Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013069.1 Corchorus olitorius cultivar O-4 contig13102, 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: 50156
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Found at i:1029 original size:44 final size:44
Alignment explanation
Indices: 966--1049 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
956 GTGTCCCAAG
* * *
966 CTATAACCAAACTATGAAATTGTGAAAACTTTCCTATGAATTTC
1 CTATAACCAAACTATGAAATTCTGAAAACCTACCTATGAATTTC
* * *
1010 CTATAATCACACTATGAAATTCTGATAACCTACCTATGAA
1 CTATAACCAAACTATGAAATTCTGAAAACCTACCTATGAA
1050 ATTTTGATAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.32
Consensus pattern (44 bp):
CTATAACCAAACTATGAAATTCTGAAAACCTACCTATGAATTTC
Found at i:1037 original size:22 final size:22
Alignment explanation
Indices: 968--1081 Score: 70
Period size: 22 Copynumber: 5.2 Consensus size: 22
958 GTCCCAAGCT
* * *
968 ATAACCAAACTATGAAATTGTG
1 ATAACCTACCTATGAAATTCTG
* * * *
990 AAAACTTTCCTATGAATTTCCT-
1 ATAACCTACCTATGAAATT-CTG
*
1012 ATAATC-ACACTATGAAATTCTG
1 ATAACCTAC-CTATGAAATTCTG
*
1034 ATAACCTACCTATGAAATTTTG
1 ATAACCTACCTATGAAATTCTG
* * * * *
1056 ATAGCCTTCTTATGGAATTTTG
1 ATAACCTACCTATGAAATTCTG
1078 ATAA
1 ATAA
1082 TGAAACTATG
Statistics
Matches: 69, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
21 3 0.04
22 63 0.91
23 3 0.04
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (22 bp):
ATAACCTACCTATGAAATTCTG
Found at i:1193 original size:22 final size:22
Alignment explanation
Indices: 1168--1209 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1158 AAATTGTGTT
*
1168 AACCTCCCTATAAAATTTTGAA
1 AACCTCACTATAAAATTTTGAA
*
1190 AACCTCACTATTAAATTTTG
1 AACCTCACTATAAAATTTTG
1210 GTAAACACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (22 bp):
AACCTCACTATAAAATTTTGAA
Found at i:6003 original size:15 final size:15
Alignment explanation
Indices: 5983--6031 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
5973 GTTGTTATTC
*
5983 TTCTTCTCCTTTTCG
1 TTCTTCTCCTTCTCG
*
5998 TTCTTCTTCTTCTCG
1 TTCTTCTCCTTCTCG
* * *
6013 TTATTCTCTTTCTCC
1 TTCTTCTCCTTCTCG
6028 TTCT
1 TTCT
6032 CTAGGTGGTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.02, C:0.33, G:0.04, T:0.61
Consensus pattern (15 bp):
TTCTTCTCCTTCTCG
Found at i:6594 original size:16 final size:16
Alignment explanation
Indices: 6573--6606 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
6563 AAATGGTCAC
6573 TGATATGTATTCTTAT
1 TGATATGTATTCTTAT
*
6589 TGATATGTGTTCTTAT
1 TGATATGTATTCTTAT
6605 TG
1 TG
6607 GTTTTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.56
Consensus pattern (16 bp):
TGATATGTATTCTTAT
Found at i:6653 original size:19 final size:19
Alignment explanation
Indices: 6629--6667 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6619 AATGGTGCAT
6629 GCTCTGTTTCTGGAAAATA
1 GCTCTGTTTCTGGAAAATA
6648 GCTCTGTTTCTGGAAAATA
1 GCTCTGTTTCTGGAAAATA
6667 G
1 G
6668 GCAGTAGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (19 bp):
GCTCTGTTTCTGGAAAATA
Found at i:10625 original size:10 final size:10
Alignment explanation
Indices: 10610--10645 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
10600 GCATCGGAAT
10610 CAAATGAAAC
1 CAAATGAAAC
10620 CAAATGAAAC
1 CAAATGAAAC
* *
10630 TAAATGGAAC
1 CAAATGAAAC
10640 CAAATG
1 CAAATG
10646 TGAGGGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.56, C:0.17, G:0.14, T:0.14
Consensus pattern (10 bp):
CAAATGAAAC
Found at i:10854 original size:7 final size:7
Alignment explanation
Indices: 10842--10880 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
10832 CAATGTTCAC
10842 ATATATA
1 ATATATA
10849 ATATATA
1 ATATATA
10856 ATATAT-
1 ATATATA
10862 ATAATATA
1 AT-ATATA
10870 ATAATATA
1 AT-ATATA
