Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013972.1 Corchorus olitorius cultivar O-4 contig14005, 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: 45114
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:8183 original size:457 final size:458
Alignment explanation
Indices: 7378--8294 Score: 1703
Period size: 457 Copynumber: 2.0 Consensus size: 458
7368 ACTTTATTAT
*
7378 AAGGGCAATTATTTGAGACACTGATAGTATAAAAAATTGGACTCTACAAGCGAAGTGAGAAGTTG
1 AAGGGCAATTATTTGAGACACTGACAGTATAAAAAATTGGACTCTACAAGCGAAGTGAGAAGTTG
*
7443 ATACACACCTATTTTATGAATTACTTTTGTTTTTAAAATTCAAAACTATTTTGTAGACGACACAT
66 ATACACACCTATTTTATGAATTACTTTTGTTTTTAAAATTCAAAACTATTTTGTAGACAACACAT
*
7508 GTCAACTCTTAACCCCCGCATGTGTAGTGTCTTAAACTCGAATGCTGTTTATTGTATAATTGATC
131 GTCAACTCTTAACCCCCGCATGTGTAGTCTCTTAAACTCGAATGCTGTTTATTGTATAATTGATC
* * * *
7573 GGTCGTTGCACAAACCACAAGATAAATCCCCACAAACCTATAACTATTAGTTAGAGCAAGTAGGG
196 GATCGTTGAACAAACCACAAGATAAATCCCCACAAACCTATAACTATTAGCTAGAACAAGTAGGG
*
7638 GTCGAATTGCAAGAGAAGGTGGAAACAAGTTAAAGCTAAATTACACTAAAGAAAGTCTTACCAAA
261 GTCGAATTGCAAGAGAAGGTGGAAACAAATTAAAGCTAAATTACACTAAAGAAAGTCTTACCAAA
*
7703 GGGGATTTTTTATGGGTTCTCAAAATAACTAAACTAAACTAGAAAACAATTATGTAAAACTAAAC
326 GGGGATTTTTTATGGGTTCTCAAAATAACTAAACTAAACTAGAAAACAATTAAGTAAAACTAAAC
7768 TAAGGATTAAGAAAACAATTAATTAAAAACATACTTCTTTTCCTCTAGGTAAGTATTTTGATCAA
391 TAAGGATTAAGAAAACAATTAATTAAAAACATACTTCTTTTCCTCTAGGTAAGTATTTTGATCAA
7833 ATA
456 ATA
*
7836 AAGGGCAATTATTTGAGACACTGACAGTAT-AAAAATTGGACTCTACAAGCGGAGTGAGAAGTTG
1 AAGGGCAATTATTTGAGACACTGACAGTATAAAAAATTGGACTCTACAAGCGAAGTGAGAAGTTG
7900 ATACACACCTATTTTATGAATTACTTTTGTTTTTAAAATTCAAAACTATTTTGTAGACAACACAT
66 ATACACACCTATTTTATGAATTACTTTTGTTTTTAAAATTCAAAACTATTTTGTAGACAACACAT
7965 GTCAACTCTTAACCCCCGCATGTGTAGTCTCTTAAACTCGAATGCTGTTTATTGTATAATTGATC
131 GTCAACTCTTAACCCCCGCATGTGTAGTCTCTTAAACTCGAATGCTGTTTATTGTATAATTGATC
8030 GATCGTTGAACAAACCACAAGATAAATCCCCACAAACCTATAACTATTAGCTAGAACAAGTAGGG
196 GATCGTTGAACAAACCACAAGATAAATCCCCACAAACCTATAACTATTAGCTAGAACAAGTAGGG
*
8095 GTCGAATT-CCAGAGAAGGTGGAAACAAAATTAAAGCTAAATTACACTAAAGAAAGTCTTACCAA
261 GTCGAATTGCAAGAGAAGGTGGAAAC-AAATTAAAGCTAAATTACACTAAAGAAAGTCTTACCAA
8159 AGGGGATTTTTTATGGGTTCTCAAAATAACTAAACTAAACTAGAAAACAATTAAGTAAAACTAAA
325 AGGGGATTTTTTATGGGTTCTCAAAATAACTAAACTAAACTAGAAAACAATTAAGTAAAACTAAA
*
8224 CTAAGGATTAAGAAAACAATTAATTAAAAACATACTTCTTTTCCTCTAGGTATGTATTTTGATCA
390 CTAAGGATTAAGAAAACAATTAATTAAAAACATACTTCTTTTCCTCTAGGTAAGTATTTTGATCA
8289 AATA
455 AATA
8293 AA
1 AA
8295 CCATGAATCC
Statistics
Matches: 446, Mismatches: 12, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
456 16 0.04
457 401 0.90
458 29 0.07
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.29
Consensus pattern (458 bp):
AAGGGCAATTATTTGAGACACTGACAGTATAAAAAATTGGACTCTACAAGCGAAGTGAGAAGTTG
ATACACACCTATTTTATGAATTACTTTTGTTTTTAAAATTCAAAACTATTTTGTAGACAACACAT
GTCAACTCTTAACCCCCGCATGTGTAGTCTCTTAAACTCGAATGCTGTTTATTGTATAATTGATC
