Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023955.1 Corchorus olitorius cultivar O-4 contig23988, 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: 21758
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:43 original size:30 final size:30
Alignment explanation
Indices: 1--615 Score: 647
Period size: 30 Copynumber: 20.5 Consensus size: 30
*
1 ACAGGATTAAAATAAAGCAACGATCCTCAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* *
31 ACAAGATAAAAATAAAGCAATGATCCTCAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* *
61 ACAAGATTAAAATGAAGTGAAGTAATGATCCTCAA
1 ACAGGATTAAAAT--A---AAGCAATGATCCTCAA
* *
96 CCAGGATT-AAATAAAGCAACGATCCTCAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
**
125 ACAGGACAAAAATAAAGCAATGATCCTCAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* * *
155 ACAGGATTATAATAAAGTAATGATCCTTAGA
1 ACAGGATTAAAATAAAGCAATGATCCTCA-A
*
186 A-AGGATTAAAAT--A--AA-GATCCTTAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* * *
210 TCAGGATTAAAATAAATCAACGATCCTCAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* **
240 ACATGAAAAAAATAAAGCAATGATCCTCAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* * *
270 ACATGATTAAAATAAAGTAATGATCCTCGA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
** *
300 ACAGGATTAAAAGGAAGCAATGATCCTCGA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* *
330 CCAGGATAAAAATAAAGCAATGATCCTCAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* *
360 ACAGGATTAAAATAGAGCGATGATCCTCAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* * *
390 ACATGATTAAAATGAAGTAATGATCCT-AA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* *
419 ACCAGGATTAACATAGAGCAAAT-ATCCTCAA
1 A-CAGGATTAAAATAAAGC-AATGATCCTCAA
* *
450 CCAGGATAAAAATAAAGCAATGATCCTCAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* * *
480 ACAGGATTAAAATGAAGTAATGATCGTCAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* * *
510 ACAGGATTAACATACAGCAACGATCCTCAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* * *
540 CCAGTATTAAAATAAAGCAATGATCCTTAA
1 ACAGGATTAAAATAAAGCAATGATCCTCAA
* *
570 CCAGGATTAAAATAAAGCAAAT-ATCCTCCA
1 ACAGGATTAAAATAAAGC-AATGATCCTCAA
*
600 CCAGGATTAAAATAAA
1 ACAGGATTAAAATAAA
616 ACTGATAACC
Statistics
Matches: 489, Mismatches: 78, Indels: 36
0.81 0.13 0.06
Matches are distributed among these distances:
24 1 0.00
25 19 0.04
26 2 0.00
27 1 0.00
28 1 0.00
29 27 0.06
30 401 0.82
31 10 0.02
32 2 0.00
34 4 0.01
35 21 0.04
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.20
Consensus pattern (30 bp):
ACAGGATTAAAATAAAGCAATGATCCTCAA
Found at i:204 original size:25 final size:25
Alignment explanation
Indices: 167--225 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
157 AGGATTATAA
* *
167 TAAAGTAATGATCCTTAGA-AAGGAT
1 TAAAATAAAGATCCTTA-ATAAGGAT
*
192 TAAAATAAAGATCCTTAATCAGGAT
1 TAAAATAAAGATCCTTAATAAGGAT
217 TAAAATAAA
1 TAAAATAAA
226 TCAACGATCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (25 bp):
TAAAATAAAGATCCTTAATAAGGAT
Found at i:1186 original size:168 final size:168
Alignment explanation
Indices: 778--1336 Score: 842
Period size: 168 Copynumber: 3.4 Consensus size: 168
768 AAACAAGGAT
* *
778 CTTAAACCTGAATTTTTGATGAAAAATTTGATGAAATCAAATGGTACCCGGAGGTTTTACCGATT
1 CTTAAACATGAATTTTTGATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTACCGATT
* *
843 GCCCAGAGGACTTATCAGAATTACTACCCGGAGGTTTCTGAATTTGTGCCCGGAAGACTTTACCA
66 GCCCGGAGGACTTATCAGAATTACTACCCGGAGGTTTCTGAATTTGTGCCCGGAGGAC-TTACCA
