Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018051.1 Corchorus olitorius cultivar O-4 contig18084, 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: 70057
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Found at i:4211 original size:21 final size:21
Alignment explanation
Indices: 4186--4225 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4176 ACGCCTCTTG
* *
4186 GGAGGTAGGAGGCATCTCCTA
1 GGAGGAAGGAAGCATCTCCTA
4207 GGAGGAAGGAAGCATCTCC
1 GGAGGAAGGAAGCATCTCC
4226 CTCTTTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.20, G:0.38, T:0.15
Consensus pattern (21 bp):
GGAGGAAGGAAGCATCTCCTA
Found at i:14691 original size:75 final size:74
Alignment explanation
Indices: 14569--14712 Score: 207
Period size: 75 Copynumber: 1.9 Consensus size: 74
14559 TAAAAAAACT
* **
14569 TTAAATTCTTATTAAAATGAAAGAATAAATTATATTCACAATAAATTAAACCATTAATACACACC
1 TTAAATTCTTATTAAAATGAAAGAATAAATTATAATCACAATAAATTAAACCAGCAATACACACC
14634 CCAATAACA
66 CCAATAACA
* * * *
14643 TTAAATTCTTGTTAAAAATGAAAGAATAATTTTTAATCACAATAAATTAAACTAGCAATACACAC
1 TTAAATTCTTATT-AAAATGAAAGAATAAATTATAATCACAATAAATTAAACCAGCAATACACAC
*
14708 TCCAA
65 CCCAA
14713 AATAGAAACG
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
74 12 0.20
75 49 0.80
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.31
Consensus pattern (74 bp):
TTAAATTCTTATTAAAATGAAAGAATAAATTATAATCACAATAAATTAAACCAGCAATACACACC
CCAATAACA
Found at i:23866 original size:24 final size:24
Alignment explanation
Indices: 23834--23881 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
23824 TGAGATGGTT
* * *
23834 TTTTCGCAGGGAAGAGCAAGAGAG
1 TTTTCGCAGGAAAAAGAAAGAGAG
23858 TTTTCGCAGGAAAAAGAAAGAGAG
1 TTTTCGCAGGAAAAAGAAAGAGAG
23882 AGAGATGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.33, T:0.17
Consensus pattern (24 bp):
TTTTCGCAGGAAAAAGAAAGAGAG
Found at i:32171 original size:76 final size:76
Alignment explanation
Indices: 32043--32284 Score: 371
Period size: 76 Copynumber: 3.2 Consensus size: 76
32033 GAAATTTTGG
* * * *
32043 AAAA-AAACGAAACGATCGTCCCCTTTGAGATTGTTTCGTCACGAACGGCCGAACACCAACCTCG
1 AAAATAAACAAAACGATCGTCTCCTTTGAGA--CTTTCTTCACGAACGGCCGAACACCAACCTCG
*
32107 GTGTCCGCGTATA
64 GTGTCCCCGTATA
32120 AAAATAAACAAAACGATCGTCTCCTTTGAGACTTTCTTCACGAACGGCCGAACACCAACCTCGGT
1 AAAATAAACAAAACGATCGTCTCCTTTGAGACTTTCTTCACGAACGGCCGAACACCAACCTCGGT
32185 GTCCCCGTATA
66 GTCCCCGTATA
* *
32196 AAAATAAACAAAACGATCGTCTCCTTTGAGACTCTCGTT-ACGAACGGCCGACCACCAACCTCGG
1 AAAATAAACAAAACGATCGTCTCCTTTGAGACTTTC-TTCACGAACGGCCGAACACCAACCTCGG
32260 TGTCCCCGTATA
65 TGTCCCCGTATA
*
32272 AAAATAAATAAAA
1 AAAATAAACAAAA
32285 GAAACGAATG
Statistics
Matches: 155, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
76 125 0.81
77 6 0.04
78 24 0.15
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (76 bp):
AAAATAAACAAAACGATCGTCTCCTTTGAGACTTTCTTCACGAACGGCCGAACACCAACCTCGGT
GTCCCCGTATA
Found at i:37445 original size:23 final size:22
Alignment explanation
Indices: 37413--37488 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
37403 ATTACACCTT
*
37413 GTAACAACAAGGGTGATGAAAA
1 GTAAAAACAAGGGTGATGAAAA
