Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014425.1 Corchorus capsularis cultivar CVL-1 contig14446, 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: 58675
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:427 original size:3 final size:3
Alignment explanation
Indices: 419--454 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
409 ACTCCATTTC
419 TCT TCT TCT TCT TCT TCT TCT TCCT TCT TCT GTCT T
1 TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT -TCT T
455 TGCTGCTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 25 0.81
4 6 0.19
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:3056 original size:13 final size:13
Alignment explanation
Indices: 3038--3062 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3028 TTTCCTTCTT
3038 TAGTCCATTTTTC
1 TAGTCCATTTTTC
3051 TAGTCCATTTTT
1 TAGTCCATTTTT
3063 GTTGGGTCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (13 bp):
TAGTCCATTTTTC
Found at i:9032 original size:9 final size:10
Alignment explanation
Indices: 9018--9062 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 10
9008 TATTCCACCC
9018 AATATAT-AT
1 AATATATAAT
9027 AATATATAAT
1 AATATATAAT
9037 AATA-ATAAT
1 AATATATAAT
*
9046 AATA-ACAAT
1 AATATATAAT
9055 AATA-ATAA
1 AATATATAA
9063 CCTAGTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
AATATATAAT
Found at i:9040 original size:3 final size:3
Alignment explanation
Indices: 9025--9062 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
9015 CCCAATATAT
*
9025 ATA ATA TATA ATA ATA ATA ATA ATA ACA ATA ATA ATA A
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
9063 CCTAGTTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:32060 original size:55 final size:55
Alignment explanation
Indices: 31968--32078 Score: 141
Period size: 55 Copynumber: 2.0 Consensus size: 55
31958 GCACCCGAGT
** ** * *
31968 TGTTAGCTTGACTGCTAGGTGCACTGTGTCTGGACCGTAAGGTCCTGGATTCAAG
1 TGTTAGCTCAACTGCTAGGTGCACCATGCCTGAACCGTAAGGTCCTGGATTCAAG
* * *
32023 TGTTAGCTCAACTGGTAGGTGCACCATGCCTGAACCGTGAGGTCCTGGGTTCAAG
1 TGTTAGCTCAACTGCTAGGTGCACCATGCCTGAACCGTAAGGTCCTGGATTCAAG
32078 T
1 T
32079 CTCACAGAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.29
Consensus pattern (55 bp):
TGTTAGCTCAACTGCTAGGTGCACCATGCCTGAACCGTAAGGTCCTGGATTCAAG
Found at i:33490 original size:2 final size:2
Alignment explanation
Indices: 33485--33540 Score: 62
Period size: 2 Copynumber: 28.0 Consensus size: 2
33475 TATATTACTG
* *
33485 TA TA TA TA TA TA TA TGA TA TA GTA TA TG TA TA TA TG TA TA TA -A
1 TA TA TA TA TA TA TA T-A TA TA -TA TA TA TA TA TA TA TA TA TA TA
33528 TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA
33541 CTAGATAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
1 2 0.04
2 40 0.87
3 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Found at i:33524 original size:26 final size:26
Alignment explanation
Indices: 33487--33537 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
33477 TATTACTGTA
*
33487 TATATATATATATGATATAGTATATG
1 TATATATATATATAATATAGTATATG
* *
33513 TATATATGTATATAATATATTATAT
1 TATATATATATATAATATAGTATAT
33538 ATACTAGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (26 bp):
TATATATATATATAATATAGTATATG
Found at i:34485 original size:234 final size:234
Alignment explanation
Indices: 34076--34543 Score: 846
Period size: 234 Copynumber: 2.0 Consensus size: 234
34066 AACTTATTTG