*
908 ATGCAAACTCTGAATAGAGACCTTAAACAAGGATTTTAAA
130 ACGCAAACTCTGAATAGAGACCTTAAACAAGGATTTT-AA
*
948 CTT----A--AATTTTTGATGAAAAATTTGATGAAATCAAATGGTACCCGGAGGTTTTACCGATT
1 CTTAAACATGAATTTTTGATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTACCGATT
*
1007 GCCCGGAGGACTTATCAGAATTACTACCCGGAGGTTTCTGACTTTGTGCCCGGAGGACTTACCAA
66 GCCCGGAGGACTTATCAGAATTACTACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAA
1072 CGCAAACTCTGAATAGAGACCTTAAACAAGGATTTTAA
131 CGCAAACTCTGAATAGAGACCTTAAACAAGGATTTTAA
* * * *
1110 CTTAAACATGAACTTTTGGTGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATT
1 CTTAAACATGAATTTTTGATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTACCGATT
* * * *
1175 GCCTGGAGGACTCATCAAAATTACTACCCGGAGGTTTCTGAATTTGTGCCCGGAGTACTTACCAA
66 GCCCGGAGGACTTATCAGAATTACTACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAA
* * * *
1240 CGCATACTATGAATAGAGACCTTGACCAAGGATTTTAA
131 CGCAAACTCTGAATAGAGACCTTAAACAAGGATTTTAA
* * * * *
1278 CTTAAACATGAATTTTTGGTGAAAAACTTGATAAAATGAAATGATACCCGGAGATTTTA
1 CTTAAACATGAATTTTTGATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTA
1337 TCAAATGGAA
Statistics
Matches: 360, Mismatches: 23, Indels: 14
0.91 0.06 0.04
Matches are distributed among these distances:
162 5 0.01
163 42 0.12
164 110 0.31
166 1 0.00
168 199 0.55
170 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (168 bp):
CTTAAACATGAATTTTTGATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTACCGATT
GCCCGGAGGACTTATCAGAATTACTACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAA
CGCAAACTCTGAATAGAGACCTTAAACAAGGATTTTAA
Found at i:1463 original size:69 final size:69
Alignment explanation
Indices: 1382--1556 Score: 287
Period size: 69 Copynumber: 2.5 Consensus size: 69
1372 AAGTAAGACT
*
1382 TGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTACATGGCTTGGATGGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTACATGGCTTGGATGGAACCAAGGCTT
1447 AAAC
66 AAAC
* ** *
1451 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCTTATGTGGCTTGGATTGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTACATGGCTTGGATGGAACCAAGGCTT
*
1516 CAAC
66 AAAC
*
1520 TGACTCGTATGGAAACGAGTTTGCCTTGTGGAAAAGC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGC
1557 ATAAAGCATT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 99 1.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (69 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTACATGGCTTGGATGGAACCAAGGCTT
AAAC
Found at i:1577 original size:69 final size:67
Alignment explanation
Indices: 1382--1577 Score: 266
Period size: 69 Copynumber: 2.8 Consensus size: 67
1372 AAGTAAGACT
* *
1382 TGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTACATGGCTTGGATGGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCATA-A-GGCTTGGATGGAACCAAGGCTT
1447 AAAC
64 AAAC
** *
1451 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCTTATGTGGCTTGGATTGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGC--ATAAGGCTTGGATGGAACCAAGGCTT
*
1516 CAAC
64 AAAC
* *
1520 TGACTCGTATGGAAACGAGTTTGCCTTGTGGAAAAGCATAAAGCATTCGGATGGAACC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCATAAGGC-TT-GGATGGAACC
1578 GATGCAAAAT
Statistics
Matches: 112, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
67 4 0.04
68 2 0.02
69 105 0.94
71 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (67 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCATAAGGCTTGGATGGAACCAAGGCTTAA
