Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007081.1 Corchorus capsularis cultivar CVL-1 contig07102, 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: 44252
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:33 original size:12 final size:12
Alignment explanation
Indices: 16--52 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
6 GAGTATTTTT
16 TTTATTAATTTA
1 TTTATTAATTTA
28 TTTATTAA-TTA
1 TTTATTAATTTA
39 GTTTATT-ATTTA
1 -TTTATTAATTTA
51 TT
1 TT
53 ATTTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTATTAATTTA
Found at i:4516 original size:30 final size:33
Alignment explanation
Indices: 4461--4523 Score: 96
Period size: 30 Copynumber: 2.0 Consensus size: 33
4451 TTATATTTTT
*
4461 CGATTGTACCCTTTATTTTTCAAAACATATTTC
1 CGATTATACCCTTTATTTTTCAAAACATATTTC
4494 CGATTATACCC-TT-TTTTT-AAAACATATTTC
1 CGATTATACCCTTTATTTTTCAAAACATATTTC
4524 TAAATTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 12 0.41
31 5 0.17
32 2 0.07
33 10 0.34
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.46
Consensus pattern (33 bp):
CGATTATACCCTTTATTTTTCAAAACATATTTC
Found at i:5456 original size:37 final size:37
Alignment explanation
Indices: 5413--5505 Score: 111
Period size: 37 Copynumber: 2.6 Consensus size: 37
5403 AATTTTGCTT
*
5413 TTTGTTTCCAACATCCTATTTAATTTTGGC-TTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTT-GCTTTTTGTC
* **
5450 TTTGTTTTCAACGTTGTATTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGCTTTTTGTC
*
5487 --TGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
5506 GGGCTTAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
35 15 0.32
36 2 0.04
37 30 0.64
ACGTcount: A:0.15, C:0.18, G:0.12, T:0.55
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCTTTTTGTC
Found at i:11761 original size:20 final size:20
Alignment explanation
Indices: 11736--11773 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11726 CACTCCCATA
*
11736 TATATCTATCCATCTATATC
1 TATATCTATACATCTATATC
11756 TATATCTATACATCTATA
1 TATATCTATACATCTATA
11774 CACTATATAA
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:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (20 bp):
TATATCTATACATCTATATC
Found at i:15580 original size:23 final size:20
Alignment explanation
Indices: 15538--15582 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
15528 GAAAACAATA
*
15538 AAATCAACATTCTCCTCTTG
1 AAATCAACATTCTCCCCTTG
15558 AAATCAACATCCTCCTCCCCTTG
1 AAATCAACAT--T-CTCCCCTTG
15581 AA
1 AA
15583 TGATCAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
22 1 0.05
23 10 0.48
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (20 bp):
AAATCAACATTCTCCCCTTG
Found at i:29168 original size:14 final size:14
Alignment explanation
Indices: 29149--29179 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
29139 CAGCTAGTAA
29149 AGTGCTGAATTCTT
1 AGTGCTGAATTCTT
29163 AGTGCTGAATTCTT
1 AGTGCTGAATTCTT
29177 AGT
1 AGT
29180 TCTAGTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (14 bp):
AGTGCTGAATTCTT
Found at i:29190 original size:12 final size:12
Alignment explanation
Indices: 29173--29197 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29163 AGTGCTGAAT
29173 TCTTAGTTCTAG
1 TCTTAGTTCTAG
29185 TCTTAGTTCTAG
1 TCTTAGTTCTAG
29197 T
1 T
29198 GATCAGTGAT
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:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (12 bp):
TCTTAGTTCTAG
Found at i:33159 original size:32 final size:32
Alignment explanation
Indices: 33114--33196 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 32
33104 GGGTTCGAGT
* *
33114 TCGGGTACT-TCGGGTTTGGGTATTTTCGGGC
1 TCGGGTAATGTCGGGTTCGGGTATTTTCGGGC
*
33145 TCAGGTTAA-GTCGGGTTCGGGTATTTTCGGGC
1 TC-GGGTAATGTCGGGTTCGGGTATTTTCGGGC
33177 TCGGGTAATGTCGGGTTCGG
1 TCGGGTAATGTCGGGTTCGG
33197 TCTCGGGTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
31 7 0.16
32 38 0.84
ACGTcount: A:0.10, C:0.16, G:0.40, T:0.35
Consensus pattern (32 bp):
TCGGGTAATGTCGGGTTCGGGTATTTTCGGGC
Found at i:33174 original size:16 final size:16
Alignment explanation
Indices: 33107--33196 Score: 67
Period size: 16 Copynumber: 5.7 Consensus size: 16
33097 ATTGGGCGGG
* *