GATCGTTGAACAAACCACAAGATAAATCCCCACAAACCTATAACTATTAGCTAGAACAAGTAGGG
GTCGAATTGCAAGAGAAGGTGGAAACAAATTAAAGCTAAATTACACTAAAGAAAGTCTTACCAAA
GGGGATTTTTTATGGGTTCTCAAAATAACTAAACTAAACTAGAAAACAATTAAGTAAAACTAAAC
TAAGGATTAAGAAAACAATTAATTAAAAACATACTTCTTTTCCTCTAGGTAAGTATTTTGATCAA
ATA
Found at i:9523 original size:21 final size:21
Alignment explanation
Indices: 9485--9529 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
9475 GACGCCCACA
* *
9485 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGTCTGAACACCCAGG
*
9506 TGGTTTGTCTGATCACCCAGG
1 TGGTTTGTCTGAACACCCAGG
9527 TGG
1 TGG
9530 GCAGTGTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (21 bp):
TGGTTTGTCTGAACACCCAGG
Found at i:13061 original size:149 final size:149
Alignment explanation
Indices: 12790--13066 Score: 439
Period size: 149 Copynumber: 1.9 Consensus size: 149
12780 TTCGTTTTAT
* * * * * *
12790 ATCTTATTGCCATAGTTTGCTTATTTACTTGGTGCTATTAATTTGTTTTGTGTTTCTAGTTTGTT
1 ATCTTATTGCCATAGTCTGCTTATTTACTTGATGCCATTAATCTATTTTGTGTTCCTAGTTTGTT
*
12855 TTCTCAAGCTTTTGTAGGTTTAAATCGTCCCTCTCTGTGGATTCGACCAATGCTTACCCTGTTCC
66 TTCTCAAGCTTTTGTAGGTTTAAATCGTCCCTCTATGTGGATTCGACCAATGCTTACCCTGTTCC
12920 ACCTATTTAGTAGTATTAC
131 ACCTATTTAGTAGTATTAC
*
12939 ATCTTATTGCCATTGTCTGCTTATTTACTTGATGCCATTAATCTATTTTGTGTTCCTAGTTTGTT
1 ATCTTATTGCCATAGTCTGCTTATTTACTTGATGCCATTAATCTATTTTGTGTTCCTAGTTTGTT
** *
13004 TTCTCAAGCTTTTGTAGGTTTAAATCGTCCCT-TGATGTGGATTCGACCCTTGTTTACCCTGTT
66 TTCTCAAGCTTTTGTAGGTTTAAATCGTCCCTCT-ATGTGGATTCGACCAATGCTTACCCTGTT
13067 TTTACCTATT
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
148 1 0.01
149 115 0.99
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.47
Consensus pattern (149 bp):
ATCTTATTGCCATAGTCTGCTTATTTACTTGATGCCATTAATCTATTTTGTGTTCCTAGTTTGTT
TTCTCAAGCTTTTGTAGGTTTAAATCGTCCCTCTATGTGGATTCGACCAATGCTTACCCTGTTCC
ACCTATTTAGTAGTATTAC
Found at i:16912 original size:36 final size:36
Alignment explanation
Indices: 16865--16935 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
16855 TAATGAGTCT
**
16865 CCTCAGCAGAAGCAAGCTTACCAGTAGAAAGTGTCG
1 CCTCAGCAGAAGCAAGCTTACCAACAGAAAGTGTCG
*
16901 CCTCAGCAGAAGTAAGCTTACCAACAGAAAGTGTC
1 CCTCAGCAGAAGCAAGCTTACCAACAGAAAGTGTC
16936 TTGTAGTAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (36 bp):
CCTCAGCAGAAGCAAGCTTACCAACAGAAAGTGTCG
Found at i:18146 original size:14 final size:14
Alignment explanation
Indices: 18127--18154 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18117 CGTTTTGGAT
18127 GTTAGAGAATAGAA
1 GTTAGAGAATAGAA
18141 GTTAGAGAATAGAA
1 GTTAGAGAATAGAA
18155 AATGACAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (14 bp):
GTTAGAGAATAGAA
Found at i:18900 original size:45 final size:45
Alignment explanation
Indices: 18850--18941 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
18840 CGAGATGCTA
18850 GAAATAAGGCAATGCCAATAGCTGCGCCTCCCTCAAATGATCCTG