AC
Found at i:3245 original size:30 final size:31
Alignment explanation
Indices: 3197--3258 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 31
3187 TGATTTGATT
*
3197 TGATTTTTTTTTTATTTTTTG-ATTTC-TGA
1 TGATTTTTTTATTATTTTTTGAATTTCTTGA
3226 TGATTTTTTTATTATTTTTTGAATTTCTTGA
1 TGATTTTTTTATTATTTTTTGAATTTCTTGA
3257 TG
1 TG
3259 GAGTGGACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 20 0.67
30 5 0.17
31 5 0.17
ACGTcount: A:0.16, C:0.03, G:0.11, T:0.69
Consensus pattern (31 bp):
TGATTTTTTTATTATTTTTTGAATTTCTTGA
Found at i:3643 original size:9 final size:8
Alignment explanation
Indices: 3623--3674 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
3613 AGTGCCTTTA
*
3623 TTTTAATT
1 TTTTCATT
3631 TTTTCATTT
1 TTTTCA-TT
3640 TTTTCA-T
1 TTTTCATT
3647 TTTTCATT
1 TTTTCATT
3655 TTTTCATT
1 TTTTCATT
**
3663 TCATCATT
1 TTTTCATT
3671 TTTT
1 TTTT
3675 TTATGGGAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
7 7 0.19
8 22 0.59
9 8 0.22
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTCATT
Found at i:3649 original size:16 final size:16
Alignment explanation
Indices: 3630--3675 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
3620 TTATTTTAAT
3630 TTTTTCATTTTTTTCA
1 TTTTTCATTTTTTTCA
3646 TTTTTCA-TTTTTTCA
1 TTTTTCATTTTTTTCA
*
3661 TTTCATCATTTTTTT
1 TTT-TTCATTTTTTT
3676 TATGGGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 11 0.41
16 10 0.37
17 6 0.22
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTCATTTTTTTCA
Found at i:3674 original size:24 final size:24
Alignment explanation
Indices: 3623--3673 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3613 AGTGCCTTTA
**
3623 TTTTAATTTTTTCATTTTTTTCAT
1 TTTTAATTTTTTCATTTTCATCAT
*
3647 TTTTCATTTTTTCA-TTTCATCAT
1 TTTTAATTTTTTCATTTTCATCAT
3670 TTTT
1 TTTT
3674 TTTATGGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTAATTTTTTCATTTTCATCAT
Found at i:7482 original size:18 final size:17
Alignment explanation
Indices: 7445--7493 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
7435 TATTGATTCC
7445 TTTCCATTTT-TTCATT
1 TTTCCATTTTCTTCATT
*
7461 TTTCCATTTTCTGTCCTT
1 TTTCCATTTTCT-TCATT
*
7479 TTTCAATTTTCTTCA
1 TTTCCATTTTCTTCA
7494 ACTTTGACCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 10 0.36
17 3 0.11
18 15 0.54
ACGTcount: A:0.12, C:0.22, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTCCATTTTCTTCATT
Found at i:10610 original size:13 final size:14
Alignment explanation
Indices: 10592--10620 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10582 TTTTTGTCCA
10592 TTTTTTG-GTTTTT
1 TTTTTTGTGTTTTT
10605 TTTTTTGTGTTTTT
1 TTTTTTGTGTTTTT
10619 TT
1 TT
10621 GCAAAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (14 bp):
TTTTTTGTGTTTTT
Found at i:11082 original size:27 final size:26
Alignment explanation
Indices: 11043--11167 Score: 103
Period size: 27 Copynumber: 4.6 Consensus size: 26
11033 TAAGGGTTCG
* *
11043 AATGACCACAATGCCCTTGACTGTACA
1 AATGACCAAAATGCCCTGGA-TGTACA
* * *
11070 AATGACTAGAATGCCCCTGGATGTGCA
1 AATGACCAAAATG-CCCTGGATGTACA
11097 AATGACCAAAATGCCCCTGGAATTGT--A
1 AATGACCAAAATG-CCCTGG-A-TGTACA
*
11124 AATGACCAAAATGCCTCTGGATTTTGA-A
1 AATGACCAAAATGCC-CTGGA-TGT-ACA
11152 AATGACCAAAATGCCC
1 AATGACCAAAATGCCC
11168 CTAGTTGATC
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
26 6 0.07
27 53 0.62
28 23 0.27
29 3 0.04
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (26 bp):
AATGACCAAAATGCCCTGGATGTACA