* * * * *
34076 GTAGAACGGTGAGATTGTTCTGGTGAGACTAAGATCATGTTTGGTACATCAGTGAGATTGGTTCG
1 GTAGAACAGTGAGATTGCTCTGATGAGACTAAGACCATGTTTGGTACACCAGTGAGATTGGTTCG
*
34141 GTAACAGTAAAATTGGTTATTTTACGGGTTAGATTTGTTACTGTACAGATAAAATTTGTTACTAA
66 GTAACAGTAAAATTGGTTATTTTACGGGTTAGATTTGTTACTGTACAAATAAAATTTGTTACTAA
34206 TTTGTTACTATACAGATGATAATATTCTCGGTGGTTGTAAAATATGTGTTTAATCGAGACCAACT
131 TTTGTTACTATACAGATGATAATATTCTCGGTGGTTGTAAAATATGTGTTTAATCGAGACCAACT
34271 GATCCCACCCTAAAAATTGTTTAGTAGGTCATCTGGGCC
196 GATCCCACCCTAAAAATTGTTTAGTAGGTCATCTGGGCC
34310 GTAGAACAGTGAGATTGCTCTGATGAGACTAAGACCATGTTTGGTACACCAGTGAGATTGGTTCG
1 GTAGAACAGTGAGATTGCTCTGATGAGACTAAGACCATGTTTGGTACACCAGTGAGATTGGTTCG
*
34375 GTAACTGTAAAATTGGTTATTTTACGGGTTAGATTTGTTACTGTACAAATAAAATTTGTTACTAA
66 GTAACAGTAAAATTGGTTATTTTACGGGTTAGATTTGTTACTGTACAAATAAAATTTGTTACTAA
*
34440 TTTGTTACTATACAGATGATAATATTCTCGGTGGTTGTAAAATATGTGTTTATTCGAGACCAACT
131 TTTGTTACTATACAGATGATAATATTCTCGGTGGTTGTAAAATATGTGTTTAATCGAGACCAACT
* *
34505 GATCCCACCCTAAAAATTGTTTAGTAGGTCGTTTGGGCC
196 GATCCCACCCTAAAAATTGTTTAGTAGGTCATCTGGGCC
34544 ATTGACCGAC
Statistics
Matches: 224, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
234 224 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.35
Consensus pattern (234 bp):
GTAGAACAGTGAGATTGCTCTGATGAGACTAAGACCATGTTTGGTACACCAGTGAGATTGGTTCG
GTAACAGTAAAATTGGTTATTTTACGGGTTAGATTTGTTACTGTACAAATAAAATTTGTTACTAA
TTTGTTACTATACAGATGATAATATTCTCGGTGGTTGTAAAATATGTGTTTAATCGAGACCAACT
GATCCCACCCTAAAAATTGTTTAGTAGGTCATCTGGGCC
Found at i:35824 original size:19 final size:18
Alignment explanation
Indices: 35789--35824 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35779 ATGTAAATCG
*
35789 ATTTTGACCAGTTCAAAT
1 ATTTTGACCAATTCAAAT
35807 ATTTTGACCAAATTCAAA
1 ATTTTGACC-AATTCAAA
35825 ACTCTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (18 bp):
ATTTTGACCAATTCAAAT
Found at i:37348 original size:45 final size:45
Alignment explanation
Indices: 37292--37381 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
37282 GATTACTTCT
* *
37292 CCAGCTTATCATTAATCCGGGGTA-GAGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTATG-GATCTTTTAATAATTCCAC
*
37337 CCAGCTCATCATTAATTCGGGGTATGGATCTTTTAATAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTATGGATCTTTTAATAATTCCAC
37382 TACTCTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 40 0.98
46 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGGGGTATGGATCTTTTAATAATTCCAC
Found at i:37729 original size:7 final size:7
Alignment explanation
Indices: 37719--37758 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
37709 CAATAAAATA
*
37719 AAAAAAT
1 AAAAAAG
37726 AAAAAAG
1 AAAAAAG
37733 AAAAAAG
1 AAAAAAG
37740 AAAAAAG
1 AAAAAAG
37747 AAAAAAG
1 AAAAAAG
37754 AAAAA
1 AAAAA
37759 TAAATATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:39041 original size:64 final size:67
Alignment explanation
Indices: 38909--39040 Score: 187
Period size: 68 Copynumber: 2.0 Consensus size: 67
38899 TTGGGTCCTG
*
38909 GTCGTGGAGAAAGAAGTCACGGAGGGAGGAAGAAAGAAGAGAAAAAAGAAAAAAAAGTAAAAAAA
1 GTCGTGGAGAAAGAAGTCACGGAGGGAGGAAAAAAGAAGAGAAAAAAGAAAAAAAAG-AAAAAAA
38974 AAA
65 AAA
* * *
38977 GTCGTGGAGAAAGAAGTCAGGGAGGGAGGAAAAAAGGAA-A-AAAAAAGGGAAAAAGAGAAAAAA
1 GTCGTGGAGAAAGAAGTCACGGAGGGAGGAAAAAA-GAAGAGAAAAAA-GAAAAAAAAGAAAAAA
39040 A
64 A
39041 GAAAAAAATG
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
67 13 0.22