* * * *
37435 GTAAATGACAAGGTTGATCACAACTT
1 GTAAA-AACAAGGGTGATGA-AA--A
37461 GTAAAAACAAGGGTGATGAAAA
1 GTAAAAACAAGGGTGATGAAAA
37483 GTAAAA
1 GTAAAA
37489 GATAGGGTTG
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
22 10 0.24
23 11 0.27
24 4 0.10
25 11 0.27
26 5 0.12
ACGTcount: A:0.49, C:0.09, G:0.24, T:0.18
Consensus pattern (22 bp):
GTAAAAACAAGGGTGATGAAAA
Found at i:37481 original size:48 final size:48
Alignment explanation
Indices: 37410--37502 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
37400 AAGATTACAC
* *
37410 CTTGTAACAACAAGGGTGATGAAAAGTAAATGACAAGGTTGATCACAA
1 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGACAAGGTTGATCACAA
* *
37458 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCA
1 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGACAAGGTTGATCA
37503 AACAAGAGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.44, C:0.10, G:0.25, T:0.22
Consensus pattern (48 bp):
CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGACAAGGTTGATCACAA
Found at i:40245 original size:23 final size:22
Alignment explanation
Indices: 40213--40336 Score: 79
Period size: 22 Copynumber: 5.3 Consensus size: 22
40203 ATTACACCTT
*
40213 GTAACAACAAGGGTGATGAAAA
1 GTAAAAACAAGGGTGATGAAAA
* * * *
40235 GTAAATGACAAGGTTGATCACAACTT
1 GTAAA-AACAAGGGTGATGA-AA--A
40261 GTAAAAACAAGGGTGATGAAAA
1 GTAAAAACAAGGGTGATGAAAA
* * * *
40283 GTAAAAGA-TAGGGTTAATCACAACTT
1 GTAAAA-ACAAGGG-TGATGA-AA--A
40309 GTAAAAACAAGGGTGATGAAAA
1 GTAAAAACAAGGGTGATGAAAA
40331 GTAAAA
1 GTAAAA
40337 GATAGGGTTG
Statistics
Matches: 75, Mismatches: 17, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
22 20 0.27
23 16 0.21
24 8 0.11
25 16 0.21
26 15 0.20
ACGTcount: A:0.48, C:0.09, G:0.23, T:0.19
Consensus pattern (22 bp):
GTAAAAACAAGGGTGATGAAAA
Found at i:40271 original size:25 final size:25
Alignment explanation
Indices: 40242--40325 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
40232 AAAGTAAATG
*
40242 ACAAGGTTGATCACAACTTGTAAAA
1 ACAAGGGTGATCACAACTTGTAAAA
* *
40267 ACAAGGGTGATGA-AA--AGTAAAA
1 ACAAGGGTGATCACAACTTGTAAAA
* *
40289 GA-TAGGGTTAATCACAACTTGTAAAA
1 -ACAAGGG-TGATCACAACTTGTAAAA
40315 ACAAGGGTGAT
1 ACAAGGGTGAT
40326 GAAAAGTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
22 10 0.23
23 5 0.11
24 4 0.09
25 15 0.34
26 10 0.23
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (25 bp):
ACAAGGGTGATCACAACTTGTAAAA
Found at i:40281 original size:48 final size:48
Alignment explanation
Indices: 40210--40350 Score: 237
Period size: 48 Copynumber: 2.9 Consensus size: 48
40200 AAGATTACAC
* * * *
40210 CTTGTAACAACAAGGGTGATGAAAAGTAAATGACAAGGTTGATCACAA
1 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCACAA
*
40258 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTAATCACAA
1 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCACAA
40306 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCA
1 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCA
40351 AACAAGAGTG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 87 1.00
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.21
