Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017356.1 Corchorus olitorius cultivar O-4 contig17389, 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: 30086
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Found at i:1312 original size:43 final size:42
Alignment explanation
Indices: 1258--1548 Score: 383
Period size: 43 Copynumber: 6.8 Consensus size: 42
1248 CATAAGGAAA
* *
1258 AATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAG
1300 AATTGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAG
1 AA-TGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTA-ATAG
* ** *
1343 -ATGCCTCTGTGTTATATATGTGTTTAAGGACTTTTGGAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTTGTAATAG
1385 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAG
1 -AATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAG
*
1428 AATTGCCCCTGTGTTATATATGTGTTTGGGGACTTGGGT-ATAG
1 AA-TGCCCCTGTGTTATATATGTGTTTGGGGACTT-TGTAATAG
* * * *
1471 -ATGCCTCTGCGTTATATATGTGTTTGAGGACTTTTGGAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTTGTAATAG
1513 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 -AATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1549 TTGGTTATTG
Statistics
Matches: 219, Mismatches: 18, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
41 55 0.25
42 21 0.10
43 85 0.39
44 58 0.26
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (42 bp):
AATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAG
Found at i:1406 original size:128 final size:128
Alignment explanation
Indices: 1257--1548 Score: 530
Period size: 128 Copynumber: 2.3 Consensus size: 128
1247 CCATAAGGAA
* *
1257 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
* *
1322 TGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTAAGGACTTTTGGAATAG
66 TGTTTGGGGACTTGGATATAGATGCCTCTGCGTTATATATGTGTTTAAGGACTTTTGGAATAG
1385 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
* *
1450 TGTTTGGGGACTTGGGTATAGATGCCTCTGCGTTATATATGTGTTTGAGGACTTTTGGAATAG
66 TGTTTGGGGACTTGGATATAGATGCCTCTGCGTTATATATGTGTTTAAGGACTTTTGGAATAG
1513 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1549 TTGGTTATTG
Statistics
Matches: 158, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 158 1.00
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (128 bp):
AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
TGTTTGGGGACTTGGATATAGATGCCTCTGCGTTATATATGTGTTTAAGGACTTTTGGAATAG
Found at i:1413 original size:85 final size:85
Alignment explanation
Indices: 1258--1548 Score: 385
Period size: 85 Copynumber: 3.4 Consensus size: 85
1248 CATAAGGAAA
* * *
1258 AATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATGT
1 AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATGCCCCTGTGTTATATATGT
1323 GTTTGGGGACTTTGATATAG
66 GTTTGGGGACTTTGATATAG
* *
1343 -ATGCCTCTGTGTTATATATGTGTTTAAGGACTTTTGGAATAGAAATGCCCCTGTGTTATATATG
1 AATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGGAATAGAAATGCCCCTGTGTTATATATG
1407 TGTTTGGGGACTTTG-TAATAG
65 TGTTTGGGGACTTTGAT-ATAG
* * * * *
1428 AATTGCCCCTGTGTTATATATGTGTTTGGGGACTTGGGTATAG--ATGCCTCTGCGTTATATATG
1 AA-TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATGCCCCTGTGTTATATATG
*
1491 TGTTTGAGGACTTTTGGA-ATAG
65 TGTTTGGGGAC-TTT-GATATAG
*
1513 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 -AATGCCCCTGTGTTATATATGTGTTTGAGGACTTT
1549 TTGGTTATTG
Statistics
Matches: 186, Mismatches: 12, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
84 59 0.32
85 88 0.47
86 12 0.06
87 27 0.15
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (85 bp):
AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATGCCCCTGTGTTATATATGT
GTTTGGGGACTTTGATATAG
Found at i:3929 original size:30 final size:31
Alignment explanation
Indices: 3881--3941 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
3871 GAAGTTCGTG
*
3881 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGACTCATTGAAGACTTATTTCAAGA
* *
3912 TTTGAAGAC-CTTTGAAGATTTATTTCAAGA
1 TTTGAAGACTCATTGAAGACTTATTTCAAGA
3942 GGAAGAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (31 bp):
TTTGAAGACTCATTGAAGACTTATTTCAAGA
Found at i:15229 original size:129 final size:128
Alignment explanation
Indices: 15088--15424 Score: 602
Period size: 129 Copynumber: 2.6 Consensus size: 128
15078 CCATAAGGAA
* *
15088 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
15153 TGTTTGGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
66 TGTTT-GGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
15217 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
* *
15282 TGTTTGGGGACTTGGGTATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
66 TGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
* *
15345 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTTGGAATAGAAATGCCCCTGTGTTATATAT
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTTGTAATAGAATTGCCCCTGTGTTATATAT
15410 GTGTTTGGGGACTTT
65 GTGTTTGGGGACTTT
15425 TTGGTTATTG
Statistics
Matches: 200, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
128 89 0.44
129 111 0.56
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (128 bp):
AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
TGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
Found at i:15275 original size:172 final size:171
Alignment explanation
Indices: 15091--15424 Score: 523
Period size: 172 Copynumber: 1.9 Consensus size: 171
15081 TAAGGAAAAA
* *
15091 TGCCTCTGTGTTATATATGTGTTTGAGGACTT-TGTAATAGAATTGCCCCTGTGTTATATATGTG
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTGGGT-ATAG-A-TGCCCCTGTGTTATATATGTG
* *
15155 TTTGGGGGAC-TTT-GATATAG-ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