Found at i:11163 original size:28 final size:27
Alignment explanation
Indices: 11069--11169 Score: 130
Period size: 27 Copynumber: 3.7 Consensus size: 27
11059 TTGACTGTAC
* * * *
11069 AAATGACTAGAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTGGATTTGA
* *
11096 AAATGACCAAAATGCCCCTGGAATTGT
1 AAATGACCAAAATGCCCCTGGATTTGA
*
11123 AAATGACCAAAATGCCTCTGGATTTTGA
1 AAATGACCAAAATGCCCCTGGA-TTTGA
11151 AAATGACCAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
11170 AGTTGATCCT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
27 43 0.67
28 21 0.33
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATTTGA
Found at i:16825 original size:298 final size:298
Alignment explanation
Indices: 16284--16863 Score: 1070
Period size: 298 Copynumber: 1.9 Consensus size: 298
16274 TTGCCTATAA
* * *
16284 TAGTGAGCATTGTCTATTGTTGACTAAGATCTTTCTAGTTCTTAAAGCAATAAATTACTTGAATC
1 TAGTAAGCATTGTCTATTGTTGACTAAGAACTTTCTAGTTCTTAAAGCAATAAATTACTTAAATC
* *
16349 TCGTAGACGCTTGGAACTAGGTTAGTATATTTGTTAGGATTTAGTCTAGGACTTGCGTCATGACT
66 TAGTACACGCTTGGAACTAGGTTAGTATATTTGTTAGGATTTAGTCTAGGACTTGCGTCATGACT
* *
16414 AATGAAGACTAAGAAAAGATACGGATTAATGGTCGATGATGTTAATCTATGCCATCTATTTATCA
131 AATGAAGACTAAGAAAAGATACGGATTAATGGTCGATGACGTTAATCTACGCCATCTATTTATCA
*
16479 AGTTAGATACCAATTGAAGCCAAGGATTAAATCCTTTTATCCCAAGAGTGTGATTGTCTTGAAAT
196 AGTTAGATACCAATTGAAGCCAAGGATCAAATCCTTTTATCCCAAGAGTGTGATTGTCTTGAAAT
16544 TGGAATATCTATTTAATTGTTTGAATCTAGTAGACGCT
261 TGGAATATCTATTTAATTGTTTGAATCTAGTAGACGCT
16582 TAGTAAGCATTGTCTATTGTTGACTAAGAACTTTCTAGTTCTTAAAGCAATAAATTACTTAAATC
1 TAGTAAGCATTGTCTATTGTTGACTAAGAACTTTCTAGTTCTTAAAGCAATAAATTACTTAAATC
*
16647 TAGTACACGCTTGGAACTAGTTTAGTATATTTGTTAGGATTTAGTCTAGGACTTGCGTCATGACT
66 TAGTACACGCTTGGAACTAGGTTAGTATATTTGTTAGGATTTAGTCTAGGACTTGCGTCATGACT
*
16712 AATGAAGACTAAGGAAAGATACGGATTAATGGTCGATGACGTTAATCTACGCCATCTATTTATCA
131 AATGAAGACTAAGAAAAGATACGGATTAATGGTCGATGACGTTAATCTACGCCATCTATTTATCA
16777 AGTTAGATACCAATTGAAGCCAAGGATCAAATCCTTTTATCCCAAGAGTGTGATTGTCTTGAAAT
196 AGTTAGATACCAATTGAAGCCAAGGATCAAATCCTTTTATCCCAAGAGTGTGATTGTCTTGAAAT
16842 TGGAATATCTATTTAATTGTTT
261 TGGAATATCTATTTAATTGTTT
16864 CTTTAATCTC
Statistics
Matches: 272, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
298 272 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (298 bp):
TAGTAAGCATTGTCTATTGTTGACTAAGAACTTTCTAGTTCTTAAAGCAATAAATTACTTAAATC
TAGTACACGCTTGGAACTAGGTTAGTATATTTGTTAGGATTTAGTCTAGGACTTGCGTCATGACT
AATGAAGACTAAGAAAAGATACGGATTAATGGTCGATGACGTTAATCTACGCCATCTATTTATCA
AGTTAGATACCAATTGAAGCCAAGGATCAAATCCTTTTATCCCAAGAGTGTGATTGTCTTGAAAT
TGGAATATCTATTTAATTGTTTGAATCTAGTAGACGCT
Found at i:17774 original size:17 final size:15
Alignment explanation
Indices: 17740--17771 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
17730 TTTTTATTTT
17740 TACATTTTCTCTCTA
1 TACATTTTCTCTCTA
17755 TACATTTTCTCTCTA
1 TACATTTTCTCTCTA
17770 TA
1 TA
17772 TACTAAATGC
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:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (15 bp):
TACATTTTCTCTCTA
Found at i:18279 original size:16 final size:16
Alignment explanation
Indices: 18258--18288 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
18248 TATAGATGAA
18258 TATTTAATTAAAGAAT
1 TATTTAATTAAAGAAT
18274 TATTTAATTAAAGAA
1 TATTTAATTAAAGAA
18289 AGAGAATGAA
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:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
TATTTAATTAAAGAAT
Done.