Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005444.1 Corchorus capsularis cultivar CVL-1 contig05462, 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: 7839
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Found at i:1187 original size:22 final size:22
Alignment explanation
Indices: 1159--1202 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1149 GCTACCCTAG
1159 TGCTTTTTCTTCGAGGGATGGT
1 TGCTTTTTCTTCGAGGGATGGT
1181 TGCTTTTTCTTCGAGGGATGGT
1 TGCTTTTTCTTCGAGGGATGGT
1203 CGGCGGATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.32, T:0.45
Consensus pattern (22 bp):
TGCTTTTTCTTCGAGGGATGGT
Found at i:1278 original size:2 final size:2
Alignment explanation
Indices: 1266--1304 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1256 TGAGTTCTTG
1266 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1305 CCACTCAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2675 original size:31 final size:31
Alignment explanation
Indices: 2637--2705 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
2627 AATTGGGCGG
*
2637 GTTCGGGTACT-TCGGGTTCTGGTATTTTCGA
1 GTTCGGGTACTGTCGGGTTCGGGTA-TTTCGA
* *
2668 GTTCGGGTTCTGTCGGGTTCGGGTATTTCGG
1 GTTCGGGTACTGTCGGGTTCGGGTATTTCGA
2699 GTTCGGG
1 GTTCGGG
2706 CCCGGGTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 22 0.65
32 12 0.35
ACGTcount: A:0.06, C:0.16, G:0.39, T:0.39
Consensus pattern (31 bp):
GTTCGGGTACTGTCGGGTTCGGGTATTTCGA
Found at i:3469 original size:16 final size:16
Alignment explanation
Indices: 3448--3507 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
3438 CGGGCTCGGG
3448 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTATTT
*
3464 TCGGGTTCGGATATTT
1 TCGGGTTCGGGTATTT
*
3480 TCGGGTTCGGGTAATT
1 TCGGGTTCGGGTATTT
3496 TCGGGTTCGGGT
1 TCGGGTTCGGGT
3508 TCGGGACGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.08, C:0.13, G:0.38, T:0.40
Consensus pattern (16 bp):
TCGGGTTCGGGTATTT
Found at i:3843 original size:2 final size:2
Alignment explanation
Indices: 3838--3887 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
3828 ATTTTTTATC
* *
3838 TA TA TA TA TA TA TA GA TA T- TA TA TA TA TA TA TA TA T- TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3878 TT TA TA TA TA
1 TA TA TA TA TA
3888 GAATAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:3862 original size:15 final size:15
Alignment explanation
Indices: 3842--3871 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3832 TTTATCTATA
3842 TATATATATAGATAT
1 TATATATATAGATAT
*
3857 TATATATATATATAT
1 TATATATATAGATAT
3872 ATTATTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TATATATATAGATAT
Found at i:3882 original size:23 final size:23
Alignment explanation
Indices: 3830--3887 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
3820 TATTTTTGAT
*
3830 TTTTTATCTATATATATATATAG
1 TTTTTATATATATATATATATAG
* *
3853 ATATTATATATATATATATATTA-
1 TTTTTATATATATATATATA-TAG
3876 TTTTTATATATA
1 TTTTTATATATA
3888 GAATAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 27 0.93
24 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTTATATATATATATATATAG
Found at i:3883 original size:17 final size:17
Alignment explanation
Indices: 3840--3887 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
3830 TTTTTATCTA
*
3840 TATATATATATAGATAT
1 TATATATATATATATAT
3857 TATATATATATATATAT
1 TATATATATATATATAT
* *
3874 TATTTTTATATATA
1 TATATATATATATA
3888 GAATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:5350 original size:114 final size:115
Alignment explanation
Indices: 5222--5441 Score: 354
Period size: 114 Copynumber: 1.9 Consensus size: 115
5212 AGTAAAATTA
* *
5222 AAATATTTATAAAGATTTAGATTTAA-TTAAAAAAATAGAGTTTTTAGTAGAGTAAAACTATAAC
1 AAATATTTATAAAGATATAG-TTTAATTTAAAAAAATAGAGTTTTTAGTAAAGTAAAACTATAAC
*
5286 AGTTTAAACAATGACAGCTTA-AAATATGTTAGAAAAATAAGGGAATAAAT
65 AGTTTAAACAATGACAGCTTAGAAATATGATAGAAAAATAAGGGAATAAAT
* * *
5336 AAATATTTATAAAGATATAGTTTAATTTTAAAAAATGGAGTTTTTAGTAAAGTAAAACTGTAACA
1 AAATATTTATAAAGATATAGTTTAATTTAAAAAAATAGAGTTTTTAGTAAAGTAAAACTATAACA
*
5401 GTTTAAACAATGACAGTTTAGAAATATGATAGAAAAATAAG
66 GTTTAAACAATGACAGCTTAGAAATATGATAGAAAAATAAG
5442 AGTAAAATGG
Statistics
Matches: 97, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
113 5 0.05
114 73 0.75
115 19 0.20
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (115 bp):
AAATATTTATAAAGATATAGTTTAATTTAAAAAAATAGAGTTTTTAGTAAAGTAAAACTATAACA
GTTTAAACAATGACAGCTTAGAAATATGATAGAAAAATAAGGGAATAAAT
Found at i:6756 original size:17 final size:17
Alignment explanation
Indices: 6612--6745 Score: 168
Period size: 17 Copynumber: 8.1 Consensus size: 17
6602 TGGTGACCTC
6612 ACCAGGTGAGTA-TTGT
1 ACCAGGTGAGTATTTGT
* *
6628 A-CTGGTTGAGTATTT-C
1 ACCAGG-TGAGTATTTGT
* *
6644 ACCAGGTGAGT-GTTGC
1 ACCAGGTGAGTATTTGT
*
6660 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
* *
6677 ACTAGGTGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
6694 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
6711 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
6728 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
6745 A
1 A
6746 TTGGGTGAGT
Statistics
Matches: 104, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
15 5 0.05
16 25 0.24
17 74 0.71
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.35
Consensus pattern (17 bp):
ACCAGGTGAGTATTTGT
Done.