33107 TTCGAGTTCGGGTA-C
1 TTCGGGTTCGGGTATT
*
33122 TTCGGGTTTGGGTATT
1 TTCGGGTTCGGGTATT
* * *
33138 TTCGGGCTCAGGT-TAA
1 TTCGGGTTCGGGTAT-T
*
33154 GTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
* *
33170 TTCGGGCTCGGGTAAT
1 TTCGGGTTCGGGTATT
*
33186 GTCGGGTTCGG
1 TTCGGGTTCGG
33197 TCTCGGGTAG
Statistics
Matches: 56, Mismatches: 16, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
15 13 0.23
16 42 0.75
17 1 0.02
ACGTcount: A:0.10, C:0.16, G:0.39, T:0.36
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:33195 original size:22 final size:23
Alignment explanation
Indices: 33170--33227 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
33160 TTCGGGTATT
*
33170 TTCGGGCTCGGGTA-A-TGTCGGG
1 TTCGGACTCGGGTAGAGT-TCGGG
*
33192 TTCGGTCTCGGGTAGAGTTCGGG
1 TTCGGACTCGGGTAGAGTTCGGG
*
33215 TTTGGACTCGGGT
1 TTCGGACTCGGGT
33228 TTTGATTTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.42
23 17 0.55
24 1 0.03
ACGTcount: A:0.09, C:0.17, G:0.43, T:0.31
Consensus pattern (23 bp):
TTCGGACTCGGGTAGAGTTCGGG
Found at i:33681 original size:31 final size:31
Alignment explanation
Indices: 33646--33717 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
33636 TAAGTTATTG
*
33646 CAAATTAAAACAAAT-TAAGCATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGCATTAAATTAAA
* *
33677 CAAA-TAATTAAAATGAAAGCCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGCATTAAATTAAA
33708 CAAATTAAAA
1 CAAATTAAAA
33718 GCAGATAGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 7 0.21
31 24 0.71
32 3 0.09
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.25
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGCATTAAATTAAA
Found at i:34782 original size:15 final size:15
Alignment explanation
Indices: 34762--34793 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
34752 ACCCTAGGTA
34762 TTGGAACTAAGTACC
1 TTGGAACTAAGTACC
34777 TTGGAACTAAGTACC
1 TTGGAACTAAGTACC
34792 TT
1 TT
34794 TTACTCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (15 bp):
TTGGAACTAAGTACC
Found at i:36779 original size:18 final size:19
Alignment explanation
Indices: 36756--36793 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
36746 GAAATAGGAT
36756 TTCAAATCCAACAGA-AGA
1 TTCAAATCCAACAGATAGA
*
36774 TTCAAATTCAACAGATAGA
1 TTCAAATCCAACAGATAGA
36793 T
1 T
36794 AGGATAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (19 bp):
TTCAAATCCAACAGATAGA
Found at i:41281 original size:18 final size:19
Alignment explanation
Indices: 41258--41295 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
41248 GAAATAGGAT
41258 TTCAAA-TCCAACAGA-AGA
1 TTCAAATTCC-ACAGATAGA
41276 TTCAAATTCCACAGATAGA
1 TTCAAATTCCACAGATAGA
41295 T
1 T
41296 AGGATAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.24
Consensus pattern (19 bp):
TTCAAATTCCACAGATAGA
Found at i:42976 original size:21 final size:21
Alignment explanation
Indices: 42930--42981 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
42920 TTTTTTGATT
*
42930 AATTTTT-TTTGAAAAAATAT
1 AATTTTTATTTGAAAAAATAA
*
42950 ATTTTTTATTT-AAAAAATGAA
1 AATTTTTATTTGAAAAAAT-AA
42971 AATTTTTATTT
1 AATTTTTATTT
42982 TTATTCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
AATTTTTATTTGAAAAAATAA
Found at i:43131 original size:17 final size:16
Alignment explanation
Indices: 43098--43154 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
43088 CCCTGACTCA
*
43098 TTTTAAAAAATATATAT
1 TTTTTAAAAA-ATATAT
*
43115 GTTTTTTAAAAATATAT
1 -TTTTTAAAAAATATAT
* *
43132 TCTTTAAAAAAAATAT
1 TTTTTAAAAAATATAT
43148 TTTTTAA
1 TTTTTAA
43155 TCAAAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 19 0.58
17 6 0.18
18 8 0.24
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
TTTTTAAAAAATATAT
Found at i:43291 original size:28 final size:29
Alignment explanation
Indices: 43235--43292 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
43225 GTCAGTCAAA
* *
43235 TTCACTTCAGGGACTAAATTACATATTTT
1 TTCACTTCAAGGACCAAATTACATATTTT
* *
43264 TTCACTTGAAGGACCAATTTAC-TATTTT
1 TTCACTTCAAGGACCAAATTACATATTTT
43292 T
1 T
43293 GCTCTACTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.43
Consensus pattern (29 bp):
TTCACTTCAAGGACCAAATTACATATTTT
Done.