAAAAGG
Found at i:38201 original size:18 final size:18
Alignment explanation
Indices: 38178--38226 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
38168 TATAATAACA
38178 ATAGTAATTAATAATTTC
1 ATAGTAATTAATAATTTC
38196 ATAGTAATTAATAATTTC
1 ATAGTAATTAATAATTTC
**
38214 -TTCTAATTAATAA
1 ATAGTAATTAATAA
38227 ATCTGCAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 11 0.38
18 18 0.62
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (18 bp):
ATAGTAATTAATAATTTC
Found at i:44137 original size:20 final size:20
Alignment explanation
Indices: 44112--44155 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
44102 TTACATGGCA
44112 TTTTTTAAT-ATTTTTAATAT
1 TTTTTTAATAATTTTTAAT-T
*
44132 TTTTTTTATAATTTTTAATT
1 TTTTTTAATAATTTTTAATT
44152 TTTT
1 TTTT
44156 AATTTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTAATAATTTTTAATT
Found at i:44138 original size:21 final size:20
Alignment explanation
Indices: 44112--44155 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
44102 TTACATGGCA
44112 TTTTTTA-ATATTTTTAATATT
1 TTTTTTATA-ATTTTTAAT-TT
44133 TTTTTTATAATTTTTAATTT
1 TTTTTTATAATTTTTAATTT
44153 TTT
1 TTT
44156 AATTTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.23
21 16 0.73
22 1 0.05
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTATAATTTTTAATTT
Found at i:44143 original size:23 final size:22
Alignment explanation
Indices: 44112--44166 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
44102 TTACATGGCA
*
44112 TTTTTTA-ATATTTTTAATATT
1 TTTTTTATAAATTTTTAATATT
*
44133 TTTTTTAT-AATTTTTAATTTT
1 TTTTTTATAAATTTTTAATATT
44154 TTAATTTTATAAA
1 TT--TTTTATAAA
44167 CCGGCTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 20 0.71
23 6 0.21
24 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTTTATAAATTTTTAATATT
Found at i:44159 original size:8 final size:8
Alignment explanation
Indices: 44111--44161 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
44101 CTTACATGGC
44111 ATTTTTTA
1 ATTTTTTA
44119 ATATTTTTA
1 AT-TTTTTA
*
44128 ATATTTT-
1 ATTTTTTA
*
44135 -TTTTATA
1 ATTTTTTA
44142 A-TTTTTA
1 ATTTTTTA
44149 ATTTTTTA
1 ATTTTTTA
44157 ATTTT
1 ATTTT
44162 ATAAACCGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
6 4 0.11
7 6 0.17
8 17 0.49
9 8 0.23
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTTTTTA
Found at i:44213 original size:31 final size:31
Alignment explanation
Indices: 44178--44238 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
44168 CGGCTCAAAG
*
44178 TACTAAATGTTTCAAAATTGGATCAATTTAA
1 TACTAAACGTTTCAAAATTGGATCAATTTAA
44209 TACTAAACGTTTCAAAATTGGATCAATTTA
1 TACTAAACGTTTCAAAATTGGATCAATTTA
44239 GATTCTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (31 bp):
TACTAAACGTTTCAAAATTGGATCAATTTAA
Found at i:45354 original size:19 final size:20
Alignment explanation
Indices: 45330--45369 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
45320 AGAAACCAAA
45330 GTACAACATCTAA-TTACAT
1 GTACAACATCTAATTTACAT
*
45349 GTACAATATCTAATTTACAT
1 GTACAACATCTAATTTACAT
45369 G
1 G
45370 GACAGCCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (20 bp):
GTACAACATCTAATTTACAT
Found at i:50429 original size:3 final size:3
Alignment explanation
Indices: 50416--50472 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
50406 CATTTATAGG
*