Consensus pattern (48 bp):
CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCACAA
Found at i:40295 original size:22 final size:22
Alignment explanation
Indices: 40270--40344 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
40260 TGTAAAAACA
40270 AGGGTGATGAAAAGTAAAAGAT
1 AGGGTGATGAAAAGTAAAAGAT
* * * *
40292 AGGGTTAATCACAACTTGTAAAA-ACA
1 AGGG-TGATGA-AA--AGTAAAAGA-T
40318 AGGGTGATGAAAAGTAAAAGAT
1 AGGGTGATGAAAAGTAAAAGAT
40340 AGGGT
1 AGGGT
40345 TGATCAAACA
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
22 15 0.38
23 5 0.13
24 4 0.10
25 5 0.13
26 10 0.26
ACGTcount: A:0.47, C:0.05, G:0.28, T:0.20
Consensus pattern (22 bp):
AGGGTGATGAAAAGTAAAAGAT
Found at i:40321 original size:26 final size:26
Alignment explanation
Indices: 40242--40322 Score: 75
Period size: 26 Copynumber: 3.3 Consensus size: 26
40232 AAAGTAAATG
40242 ACAA-GGTTGATCACAACTTGTAAAA
1 ACAAGGGTTGATCACAACTTGTAAAA
* *
40267 ACAAGGG-TGATGA-AA--AGTAAAA
1 ACAAGGGTTGATCACAACTTGTAAAA
* *
40289 GA-TAGGGTTAATCACAACTTGTAAAA
1 -ACAAGGGTTGATCACAACTTGTAAAA
40315 ACAAGGGT
1 ACAAGGGT
40323 GATGAAAAGT
Statistics
Matches: 42, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
22 10 0.24
23 5 0.12
24 4 0.10
25 10 0.24
26 13 0.31
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.21
Consensus pattern (26 bp):
ACAAGGGTTGATCACAACTTGTAAAA
Found at i:42701 original size:63 final size:63
Alignment explanation
Indices: 42602--42727 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
42592 ACACTCAAAC
*
42602 CCGCTTGTGATTTTCTTGTCTCCGGCAACCGTGGCTTGCCTGAATTTGAAATGTCAGAGAGAG
1 CCGCTTGTGATTTTCTTGTCTCCGACAACCGTGGCTTGCCTGAATTTGAAATGTCAGAGAGAG
42665 CCGCTTGTGATTTTCTTGTCTCCGACAACCGTGGCTTGCCTGAATTTGAAATGTCAGAGAGAG
1 CCGCTTGTGATTTTCTTGTCTCCGACAACCGTGGCTTGCCTGAATTTGAAATGTCAGAGAGAG
42728 GTTTCCTCTG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (63 bp):
CCGCTTGTGATTTTCTTGTCTCCGACAACCGTGGCTTGCCTGAATTTGAAATGTCAGAGAGAG
Found at i:47004 original size:29 final size:29
Alignment explanation
Indices: 46962--47030 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
46952 TGCGGTGTCT
46962 AATGGCAAAGCTAGGTCAGAGACATTGCC
1 AATGGCAAAGCTAGGTCAGAGACATTGCC
46991 AATGGCAAAGCTAGGTCAGAGACATTGCC
1 AATGGCAAAGCTAGGTCAGAGACATTGCC
*
47020 AGTGGCAAAGC
1 AATGGCAAAGC
47031 AGCTAGTATG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.16
Consensus pattern (29 bp):
AATGGCAAAGCTAGGTCAGAGACATTGCC
Found at i:52872 original size:54 final size:54
Alignment explanation
Indices: 52808--52914 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
52798 TTTAAACAAG
52808 TTTATTTGAAACAAGCATTAAACCAATAAATAAAGATTCATCCTATTATTACTT
1 TTTATTTGAAACAAGCATTAAACCAATAAATAAAGATTCATCCTATTATTACTT
52862 TTTATTTGAAACAAGCATTAAACCAATAAATAAAGATTCATCCTATTATTACT
1 TTTATTTGAAACAAGCATTAAACCAATAAATAAAGATTCATCCTATTATTACT
52915 GAAATGAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (54 bp):
TTTATTTGAAACAAGCATTAAACCAATAAATAAAGATTCATCCTATTATTACTT
Found at i:53080 original size:66 final size:66
Alignment explanation
Indices: 53003--53140 Score: 249
Period size: 66 Copynumber: 2.1 Consensus size: 66