1 GAAATAAGGCAATGCCAATAGCTGCGCCTCCCTCAAATGATCCTG
18895 GAAATAAGGCAATGCCAATAGCTGCGCCTCCCTCAAATGATCCTG
1 GAAATAAGGCAATGCCAATAGCTGCGCCTCCCTCAAATGATCCTG
18940 GA
1 GA
18942 CCAAGTGGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.20
Consensus pattern (45 bp):
GAAATAAGGCAATGCCAATAGCTGCGCCTCCCTCAAATGATCCTG
Found at i:19452 original size:13 final size:13
Alignment explanation
Indices: 19413--19457 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
19403 ATTTAATTCG
19413 ACAATACTTTAAA
1 ACAATACTTTAAA
** *
19426 TGATTACTTCTAAA
1 ACAATACTT-TAAA
19440 ACAATACTTTAAA
1 ACAATACTTTAAA
19453 ACAAT
1 ACAAT
19458 GCAGTCTGGC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (13 bp):
ACAATACTTTAAA
Found at i:19544 original size:21 final size:21
Alignment explanation
Indices: 19518--19558 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
19508 CATCTACAAT
19518 GGTTGCTTCTGCTTCTGCAAG
1 GGTTGCTTCTGCTTCTGCAAG
*
19539 GGTTGCTTCTTCTTCTGCAA
1 GGTTGCTTCTGCTTCTGCAA
19559 CACAGTCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.41
Consensus pattern (21 bp):
GGTTGCTTCTGCTTCTGCAAG
Found at i:19706 original size:27 final size:26
Alignment explanation
Indices: 19668--19752 Score: 107
Period size: 27 Copynumber: 3.2 Consensus size: 26
19658 GTGTCAAAAA
*
19668 GTCTTAAGTTTAGGAGCTAAATCATTT
1 GTCTAAAGTTTAGGAGCTAAATC-TTT
19695 GTCTAAAGTTTAGGAGCTAAATCTTTT
1 GTCTAAAGTTTAGGAGCTAAATC-TTT
** *
19722 GTCTAAAGTAAAGGAGATAAATCTTT
1 GTCTAAAGTTTAGGAGCTAAATCTTT
19748 CGTCT
1 -GTCT
19753 TAACTTTATA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
26 3 0.06
27 49 0.94
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (26 bp):
GTCTAAAGTTTAGGAGCTAAATCTTT
Found at i:22250 original size:31 final size:31
Alignment explanation
Indices: 22215--22286 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
22205 TAAATTATTG
*
22215 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
22246 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
22277 CAAATTAAAA
1 CAAATTAAAA
22287 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:24689 original size:109 final size:109
Alignment explanation
Indices: 24498--24715 Score: 409
Period size: 109 Copynumber: 2.0 Consensus size: 109
24488 CTATTATATA
*
24498 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAATAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
24563 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
*
24607 TATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
*
24672 CAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
24716 AAAATGACTA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 106 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (109 bp):
TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
Found at i:25662 original size:14 final size:15
Alignment explanation
Indices: 25643--25672 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25633 AACTAGGAAA