50416 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT GA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
50461 TAT TAC TAT TAT
1 TAT TAT TAT TAT
50473 ATATATTACT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 5 0.11
3 42 0.89
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:50433 original size:14 final size:14
Alignment explanation
Indices: 50416--50480 Score: 89
Period size: 14 Copynumber: 4.7 Consensus size: 14
50406 CATTTATAGG
50416 TATTATATTATTAT
1 TATTATATTATTAT
50430 TA-T-TATTATTAT
1 TATTATATTATTAT
50442 TATTATATTATTAT
1 TATTATATTATTAT
* *
50456 TATGATATTACTAT
1 TATTATATTATTAT
50470 TATATATATTA
1 TAT-TATATTA
50481 CTTGCGGTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.24
13 2 0.04
14 26 0.58
15 6 0.13
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:50438 original size:26 final size:26
Alignment explanation
Indices: 50415--50480 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
50405 ACATTTATAG
50415 GTATTATATTATTATTATTATTATTA
1 GTATTATATTATTATTATTATTATTA
* *
50441 TTATTATATTATTATTATGA-TATTA
1 GTATTATATTATTATTATTATTATTA
*
50466 CTATTATATATATTA
1 GTATTATAT-TATTA
50481 CTTGCGGTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 13 0.36
26 23 0.64
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (26 bp):
GTATTATATTATTATTATTATTATTA
Found at i:57026 original size:41 final size:41
Alignment explanation
Indices: 56966--57114 Score: 138
Period size: 41 Copynumber: 3.9 Consensus size: 41
56956 TCAAATTATC
**
56966 ATCAATTCAAGAACAAGTCATCGAGACCCTTGAATTAAATT
1 ATCAATTCAAGATTAAGTCATCGAGACCCTTGAATTAAATT
* * *
57007 ATCAATTCAAGATTGAGTCATCGAAACCCTTG-------TC
1 ATCAATTCAAGATTAAGTCATCGAGACCCTTGAATTAAATT
* *
57041 ATCAATTCAAGATTAAGTCGTCAAGA-CCTTGAATTAAATT
1 ATCAATTCAAGATTAAGTCATCGAGACCCTTGAATTAAATT
**
57081 ATCAATTCAAGACCAAGTCATTC--GACCCTTGAAT
1 ATCAATTCAAGATTAAGTCA-TCGAGACCCTTGAAT
57115 CAATCAAATC
Statistics
Matches: 86, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
33 5 0.06
34 23 0.27
39 2 0.02
40 26 0.30
41 30 0.35
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.29
Consensus pattern (41 bp):
ATCAATTCAAGATTAAGTCATCGAGACCCTTGAATTAAATT
Found at i:57188 original size:62 final size:62
Alignment explanation
Indices: 57081--57248 Score: 239
Period size: 62 Copynumber: 2.7 Consensus size: 62
57071 GAATTAAATT
* **
57081 ATCAA-TTCAAGACCAAGTCATTCGACCCTTGAATCAATCAAATCAAATCAAGTTCTCAAATTAT
1 ATCAAGTTCAAGATCAAGTCATTCGACCCTT--A--AATCAAATCAAATCAAACTCTCAAATTAT
57145 C
62 C
*
57146 ATCAAGTTCAAGATCAAGTCATTTGACCCTTAAATCAAATCAAATCAAACTCTCAAATTATC
1 ATCAAGTTCAAGATCAAGTCATTCGACCCTTAAATCAAATCAAATCAAACTCTCAAATTATC
* *
57208 ATCAAGTTCAAGATCAAGTAATTCGACCCTTAAAGCAAATC
1 ATCAAGTTCAAGATCAAGTCATTCGACCCTTAAATCAAATC
57249 TTGAAGCATA
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
62 66 0.69
64 1 0.01
65 5 0.05
66 23 0.24
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.27
Consensus pattern (62 bp):
ATCAAGTTCAAGATCAAGTCATTCGACCCTTAAATCAAATCAAATCAAACTCTCAAATTATC
Found at i:57952 original size:12 final size:12
Alignment explanation
Indices: 57935--57959 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57925 GAACTTGATG
57935 ATGACGATGAAA
1 ATGACGATGAAA
57947 ATGACGATGAAA
1 ATGACGATGAAA
57959 A
1 A
57960 GTGAGTAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (12 bp):
ATGACGATGAAA
Found at i:58259 original size:20 final size:20
