Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007716.1 Corchorus capsularis cultivar CVL-1 contig07737, 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: 124301
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13468 original size:15 final size:15
Alignment explanation
Indices: 13448--13480 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
13438 CATTTACAAG
13448 ACTACGATATTGAAA
1 ACTACGATATTGAAA
13463 ACTACGATATTGAAA
1 ACTACGATATTGAAA
13478 ACT
1 ACT
13481 TATTTAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (15 bp):
ACTACGATATTGAAA
Found at i:15370 original size:16 final size:16
Alignment explanation
Indices: 15351--15383 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
15341 GGTGAGTATT
15351 GCATTGCACCAGGTGA
1 GCATTGCACCAGGTGA
15367 GCATTGCACCAGGTGA
1 GCATTGCACCAGGTGA
15383 G
1 G
15384 TGTTTTTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.18
Consensus pattern (16 bp):
GCATTGCACCAGGTGA
Found at i:15400 original size:17 final size:17
Alignment explanation
Indices: 15374--15425 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
15364 TGAGCATTGC
*
15374 ACCAGGTGAGTGTTTTT
1 ACCAGGTGAGTGTTTGT
* *
15391 ACCGGGTGAGTATTTGT
1 ACCAGGTGAGTGTTTGT
15408 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTGTTTGT
15425 A
1 A
15426 TTGGGTGAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.19, C:0.12, G:0.33, T:0.37
Consensus pattern (17 bp):
ACCAGGTGAGTGTTTGT
Found at i:15432 original size:17 final size:17
Alignment explanation
Indices: 15378--15435 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
15368 CATTGCACCA
*
15378 GGTGAGTGTTTTTACCG
1 GGTGAGTGTTTGTACCG
* *
15395 GGTGAGTATTTGTACCA
1 GGTGAGTGTTTGTACCG
**
15412 GGTGAGTGTTTGTATTG
1 GGTGAGTGTTTGTACCG
15429 GGTGAGT
1 GGTGAGT
15436 TGGGTAGGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.16, C:0.07, G:0.38, T:0.40
Consensus pattern (17 bp):
GGTGAGTGTTTGTACCG
Found at i:28208 original size:210 final size:210
Alignment explanation
Indices: 27846--28231 Score: 700
Period size: 210 Copynumber: 1.8 Consensus size: 210
27836 GTCACTTTGC
* * *
27846 ACACCATAACTATAGGGATCTATCACCAAACATCAGACTATAGAATTGCCCCATGAAATCTAAAC
1 ACACCATAACCATAGGGAGCTATCACCAAACATCAGACTATAGAATAGCCCCATGAAATCTAAAC
27911 AAATAATATGAAGAGAGCTAAAGAAGTAGAATTATCAGATTCAAAGTCAGCTACTGAAGCATAAA
66 AAATAATATGAAGAGAGCTAAAGAAGTAGAATTATCAGATTCAAAGTCAGCTACTGAAGCATAAA
27976 AACCCAACTCCATTCTCTCGAGCAGCAAAAATTGCATTTAAGAACATCGGATTATAGAGCAGCAA
131 AACCCAACTCCATTCTCTCGAGCAGCAAAAATTGCATTTAAGAACATCGGATTATAGAGCAGCAA
28041 AATTTGCATTTAAGA
196 AATTTGCATTTAAGA
28056 ACACCATAACCATAGGGAGCTATCACCAAACATCAGACTATAGAATAGCCCCATGAAATCTAAAC
1 ACACCATAACCATAGGGAGCTATCACCAAACATCAGACTATAGAATAGCCCCATGAAATCTAAAC
** * *
28121 AAATAATATGGGGAGCGCTAAAGAAGTAGAATTATCAGATTCAAAGTCAGCTGCTGAAGCATAAA
66 AAATAATATGAAGAGAGCTAAAGAAGTAGAATTATCAGATTCAAAGTCAGCTACTGAAGCATAAA
*
28186 AACCCAACTCCATTCTCTCGAGCAGCAAAACTTGCATTTAAGAACA
131 AACCCAACTCCATTCTCTCGAGCAGCAAAAATTGCATTTAAGAACA
28232 ACTAAAAATG
Statistics
Matches: 168, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
210 168 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (210 bp):
ACACCATAACCATAGGGAGCTATCACCAAACATCAGACTATAGAATAGCCCCATGAAATCTAAAC
AAATAATATGAAGAGAGCTAAAGAAGTAGAATTATCAGATTCAAAGTCAGCTACTGAAGCATAAA
AACCCAACTCCATTCTCTCGAGCAGCAAAAATTGCATTTAAGAACATCGGATTATAGAGCAGCAA