63 TTT-GAGGACTTTTGGA-ATAGAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
15217 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAAT
126 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAAT
* *
15263 TGCCCCTGTGTTATATATGTGTTTGGGGACTTGGGTATAGATGCCTCTGTGTTATATATGTGTTT
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTGGGTATAGATGCCCCTGTGTTATATATGTGTTT
*
15328 GAGGACTTTTGGAATAGAAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTTGGAATAGAAAT
66 GAGGACTTTTGGAATAG-AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAAAT
15393 GCCCCTGTGTTATATATGTGTTTGGGGACTTT
130 GCCCCTGTGTTATATATGTGTTTGGGGACTTT
15425 TTGGTTATTG
Statistics
Matches: 150, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
169 5 0.03
170 30 0.20
171 3 0.02
172 110 0.73
173 2 0.01
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.41
Consensus pattern (171 bp):
TGCCCCTGTGTTATATATGTGTTTGAGGACTTGGGTATAGATGCCCCTGTGTTATATATGTGTTT
GAGGACTTTTGGAATAGAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAAATG
CCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAAT
Found at i:15425 original size:44 final size:43
Alignment explanation
Indices: 15088--15424 Score: 486
Period size: 44 Copynumber: 7.8 Consensus size: 43
15078 CCATAAGGAA
* * *
15088 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGGAATAG
*
15131 AATTGCCCCTGTGTTATATATGTGTTTGGGGGACTTT-GATATAG
1 AAATGCCCCTGTGTTATATATGTGTTT-GGGGACTTTGGA-ATAG
* *
15175 --ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTTGGAATAG
*
15217 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAG
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGGAATAG
* * *
15260 AATTGCCCCTGTGTTATATATGTGTTTGGGGACTTGGGTATAG
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGGAATAG
* *
15303 --ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTTGGAATAG
15345 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTTGGAATAG
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTTGGAATAG
15389 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
15425 TTGGTTATTG
Statistics
Matches: 264, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
41 33 0.12
42 38 0.14
43 79 0.30
44 114 0.43
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (43 bp):
AAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGGAATAG
Found at i:17377 original size:14 final size:14
Alignment explanation
Indices: 17360--17390 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
17350 AACCAAGCAG
17360 AACCCCACCAACAA
1 AACCCCACCAACAA
17374 AACCCCACCAACAA
1 AACCCCACCAACAA
17388 AAC
1 AAC
17391 AAATCCCAAA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (14 bp):
AACCCCACCAACAA
Found at i:19225 original size:20 final size:20
Alignment explanation
Indices: 19200--19238 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
19190 AGCAATCAAA
19200 GCAATCAAAGTAATTGATTT
1 GCAATCAAAGTAATTGATTT
19220 GCAATCAAAGTAATTGATT
1 GCAATCAAAGTAATTGATT
19239 GACCAAGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (20 bp):
GCAATCAAAGTAATTGATTT
Found at i:23858 original size:20 final size:20
Alignment explanation
Indices: 23833--23871 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
23823 AGCAATCAAA
23833 GCAATCAAAGTAATTGATTT
1 GCAATCAAAGTAATTGATTT
23853 GCAATCAAAGTAATTGATT
1 GCAATCAAAGTAATTGATT
23872 GACCAAGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (20 bp):
GCAATCAAAGTAATTGATTT
Found at i:27416 original size:100 final size:104
Alignment explanation
Indices: 27289--27536 Score: 299
Period size: 107 Copynumber: 2.4 Consensus size: 104
27279 AATTTTTCTA
* **
27289 ACCCTTAAAATAAAATTTTAATTTTAATTT-AGACTAAAC-GTG-AATTAGCTATATATTTTA-T
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGACTAAACTGTGAAATTAGCTATATATTTTAGT
*
27350 TTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
66 TT-TAAAACCCTATAACAATAATTATTAATTATGAAATTT
* * * * *
27389 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGACTAAAC-T-GTGAAATTAGCTATATATTTTA
*
27454 GTTTTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
64 GTTTTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
* * * *
27496 ACGCTTAAAATAAAAACAAAATTTTAATTTGGGGCTAAACT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGACTAAACT
27537 TAGGGGTTGT
Statistics
Matches: 128, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
100 27 0.21
101 7 0.05
104 3 0.02
105 32 0.25
106 4 0.03
107 55 0.43
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (104 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGAGACTAAACTGTGAAATTAGCTATATATTTTAGT
TTTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:27517 original size:107 final size:105
Alignment explanation
Indices: 27342--27539 Score: 326
Period size: 107 Copynumber: 1.9 Consensus size: 105
27332 ATTAGCTATA
* *
27342 TATTTTATTTCTAAAACCCTATAACAATATTATTAATTATGGAATTTACCCTTAAAATAAAAATA
1 TATTTTATTTCTAAAACCCTATAACAATATTATTAATTATGAAATTTACCCTTAAAATAAAAACA
27407 AAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTG
66 AAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTG
* *
27447 TATTTTAGTTT-TAAAACCCTATAACAATAAATTATTAATTTTGAAATTTACGCTTAAAATAAAA
1 TATTTTA-TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTTACCCTTAAAATAAAA
27511 ACAAAATTTTAATTTGGGGCTAAACTTAG
63 ACAAAATTTTAATTTGGGGCTAAACTTAG
27540 GGGTTGTTTG
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
105 24 0.28
106 3 0.03
107 59 0.69
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (105 bp):
TATTTTATTTCTAAAACCCTATAACAATATTATTAATTATGAAATTTACCCTTAAAATAAAAACA
AAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTG
Done.