52993 AAATTAGTAG
53003 TAAGTCTTTTTGCAAGGATTTACATGAATTACAGTTTTCTCATATACAAAGTTGCAAATATATGA
1 TAAGTCTTTTTGCAAGGATTTACATGAATTACAGTTTTCTCATATACAAAGTTGCAAATATATGA
53068 A
66 A
* *
53069 TAAGTCTTTTTGCAAGGATTTACATGAATTATAGTTTTCTCATATGCAAAGTTGCAAATATATGA
1 TAAGTCTTTTTGCAAGGATTTACATGAATTACAGTTTTCTCATATACAAAGTTGCAAATATATGA
53134 A
66 A
*
53135 CAAGTC
1 TAAGTC
53141 AAGCAGCAGC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (66 bp):
TAAGTCTTTTTGCAAGGATTTACATGAATTACAGTTTTCTCATATACAAAGTTGCAAATATATGA
A
Found at i:55150 original size:13 final size:13
Alignment explanation
Indices: 55132--55161 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
55122 AGTTCTTCCT
*
55132 ACCATATTCAAAG
1 ACCATATTCAAAA
55145 ACCATATTCAAAA
1 ACCATATTCAAAA
55158 ACCA
1 ACCA
55162 ACTTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.27, G:0.03, T:0.20
Consensus pattern (13 bp):
ACCATATTCAAAA
Found at i:59210 original size:13 final size:13
Alignment explanation
Indices: 59191--59226 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
59181 CTCCATCCAA
59191 CCAATCCAATGAAT
1 CCAATCCAATG-AT
59205 CC-ATCCAATGAT
1 CCAATCCAATGAT
59217 CCAATCCAAT
1 CCAATCCAAT
59227 TAGCAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 15 0.71
14 2 0.10
ACGTcount: A:0.39, C:0.33, G:0.06, T:0.22
Consensus pattern (13 bp):
CCAATCCAATGAT
Found at i:63489 original size:9 final size:9
Alignment explanation
Indices: 63475--63566 Score: 65
Period size: 9 Copynumber: 10.8 Consensus size: 9
63465 TTAAAAATAA
*
63475 ATATTATTT
1 ATATTATAT
63484 ATATTATAT
1 ATATTATAT
*
63493 ATA-TAAAT
1 ATATTATAT
*
63501 ATATTATCAG
1 ATATTAT-AT
63511 ATA-TATAT
1 ATATTATAT
*
63519 A-A-TATAA
1 ATATTATAT
63526 ATA-TAT-T
1 ATATTATAT
63533 ATTATTAT-T
1 A-TATTATAT
63542 ATTATTATAT
1 A-TATTATAT
63552 ATA-TATAT
1 ATATTATAT
63560 ATATTAT
1 ATATTAT
63567 TCGGTCGGTA
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
7 7 0.10
8 23 0.33
9 33 0.48
10 6 0.09
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (9 bp):
ATATTATAT
Found at i:63495 original size:2 final size:2
Alignment explanation
Indices: 63483--63563 Score: 63
Period size: 2 Copynumber: 44.5 Consensus size: 2
63473 AAATATTATT
* *
63483 TA TA T- TA TA TA TA TA AA TA TA T- TA TCA GA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
*
63523 TA AA TA TA T- TA T- TA T- TA T- TA T- TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63559 TA TA T
1 TA TA T
63564 TATTCGGTCG
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
1 9 0.14
2 53 0.84
3 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64572 original size:22 final size:22
Alignment explanation
Indices: 64516--64582 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
64506 AATTTATTAT
* *
64516 ATATCTTTTATACATATCATAA
1 ATATATTTTATATATATCATAA
64538 ATATATTTTATATATATCATAA
1 ATATATTTTATATATATCATAA
*
64560 ATATATTTTATATAATACCATAA
1 ATATATTTTATAT-ATATCATAA
64583 TCGGTCGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 33 0.80
23 8 0.20
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATATTTTATATATATCATAA
Done.