AATTTGCATTTAAGA
Found at i:38043 original size:25 final size:25
Alignment explanation
Indices: 38015--38066 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
38005 CTGCAATCAT
38015 ATGTACCTCTCTTAACTAATTAATA
1 ATGTACCTCTCTTAACTAATTAATA
38040 ATGTACCTCTCTTAACTAATTAATA
1 ATGTACCTCTCTTAACTAATTAATA
38065 AT
1 AT
38067 TAACGGGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (25 bp):
ATGTACCTCTCTTAACTAATTAATA
Found at i:40867 original size:6 final size:6
Alignment explanation
Indices: 40834--40865 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
40824 AGGTGATGCA
*
40834 GACCTT GACCTT GACCTT GACCTT GATCTT GA
1 GACCTT GACCTT GACCTT GACCTT GACCTT GA
40866 TCGTGATCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (6 bp):
GACCTT
Found at i:48792 original size:229 final size:229
Alignment explanation
Indices: 48391--48852 Score: 915
Period size: 229 Copynumber: 2.0 Consensus size: 229
48381 TAAAGATAAC
48391 AACTCTAGTAGACGGTCCATGTTTGCAAGTTACTTAGAGTTAGCATTTCTGCCTTGTCGAAGCCT
1 AACTCTAGTAGACGGTCCATGTTTGCAAGTTACTTAGAGTTAGCATTTCTGCCTTGTCGAAGCCT
48456 CAAGCTATACATTAACTGTGTGGCTTAACAAGTTGAGCAACATCATTTAGGCCCATTAACATACC
66 CAAGCTATACATTAACTGTGTGGCTTAACAAGTTGAGCAACATCATTTAGGCCCATTAACATACC
48521 AGTTTCACAACATCATTTAGGCCCATTACGCACTTCTCTTGTATACAAGTTTCAGTGGCACGAAC
131 AGTTTCACAACATCATTTAGGCCCATTACGCACTTCTCTTGTATACAAGTTTCAGTGGCACGAAC
48586 ACTTATCTGTGTTTTCTTAATTGGTTAATTAAAT
196 ACTTATCTGTGTTTTCTTAATTGGTTAATTAAAT
48620 AACTCTAGTAGACGGTCCATGTTTGCAAGTTACTTAGAGTTAGCATTTCTGCCTTGTCGAAGCCT
1 AACTCTAGTAGACGGTCCATGTTTGCAAGTTACTTAGAGTTAGCATTTCTGCCTTGTCGAAGCCT
48685 CAAGCTATACATTAACTGTGTGGCTTAACAAGTTGAGCAACATCATTTAGGCCCATTAACATACC
66 CAAGCTATACATTAACTGTGTGGCTTAACAAGTTGAGCAACATCATTTAGGCCCATTAACATACC
48750 AGTTTCACAACATCATTTAGGCCCATTACGCACTTCTCTTGTATACAAGTTTCAGTGGCACGAAC
131 AGTTTCACAACATCATTTAGGCCCATTACGCACTTCTCTTGTATACAAGTTTCAGTGGCACGAAC
*
48815 ACTTATCTGTGTTTTTTTAATTGGTTAATTAAAT
196 ACTTATCTGTGTTTTCTTAATTGGTTAATTAAAT
48849 AACT
1 AACT
48853 TCTTTAGACC
Statistics
Matches: 232, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
229 232 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Consensus pattern (229 bp):
AACTCTAGTAGACGGTCCATGTTTGCAAGTTACTTAGAGTTAGCATTTCTGCCTTGTCGAAGCCT
CAAGCTATACATTAACTGTGTGGCTTAACAAGTTGAGCAACATCATTTAGGCCCATTAACATACC
AGTTTCACAACATCATTTAGGCCCATTACGCACTTCTCTTGTATACAAGTTTCAGTGGCACGAAC
ACTTATCTGTGTTTTCTTAATTGGTTAATTAAAT
Found at i:64105 original size:3 final size:3
Alignment explanation
Indices: 64097--64125 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
64087 TAATCTATTT
64097 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
64126 TTTGTCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:68128 original size:19 final size:19
Alignment explanation
Indices: 68104--68140 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
68094 ATACAGTACC
68104 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
68123 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
68141 TGCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:82595 original size:13 final size:13
Alignment explanation
Indices: 82577--82602 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
82567 ATTCTTTTTC
82577 TTTCTCTTTCTCT
1 TTTCTCTTTCTCT
82590 TTTCTCTTTCTCT
1 TTTCTCTTTCTCT
82603 CACTCTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCTCTTTCTCT
Found at i:82599 original size:6 final size:6
Alignment explanation
Indices: 82569--82602 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
82559 TAAAAGCGAT
*
82569 TCTTTT TCTTTC TCTTTC TCTTTTC TCTTTC TCT
1 TCTTTC TCTTTC TCTTTC TC-TTTC TCTTTC TCT
82603 CACTCTTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (6 bp):
TCTTTC
Found at i:82608 original size:19 final size:18
Alignment explanation
Indices: 82569--82609 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
82559 TAAAAGCGAT
**
82569 TCTTTTTCTTTCTCTTTC
1 TCTTTTTCTTTCTCTCAC
82587 TCTTTTCTCTTTCTCTCAC
1 TCTTTT-TCTTTCTCTCAC
82606 TCTT
1 TCTT
82610 AACCTCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (18 bp):
TCTTTTTCTTTCTCTCAC
Found at i:85884 original size:17 final size:18
Alignment explanation
Indices: 85862--85895 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
85852 TACAATATAC
85862 TCCTTTT-ATCTCTTTTT
1 TCCTTTTCATCTCTTTTT
85879 TCCTTTTCATCTCTTTT
1 TCCTTTTCATCTCTTTT
85896 GATTTTGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (18 bp):
TCCTTTTCATCTCTTTTT
Found at i:103364 original size:17 final size:17
Alignment explanation
Indices: 103344--103378 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
103334 CAAAATTTAG
*
103344 CTAATTGATACTCCCTC
1 CTAATTGATACCCCCTC
103361 CTAATTGATACCCCCTC
1 CTAATTGATACCCCCTC
103378 C
1 C
103379 GTCTCATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.06, T:0.31
Consensus pattern (17 bp):
CTAATTGATACCCCCTC
Found at i:121818 original size:25 final size:26
Alignment explanation
Indices: 121763--121820 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 26
121753 TCTTTCTATT
* *
121763 TTAACTAAAAACTTTATTTTTTTTGGCAA
1 TTAACTAAAAACTTTA---TTTTAGGAAA
121792 TTAACTAAAAACTTTA-TTTAGGAAA
1 TTAACTAAAAACTTTATTTTAGGAAA
121817 TTAA
1 TTAA
121821 ATGTAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 11 0.41
29 16 0.59
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (26 bp):
TTAACTAAAAACTTTATTTTAGGAAA
Found at i:122801 original size:19 final size:20
Alignment explanation
Indices: 122755--122802 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
122745 TGTGGCACGC
*
122755 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
122777 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
122796 CACATGT
1 CACATGT
122803 CACGCCACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:122807 original size:53 final size:53
Alignment explanation
Indices: 122722--122824 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
122712 GACGTGGCAC
* * **
122722 GCCACGTGTACCAAAAAGTGATATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
*
122775 GCCACATGTACCAAAAAGTGACACATGTCACGCCACATGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
122825 GACACGTGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:122852 original size:31 final size:31
Alignment explanation
Indices: 122774--122872 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
122764 CAAAAAGTCG
* *
122774 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
*
122805 CGCCACATGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** * * *
122836 TGCCACATGTTTCAAAAAATGGCACGTGGTA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
122867 TGCCAC
1 TGCCAC
122873 GTGCACAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.19
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Done.