Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024230.1 Corchorus olitorius cultivar O-4 contig24263, 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: 39513
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:10468 original size:4 final size:4
Alignment explanation
Indices: 10453--10515 Score: 117
Period size: 4 Copynumber: 15.8 Consensus size: 4
10443 CATTTTGACC
*
10453 TTTA TCTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
10501 TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTT
10516 TATTAAATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:14009 original size:2 final size:2
Alignment explanation
Indices: 14002--14077 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
13992 TGCTTTGCTT
14002 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
14044 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
14078 TATTGATAAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:14461 original size:107 final size:107
Alignment explanation
Indices: 14263--14515 Score: 381
Period size: 107 Copynumber: 2.4 Consensus size: 107
14253 AAAAATCATG
* *
14263 CCTATAACAAT--ATTATTAATTATGGAATTTACCCTT-AAATAAAAATAAAATTTTAATTTGGG
1 CCTATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAATTTTAATTTGGG
*
14325 GCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAAC
66 GCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
14367 CCTATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAATTTTAATTTGGG
1 CCTATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAATTTTAATTTGGG
14432 GCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
66 GCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
* * * * *
14474 TCTATAATAA-AAAATATTTAA-TTTCATAATTTACTCTTAAAA
1 CCTATAACAATAAATTA-TTAATTTTGA-AATTTACCCTTAAAA
14516 ATTAAATTTC
Statistics
Matches: 136, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
104 11 0.08
106 32 0.24
107 93 0.68
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (107 bp):
CCTATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAATTTTAATTTGGG
GCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
Found at i:14937 original size:129 final size:130
Alignment explanation
Indices: 14789--15041 Score: 454
Period size: 129 Copynumber: 2.0 Consensus size: 130
14779 CATTGTTTAA
*
14789 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATTTAATATCCTTATAAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
* *
14854 TATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAA-TTATATATATTAGAATTTTAAATAT
66 TATTTAATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTAAATAT
*
14918 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
*
14983 TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTT
66 TATTTAATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTT
15042 TAAAACTATT
Statistics
Matches: 118, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
129 100 0.85
130 18 0.15
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (130 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
TATTTAATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTAAATAT
Found at i:15723 original size:75 final size:75
Alignment explanation
Indices: 15600--15762 Score: 245
Period size: 75 Copynumber: 2.2 Consensus size: 75
15590 CTCATCTGGA
* *
15600 TTCAGGTCATTCGGATCTCGGATTTACTGGGTTTAGGATCATACGAGTTCGGGTTTTGCCCTCAA
1 TTCAGGTCATTCGGATCTCGGATATACTGGGTTTAGGATCAGACGAGTTCGGGTTTTGCCCTCAA
*
15665 GTCACTCGGG
66 GTCACTCGGC
* * * *
15675 TTCAGGTCATTCGGGTCTCGGATATGCTGGGTTTAGGGTCAGACGAGTTCGGGTTTTGGCCTCAA
1 TTCAGGTCATTCGGATCTCGGATATACTGGGTTTAGGATCAGACGAGTTCGGGTTTTGCCCTCAA
15740 GTCACTCGGC
66 GTCACTCGGC
*
15750 TTCTGGGTCATTC
1 TTC-AGGTCATTC
15763 AGATTTTGGG
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 71 0.90
76 8 0.10
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.33
Consensus pattern (75 bp):
TTCAGGTCATTCGGATCTCGGATATACTGGGTTTAGGATCAGACGAGTTCGGGTTTTGCCCTCAA
GTCACTCGGC
Found at i:16152 original size:28 final size:28
Alignment explanation
Indices: 16117--16174 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
16107 ATATATATAT
16117 AATAATTGTTCATATAGTGAAATTTAGC
1 AATAATTGTTCATATAGTGAAATTTAGC
16145 AATAATTGTTCATATAGTGAAATTTAGC
1 AATAATTGTTCATATAGTGAAATTTAGC
16173 AA
1 AA
16175 ATTTAATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (28 bp):
AATAATTGTTCATATAGTGAAATTTAGC
Found at i:16189 original size:28 final size:28
Alignment explanation
Indices: 16117--16208 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 28
16107 ATATATATAT
**
16117 AATAATTGTTCATATAGTGAAATTTAGC
1 AATAATTAATCATATAGTGAAATTTAGC
**
16145 AATAATTGTTCATATAGTGAAATTTAGC
1 AATAATTAATCATATAGTGAAATTTAGC
* * *
16173 AA-ATTTAATCATAATAGGTAAAATTATAAC
1 AATAATTAATCAT-ATA-GTGAAATT-TAGC
16203 AATAAT
1 AATAAT
16209 ATAAATTGTA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 7 0.13
28 33 0.61
29 7 0.13
30 5 0.09
31 2 0.04
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (28 bp):
AATAATTAATCATATAGTGAAATTTAGC
Found at i:20800 original size:2 final size:2
Alignment explanation
Indices: 20793--20823 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20783 TTATAAATAC
20793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20824 GAAGAGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32118 original size:10 final size:10
Alignment explanation
Indices: 32103--32130 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
32093 AATTATTCAA
32103 AAAAAAAAGG
1 AAAAAAAAGG
32113 AAAAAAAAGG
1 AAAAAAAAGG
32123 AAAAAAAA
1 AAAAAAAA
32131 ACACTGTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:34664 original size:25 final size:24
Alignment explanation
Indices: 34636--34692 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
34626 GTGGATTGTA
*
34636 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
34661 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
34685 AAA-AAATT
1 AAATAAATT
34693 CAAGGCTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:35666 original size:105 final size:106
Alignment explanation
Indices: 35431--35622 Score: 287
Period size: 105 Copynumber: 1.8 Consensus size: 106
35421 AGTAAAATGG
* *
35431 TAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTATTTGAGT
1 TAAAAATTAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGT
*** * *
35496 AAAACTATAAAAGTATATTTAAAAATTCTAATATATAAAAA
66 AAAACTATAAAAGTATAAACAAAAATTCTAAGAAATAAAAA
*
35537 TAAAAATTAAATAGTTATAAGGATATTAGATTTAATTAAAT-AAAAATAGAGTTTTTAGTTGAGT
1 TAAAAATTAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGT
* *
35601 AAAACTATGAAAGTTTAAACAA
66 AAAACTATAAAAGTATAAACAA
35623 TGACATTTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
105 39 0.50
106 39 0.50
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (106 bp):
TAAAAATTAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGT
AAAACTATAAAAGTATAAACAAAAATTCTAAGAAATAAAAA
Found at i:37685 original size:22 final size:22
Alignment explanation
Indices: 37658--37704 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
37648 GCAAATCAAA
37658 TCAAGCTCCGT-GCTTACAACTC
1 TCAAGC-CCGTGGCTTACAACTC
* *
37680 TCAAGCCCTTGGCTTTCAACTC
1 TCAAGCCCGTGGCTTACAACTC
37702 TCA
1 TCA
37705 TTTGTAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.21, C:0.36, G:0.13, T:0.30
Consensus pattern (22 bp):
TCAAGCCCGTGGCTTACAACTC
Done.