25643 AATAAAT-AACAAGG
1 AATAAATAAACAAGG
25657 AATAAATAAACAAGG
1 AATAAATAAACAAGG
25672 A
1 A
25673 TTGGACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAAATAAACAAGG
Found at i:30002 original size:20 final size:20
Alignment explanation
Indices: 29977--30023 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
29967 AATCAAAAAG
29977 CCCCAATTACCCTACTAAGA
1 CCCCAATTACCCTACTAAGA
29997 CCCCAATTACCCTACTAAGA
1 CCCCAATTACCCTACTAAGA
30017 CCCCAAT
1 CCCCAAT
30024 CACCTTGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.43, G:0.04, T:0.19
Consensus pattern (20 bp):
CCCCAATTACCCTACTAAGA
Found at i:38681 original size:193 final size:198
Alignment explanation
Indices: 38334--38699 Score: 553
Period size: 193 Copynumber: 1.9 Consensus size: 198
38324 TTTTCAAAAA
* *
38334 AACTTCTTAACCCGCTTATGGAGTCCAAATTTTACACTGACAGTGTATTATATAATAATCCTATA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGAAAGTGTATTATATAATAATCCTATA
* * * * *
38399 AGAAAATTTATATAATACATCGTCAGTGGAGTTTAGCCGACTGCACGTGCGGGGTTTAACTTTAA
66 AGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGAGG--T-ACTTTAA
38464 GGGTTGACATGTGTACCCTTAGGGAATATGCATTAATATTAAATATTTGATTATGACATGGAGTA
128 GGGTTGACATGTGTACCCTTAGGGAATATGCATTAATATTAAATATTTGATTATGACATGGAGTA
38529 TGTGTC
193 TGTGTC
* *
38535 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTATACTGAAATTGTATT-TATAATAATCCTATA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGAAAGTGTATTATATAATAATCCTATA
* *
38599 AGAAAAATTATACAATAC-CCGTTAGTGGATTTTAGCAGACTGCACGTGC-AGG-A-TTTAAGGG
66 AGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGAGGTACTTTAAGGG
* *
38660 TTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAA
131 TTGACATGTGTACCCTTAGGGAATATGCATTAATATTAAA
38700 CAAGTTGATC
Statistics
Matches: 152, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
193 46 0.30
194 1 0.01
198 2 0.01
199 27 0.18
200 31 0.20
201 45 0.30
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (198 bp):
AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGAAAGTGTATTATATAATAATCCTATA
AGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGAGGTACTTTAAGGG
TTGACATGTGTACCCTTAGGGAATATGCATTAATATTAAATATTTGATTATGACATGGAGTATGT
GTC
Found at i:39889 original size:11 final size:11
Alignment explanation
Indices: 39873--39901 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
39863 ATCTAAACTA
39873 AATAAAGATAG
1 AATAAAGATAG
39884 AATAAAGATAG
1 AATAAAGATAG
39895 AATAAAG
1 AATAAAG
39902 CCCACAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (11 bp):
AATAAAGATAG
Found at i:40175 original size:21 final size:21
Alignment explanation
Indices: 40149--40190 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
40139 GCACCTTAGG
*
40149 CAACTCCGATGAGTTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
40170 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
40191 TTCTTTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Done.