10878 ATA
1 ATA
10881 AGTGCAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 2 0.07
7 18 0.60
8 10 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATATATA
Found at i:10863 original size:16 final size:17
Alignment explanation
Indices: 10842--10881 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
10832 CAATGTTCAC
10842 ATATATAATAT-ATAAT
1 ATATATAATATAATAAT
10858 ATATATAATATAATAAT
1 ATATATAATATAATAAT
10875 ATA-ATAA
1 ATATATAA
10882 GTGCAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATATAATATAATAAT
Found at i:17394 original size:5 final size:5
Alignment explanation
Indices: 17379--17411 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
17369 GATAAATCTG
*
17379 TTTTC TGTTC TTTTC TTTTC TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
17412 GTTTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:17547 original size:26 final size:26
Alignment explanation
Indices: 17518--17569 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
17508 TGCCGCCTCA
17518 CTACTATACCAACAACTAAGTTTGTC
1 CTACTATACCAACAACTAAGTTTGTC
17544 CTACTATACCAACAACTAAGTTTGTC
1 CTACTATACCAACAACTAAGTTTGTC
17570 TTGAGTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (26 bp):
CTACTATACCAACAACTAAGTTTGTC
Found at i:17932 original size:102 final size:102
Alignment explanation
Indices: 17756--17949 Score: 343
Period size: 102 Copynumber: 1.9 Consensus size: 102
17746 GAAAAACAAT
* *
17756 AATAATTATAGGAAGTGAAAGTACCAAAAAATCAGTCAAAAGATTTAACCTTATTAATTTGATTA
1 AATAATTATAGGAAGTGAAAGTACCAAAAAACCAATCAAAAGATTTAACCTTATTAATTTGATTA
*
17821 CTATTTAGCTTGGTTTTTCCGTCATTTATACAAAAAC
66 CTATTTAGCTTGATTTTTCCGTCATTTATACAAAAAC
*
17858 AATAATTATAGGAAGTGAAAGTACTAAAAAACCAATCAAAAGATTTAACCTTATTAATTTGATTA
1 AATAATTATAGGAAGTGAAAGTACCAAAAAACCAATCAAAAGATTTAACCTTATTAATTTGATTA
*
17923 CTATTTAGCTTGATTTTTTCGTCATTT
66 CTATTTAGCTTGATTTTTCCGTCATTT
17950 CAATATAGGT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 87 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (102 bp):
AATAATTATAGGAAGTGAAAGTACCAAAAAACCAATCAAAAGATTTAACCTTATTAATTTGATTA
CTATTTAGCTTGATTTTTCCGTCATTTATACAAAAAC
Found at i:18371 original size:178 final size:178
Alignment explanation
Indices: 18102--18431 Score: 500
Period size: 178 Copynumber: 1.9 Consensus size: 178
18092 CTGATTAAGG
* *
18102 TGATTTAAGTGTCTATTAAAAGATTGTTCCATGATTTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * ** * *
18167 AATTTAATGTTTCAAGCATCAAAAATGCTTCCGAAAAATTTGTTGTTTTAGTTAACGGGAATAGA
66 AATTTAATGTTTCAAGCATAAAAAATGCTTCCAAAAAATTAATTGTTTCAGTTAACGGAAATAGA
*
18232 CGGTCCACTTAATATTATATAACTTTTGCTTCAGTTGTCTAATCGAGA
131 CGGTCCACTTAATATTACATAACTTTTGCTTCAGTTGTCTAATCGAGA
* * *
18280 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * *
18345 AATTTATTG-TTCAAGGTATAAAAAATGCTTCCAAAAAATTAATTGTTTCGGTTAACGGAAATAG
66 AATTTAATGTTTCAA-GCATAAAAAATGCTTCCAAAAAATTAATTGTTTCAGTTAACGGAAATAG
*
18409 ACGGTCTACTTAATATTACATAA
130 ACGGTCCACTTAATATTACATAA
18432 TTTGCGCTTA
Statistics
Matches: 135, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
177 5 0.04
178 130 0.96
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGCATAAAAAATGCTTCCAAAAAATTAATTGTTTCAGTTAACGGAAATAGA
CGGTCCACTTAATATTACATAACTTTTGCTTCAGTTGTCTAATCGAGA
Found at i:25629 original size:18 final size:19
Alignment explanation
Indices: 25591--25654 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 19
25581 TTTTTTCTTG
* *
25591 GGTATGAACTTTGTTTTTT
1 GGTATGAACTCTGTCTTTT
25610 GGTATGAACTCT-TCTTTT
1 GGTATGAACTCTGTCTTTT
* *
25628 GGTATGGACTGTG-C-TTT
1 GGTATGAACTCTGTCTTTT
*
25645 GGTGTGAACT
1 GGTATGAACT
25655 GGTTTTTTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
17 11 0.29
18 16 0.42
19 11 0.29
ACGTcount: A:0.16, C:0.11, G:0.27, T:0.47