68 42 0.72
69 3 0.05
ACGTcount: A:0.59, C:0.04, G:0.32, T:0.05
Consensus pattern (67 bp):
GTCGTGGAGAAAGAAGTCACGGAGGGAGGAAAAAAGAAGAGAAAAAAGAAAAAAAAGAAAAAAAA
AA
Found at i:39376 original size:44 final size:45
Alignment explanation
Indices: 39260--39381 Score: 219
Period size: 45 Copynumber: 2.7 Consensus size: 45
39250 GCATTTTGCC
* *
39260 TTAATCCGGGGTAGGGATCTTTTAGTAAATCCACCCAGCTCATCA
1 TTAATTCGGGGTAGGGATCTTTTAGTAATTCCACCCAGCTCATCA
39305 TTAATTCGGGGTAGGGATCTTTTAGTAATTCCACCCAGCTCATCA
1 TTAATTCGGGGTAGGGATCTTTTAGTAATTCCACCCAGCTCATCA
39350 TTAATTC-GGGTAGGGATCTTTTAGTAATTCCA
1 TTAATTCGGGGTAGGGATCTTTTAGTAATTCCA
39382 TTACTCTATT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
44 25 0.33
45 50 0.67
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (45 bp):
TTAATTCGGGGTAGGGATCTTTTAGTAATTCCACCCAGCTCATCA
Found at i:42361 original size:127 final size:127
Alignment explanation
Indices: 42209--42462 Score: 499
Period size: 127 Copynumber: 2.0 Consensus size: 127
42199 TTTCTCACTT
42209 TGGAGAGAAAGTTTCTGGGTCAGTTAAAACTTTCTCACCCTAAACTTTCTCTTAAAAAAATAACC
1 TGGAGAGAAAGTTTCTGGGTCAGTTAAAACTTTCTCACCCTAAACTTTCTCTTAAAAAAATAACC
*
42274 AAACATGCTAAAGTTATTTCCTACCCTATACTTTCTATAGAAAGTGATTAAATTACATCAAA
66 AAACATGCTAAAGTTATTTCCTACCCTATACTTTCTATAAAAAGTGATTAAATTACATCAAA
42336 TGGAGAGAAAGTTTCTGGGTCAGTTAAAACTTTCTCACCCTAAACTTTCTCTTAAAAAAATAACC
1 TGGAGAGAAAGTTTCTGGGTCAGTTAAAACTTTCTCACCCTAAACTTTCTCTTAAAAAAATAACC
42401 AAACATGCTAAAGTTATTTCCTACCCTATACTTTCTATAAAAAGTGATTAAATTACATCAAA
66 AAACATGCTAAAGTTATTTCCTACCCTATACTTTCTATAAAAAGTGATTAAATTACATCAAA
42463 ACAAACGATT
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 126 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (127 bp):
TGGAGAGAAAGTTTCTGGGTCAGTTAAAACTTTCTCACCCTAAACTTTCTCTTAAAAAAATAACC
AAACATGCTAAAGTTATTTCCTACCCTATACTTTCTATAAAAAGTGATTAAATTACATCAAA
Found at i:53573 original size:30 final size:32
Alignment explanation
Indices: 53520--53587 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 32
53510 GGGAAACTTT
53520 ATATTTTCCGATTGTACCCTTTTTCCAAAAAC
1 ATATTTTCCGATTGTACCCTTTTTCCAAAAAC
***
53552 ATATTTT-CGATTGTA-CCTTTTTTTTAAAAC
1 ATATTTTCCGATTGTACCCTTTTTCCAAAAAC
53582 ATATTT
1 ATATTT
53588 CTAAATTGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 18 0.55
31 8 0.24
32 7 0.21
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.49
Consensus pattern (32 bp):
ATATTTTCCGATTGTACCCTTTTTCCAAAAAC
Found at i:53791 original size:37 final size:37
Alignment explanation
Indices: 53741--53835 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 37
53731 AATTTTACTT
53741 TTTGTTTCCAACGTCCTATTTAATTTTGAC-TTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTG-CTTTTTGTC
** *
53778 TTTGTTTCCAACGTTGTATTTCATTTTGCTTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGCTTTTTGTC
* *
53815 TTTGTCTCCAACATCCTATTT
1 TTTGTTTCCAACGTCCTATTT
53836 GGGCATAGAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 1 0.02
37 49 0.98
ACGTcount: A:0.15, C:0.20, G:0.11, T:0.55
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCTTTTTGTC
Found at i:57941 original size:13 final size:13
Alignment explanation
Indices: 57923--57947 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57913 ATTGATGGTC
57923 AAAATCTAAAGGT
1 AAAATCTAAAGGT
57936 AAAATCTAAAGG
1 AAAATCTAAAGG
57948 GAATGGTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (13 bp):
AAAATCTAAAGGT
Done.