Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008120.1 Corchorus capsularis cultivar CVL-1 contig08141, 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: 24508
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:4664 original size:1 final size:1
Alignment explanation
Indices: 4654--4690 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
4644 ATTTCAATTC
*
4654 AAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4691 CTTTTTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:10441 original size:7 final size:7
Alignment explanation
Indices: 10429--10458 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
10419 AGTTAGGTGA
10429 GACTCTG
1 GACTCTG
10436 GACTCTG
1 GACTCTG
10443 GACTCTG
1 GACTCTG
10450 GACTCTG
1 GACTCTG
10457 GA
1 GA
10459 GTGGAGATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GACTCTG
Found at i:10792 original size:16 final size:18
Alignment explanation
Indices: 10744--10792 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 18
10734 TAATACTTGT
10744 AATATTAATTGAAAATAAA
1 AATATT-ATTGAAAATAAA
10763 AATATTATTG---ATAAA
1 AATATTATTGAAAATAAA
10778 AA-A-TATTGAAAATAA
1 AATATTATTGAAAATAA
10793 TTTTTGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
13 5 0.19
14 1 0.04
15 7 0.26
16 4 0.15
18 4 0.15
19 6 0.22
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
AATATTATTGAAAATAAA
Found at i:10850 original size:13 final size:13
Alignment explanation
Indices: 10834--10866 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
10824 AAATTAAGTC
10834 TTAAAAATAATTA
1 TTAAAAATAATTA
10847 TTAAAAATAATTA
1 TTAAAAATAATTA
*
10860 TGAAAAA
1 TTAAAAA
10867 ACATATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
TTAAAAATAATTA
Found at i:12265 original size:31 final size:30
Alignment explanation
Indices: 12227--12318 Score: 121
Period size: 31 Copynumber: 3.0 Consensus size: 30
12217 AATTTTATGT
*
12227 TTTCCGATTGGACCATTTTTTTAAAAATATA
1 TTTCCGATTGTACC-TTTTTTTAAAAATATA
* *
12258 TTTCCGATTGTACCCTTTTTTAAAAAACATA
1 TTTCCGATTGTA-CCTTTTTTTAAAAATATA
*
12289 TTTCCGATTGTACCCTTTTTTAAAACATAT
1 TTTCCGATTGTACCTTTTTTTAAAA-ATAT
12319 TTCTTAATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 11 0.21
31 40 0.75
32 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (30 bp):
TTTCCGATTGTACCTTTTTTTAAAAATATA
Found at i:12460 original size:152 final size:152
Alignment explanation
Indices: 12299--12604 Score: 528
Period size: 152 Copynumber: 2.0 Consensus size: 152
12289 TTTCCGATTG
* *
12299 TACCCTTTTTTAAAACATATTTCTTAATT-ACCATTACTAAATAATATTTTAATTATTCCATTAT
1 TACCCTTTTTTAAAACATATTTCTAAATTGA-CATTACTAAATAATATTTTAATTATTCAATTAT
12363 TTTTTTACCATAAATTA-TTCTATTA-TTTTTTTCTAAGAAAAAATTATTCCATTATTAATTATT
65 TTTTTTACCATAAATTATTTC-ATTATTTTTTTTCTAAG-AAAAATTATTCCATTATTAATTATT
*
12426 AGATTATAATATGTATATTAAATTA
128 AGATTATAATACGTATATTAAATTA
*
12451 TACCCTTTTTTAAAGCATATTTCTAAATTGACATTACTAAATAATATTTTAATTATTCAATTATT
1 TACCCTTTTTTAAAACATATTTCTAAATTGACATTACTAAATAATATTTTAATTATTCAATTATT
12516 TTTTTACCATAAATTATTTCATTATTTTTTTTCTAAGAAAAATTATTCCATTATTAATTATTAGA
66 TTTTTACCATAAATTATTTCATTATTTTTTTTCTAAGAAAAATTATTCCATTATTAATTATTAGA
12581 TTATAATACGTATATTAAATTA
131 TTATAATACGTATATTAAATTA
12603 TA
1 TA
12605 AAAAAAAAAG
Statistics
Matches: 147, Mismatches: 4, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
152 131 0.89
153 16 0.11
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (152 bp):
TACCCTTTTTTAAAACATATTTCTAAATTGACATTACTAAATAATATTTTAATTATTCAATTATT
TTTTTACCATAAATTATTTCATTATTTTTTTTCTAAGAAAAATTATTCCATTATTAATTATTAGA
TTATAATACGTATATTAAATTA
Found at i:12677 original size:37 final size:37
Alignment explanation
Indices: 12627--12721 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 37
12617 AATTTTGCTT
12627 TTTGTTTCCAACGTCCTATTTAATTTTGGCTTTTATC
1 TTTGTTTCCAACGTCCTATTTAATTTTGGCTTTTATC
* ** * * *
12664 TTTGTTTTCAACGTTGTATTAAATTTTGTCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGGCTTTTATC
*
12701 TTTGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
12722 GGGCTTAGAT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.55
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGGCTTTTATC
Found at i:15666 original size:23 final size:23
Alignment explanation
Indices: 15624--15667 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
15614 ATTCAACTAA
*
15624 GCTCCGCGCTTATTTTCTCTTTG
1 GCTCCGCGCTTATTTACTCTTTG
15647 GCTCCGCGCCTT-TTTACTCTT
1 GCTCCGCG-CTTATTTACTCTT
15668 GTTCATCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.05, C:0.34, G:0.16, T:0.45
Consensus pattern (23 bp):
GCTCCGCGCTTATTTACTCTTTG
Found at i:17202 original size:15 final size:17
Alignment explanation
Indices: 17183--17216 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17173 CTTCTAACCT
*
17183 TTTTTTTTAT-TCTCTC
1 TTTTTTCTATCTCTCTC
17199 TTTTTTCTATCTCTCTC
1 TTTTTTCTATCTCTCTC
17216 T
1 T
17217 CATTCCCGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTCTATCTCTCTC
Found at i:17251 original size:13 final size:13
Alignment explanation
Indices: 17235--17261 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17225 CTTCTAACAT
17235 TTTTTTCTCTCTC
1 TTTTTTCTCTCTC
17248 TTTTTTCTCTCTC
1 TTTTTTCTCTCTC
17261 T
1 T
17262 CCCATTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTCTCTCTC
Found at i:17252 original size:15 final size:15
Alignment explanation
Indices: 17234--17262 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17224 GCTTCTAACA
17234 TTTTTT-TCTCTCTC
1 TTTTTTCTCTCTCTC
17248 TTTTTTCTCTCTCTC
1 TTTTTTCTCTCTCTC
17263 CCATTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTCTCTCTCTC
Found at i:20677 original size:16 final size:16
Alignment explanation
Indices: 20656--20686 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20646 ACAGTCTGAT
20656 CTGTGGAACATTGTTA
1 CTGTGGAACATTGTTA
20672 CTGTGGAACATTGTT
1 CTGTGGAACATTGTT
20687 TCAATTGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (16 bp):
CTGTGGAACATTGTTA
Done.