Consensus pattern (19 bp):
GGTATGAACTCTGTCTTTT
Found at i:32491 original size:65 final size:65
Alignment explanation
Indices: 32387--32511 Score: 232
Period size: 65 Copynumber: 1.9 Consensus size: 65
32377 AACTGGTCAT
* *
32387 ACCCATGCATGGGGTACCCTTGGCCTACCCACGCTTGGGCTAGTGCAGAAAGTTTGAATCGTCCA
1 ACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATCGTCCA
32452 ACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
1 ACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
32512 AATAGCAAGC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.22
Consensus pattern (65 bp):
ACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATCGTCCA
Found at i:32760 original size:21 final size:21
Alignment explanation
Indices: 32705--32775 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
32695 CTTAGGCAAT
*
32705 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
32726 CCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
32747 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
32768 TCCAATGA
1 TCCAATGA
32776 ACTCCTAACA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 3 0.07
21 43 0.93
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:38470 original size:66 final size:66
Alignment explanation
Indices: 38358--38483 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 66
38348 TGAATATTTT
* * * * * *
38358 TATGAAATTTTGATAACTACCCTATTAAATTTTGATAATCACACTATGAAATTTTGATAATTTAC
1 TATGAAATTGTGATAACTACCATATAAAACTTTGATAAACACACTATGAAATTTTAATAATTTAC
38423 C
66 C
38424 TATGAAATTGTGATAAACT-CCATATAAAACTTTGATAAACTA-ACTATGAAATTTTAATAA
1 TATGAAATTGTGAT-AACTACCATATAAAACTTTGATAAAC-ACACTATGAAATTTTAATAA
38484 ACCTTCCTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 47 0.90
67 5 0.10
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (66 bp):
TATGAAATTGTGATAACTACCATATAAAACTTTGATAAACACACTATGAAATTTTAATAATTTAC
C
Found at i:38484 original size:22 final size:22
Alignment explanation
Indices: 38358--38516 Score: 137
Period size: 22 Copynumber: 7.2 Consensus size: 22
38348 TGAATATTTT
38358 TATGAAATTTTGAT-AACTACCC
1 TATGAAATTTTGATAAACTA-CC
* *
38380 TATTAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAAACTAC-C
**
38402 TATGAAATTTTGATAATTTACC
1 TATGAAATTTTGATAAACTACC
*
38424 TATGAAATTGTGATAAACT-CC
1 TATGAAATTTTGATAAACTACC
* * *
38445 ATATAAAACTTTGATAAACTAAC
1 -TATGAAATTTTGATAAACTACC
* *
38468 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGATAAA-CTACC
* * *
38491 TATGAAAATTTG-TAACCTTCC
1 TATGAAATTTTGATAAACTACC
38512 TATGA
1 TATGA
38517 TTTTTTATAA
Statistics
Matches: 112, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
21 13 0.12
22 81 0.72
23 18 0.16
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAAACTACC
Found at i:38528 original size:21 final size:21
Alignment explanation
Indices: 38467--38516 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
38457 GATAAACTAA
*
38467 CTATGAAATTTTAATAAACCTTC
1 CTATGAAAATTT-AT-AACCTTC
*
38490 CTATGAAAATTTGTAACCTTC
1 CTATGAAAATTTATAACCTTC
38511 CTATGA
1 CTATGA
38517 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.52
22 1 0.04
23 11 0.44
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (21 bp):
CTATGAAAATTTATAACCTTC
Found at i:46005 original size:31 final size:31
Alignment explanation
Indices: 45970--46033 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
45960 AGAGTTTGTC
45970 TTTATTTTCTTA-TTTAGATTAGTATTAGGCT
1 TTTATTTTCTTATTTTAG-TTAGTATTAGGCT
*
46001 TTTATTTTCTTATTTTAGTTAGTATTGGGCT
1 TTTATTTTCTTATTTTAGTTAGTATTAGGCT
46032 TT
1 TT
46034 ATTGGCTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.19, C:0.06, G:0.14, T:0.61
Consensus pattern (31 bp):
TTTATTTTCTTATTTTAGTTAGTATTAGGCT
Done.