Alignment explanation
Indices: 58231--58271 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
58221 TACCCATTTG
*
58231 AAAATAAACCACCAATTTAA
1 AAAAAAAACCACCAATTTAA
*
58251 AAAAAAAACTACCAATTTAA
1 AAAAAAAACCACCAATTTAA
58271 A
1 A
58272 TGTGCCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.63, C:0.17, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAAAAACCACCAATTTAA
Found at i:58459 original size:3 final size:3
Alignment explanation
Indices: 58451--58484 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
58441 TAATAAGTTT
* *
58451 ACA ACA ACA ACA ACA ACA ACA ATA ATA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
58485 GAGGGATAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.06
Consensus pattern (3 bp):
ACA
Found at i:61136 original size:13 final size:12
Alignment explanation
Indices: 61120--61188 Score: 56
Period size: 13 Copynumber: 5.8 Consensus size: 12
61110 ATGAGGGAGG
61120 AAGAAATGAAGAA
1 AAGAAA-GAAGAA
61133 AAGAAA-AA-AA
1 AAGAAAGAAGAA
61143 AAGAAAGAAGAA
1 AAGAAAGAAGAA
61155 GAAGAAGAGAA-AA
1 -AAGAA-AGAAGAA
*
61168 AAGTGAA-AAGAA
1 AAG-AAAGAAGAA
*
61180 AAAAAAGAA
1 AAGAAAGAA
61189 TTAAAAATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
10 8 0.17
11 8 0.17
12 12 0.26
13 14 0.30
14 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (12 bp):
AAGAAAGAAGAA
Found at i:64760 original size:21 final size:22
Alignment explanation
Indices: 64735--64781 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
64725 AACTAAGGTT
64735 AAAACATATATTTCAGAAGT-A
1 AAAACATATATTTCAGAAGTGA
*
64756 AAAACATATATTTCTGAAGTGA
1 AAAACATATATTTCAGAAGTGA
64778 AAAA
1 AAAA
64782 GCCAATATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (22 bp):
AAAACATATATTTCAGAAGTGA
Found at i:65103 original size:37 final size:36
Alignment explanation
Indices: 65062--65131 Score: 113
Period size: 37 Copynumber: 1.9 Consensus size: 36
65052 CATGTGGTTA
**
65062 TTCGAAAATTAGGGTTATTGATTTGGGGTTTTTCATT
1 TTCGAAAATTAGGGTTAGGGATTT-GGGTTTTTCATT
65099 TTCGAAAATTAGGGTTAGGGATTTGGGTTTTTC
1 TTCGAAAATTAGGGTTAGGGATTTGGGTTTTTC
65132 GAAAATTAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 9 0.29
37 22 0.71
ACGTcount: A:0.21, C:0.06, G:0.27, T:0.46
Consensus pattern (36 bp):
TTCGAAAATTAGGGTTAGGGATTTGGGTTTTTCATT
Found at i:65463 original size:2 final size:2
Alignment explanation
Indices: 65456--65490 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
65446 ATCTATCTTA
65456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
65491 CTAGTAATTG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:66609 original size:21 final size:20
Alignment explanation
Indices: 66580--66620 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
66570 ATTTTCATGT
*
66580 CTAATAAGGTTACTAAAAAAA
1 CTAAAAAGGTTA-TAAAAAAA
66601 CTAAAAAGGTTATAAAAAAA
1 CTAAAAAGGTTATAAAAAAA
66621 TTAAGGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22
Consensus pattern (20 bp):
CTAAAAAGGTTATAAAAAAA
Found at i:67160 original size:23 final size:23
Alignment explanation
Indices: 67134--67177 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
67124 TCTTAATTGA
*
67134 TTAAC-AAATTTATTTAACTTCTC
1 TTAACTAAAATTA-TTAACTTCTC
67157 TTAACTAAAATTATTAACTTC
1 TTAACTAAAATTATTAACTTC
67178 AAGAAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAACTAAAATTATTAACTTCTC
Done.