Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009467.1 Corchorus capsularis cultivar CVL-1 contig09488, 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: 17149
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1863 original size:70 final size:70
Alignment explanation
Indices: 1786--2088 Score: 325
Period size: 70 Copynumber: 4.3 Consensus size: 70
1776 AAAAAGTAGA
* * * *
1786 AATCAGTAAATCAGTAATTAAGTAAAAGAGATTAATCAGTAAAGTGATAATCAAGAATCAAGGCA
1 AATCAGTAAATCAGTAATTAAGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTA
1851 ATAGT
66 ATAGT
* *
1856 AATCAGTAAATCAG----T-A--AAAAGAGATCAATCAGCAAATTGATAATTAAGAGTCAAGGTA
1 AATCAGTAAATCAGTAATTAAGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTA
*
1914 ATGGT
66 ATAGT
* *
1919 AATCAGCAAGTCAGTAATTAAGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTA
1 AATCAGTAAATCAGTAATTAAGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTA
1984 ATAGT
66 ATAGT
* * * * *
1989 GATCAGTAAAGTCAGTAATCAAGAGTCAAGGTAA-AAATGGTAATCAGTAAATCGATAATGAAGA
1 AATCAGTAAA-TCAGTAAT-TA-AGT-AA---AAGAGAT--TAATCAGTAAATTGATAATTAAGA
* *
2053 GTCAAAGTGATAGT
57 GTCAAGGTAATAGT
2067 AATCAGTAAATCAGTAATTAAG
1 AATCAGTAAATCAGTAATTAAG
2089 AGTTGAGTGA
Statistics
Matches: 194, Mismatches: 23, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
63 52 0.27
65 1 0.01
66 1 0.01
67 1 0.01
68 1 0.01
70 65 0.34
71 8 0.04
72 1 0.01
73 3 0.02
74 2 0.01
75 2 0.01
76 4 0.02
77 10 0.05
78 43 0.22
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.25
Consensus pattern (70 bp):
AATCAGTAAATCAGTAATTAAGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTA
ATAGT
Found at i:1897 original size:63 final size:63
Alignment explanation
Indices: 1794--2006 Score: 239
Period size: 63 Copynumber: 3.3 Consensus size: 63
1784 GAAATCAGTA
* * * * * *
1794 AATCAGTAATTAAGT-AAAAGAGATTAATCAGTAAAGTGATAATCAAGAATCAAGGCAATAGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGT
* * *
1856 AATCAGTAAATCAGTAAAAAGAGATCAATCAGCAAATTGATAATTAAGAGTCAAGGTAATGGT
1 AATCAGTAAATCAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGT
* *
1919 AATCAGCAAGTCAGTAATTAAGTAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTA
1 AATCAGTAAATCAG----T-A--AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTA
1984 ATAGT
59 ATAGT
*
1989 GATCAGTAAAGTCAGTAA
1 AATCAGTAAA-TCAGTAA
2007 TCAAGAGTCA
Statistics
Matches: 125, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
62 13 0.10
63 52 0.42
64 1 0.01
66 1 0.01
67 2 0.02
68 1 0.01
70 51 0.41
71 4 0.03
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.25
Consensus pattern (63 bp):
AATCAGTAAATCAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGT
Found at i:2591 original size:16 final size:16
Alignment explanation
Indices: 2570--2627 Score: 80
Period size: 16 Copynumber: 3.5 Consensus size: 16
2560 TAAACAAGAG
*
2570 AGTAAAAATGGTATCA
1 AGTAAAAATGGTATTA
*
2586 AGTAAAGATGGTATTA
1 AGTAAAAATGGTATTA
2602 AGGTCAAAAATGGTATTA
1 A-GT-AAAAATGGTATTA
2620 AGTAAAAA
1 AGTAAAAA
2628 GGGTCAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 20 0.54
17 4 0.11
18 13 0.35
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (16 bp):
AGTAAAAATGGTATTA
Found at i:2611 original size:61 final size:60
Alignment explanation
Indices: 2549--2664 Score: 166
Period size: 60 Copynumber: 1.9 Consensus size: 60
2539 AAGAGTTAAA
*
2549 AAAAATGGTATTAA-ACAAGAGAGT-AAAAATGGTATCAAGTAAAG-ATGGTATTAAGGTC
1 AAAAATGGTATTAAGA-AAAAGAGTCAAAAATGGTATCAAGTAAAGTATGGTATTAAGGTC
* *
2607 AAAAATGGTATTAAGTAAAAAGGGTCAAAATTGGTATCAAGTAAAGTATGGTATTAAG
1 AAAAATGGTATTAAG-AAAAAGAGTCAAAAATGGTATCAAGTAAAGTATGGTATTAAG
2665 TAAGAAGGTC
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
58 14 0.27
59 6 0.12
60 20 0.39
61 11 0.22
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.26
Consensus pattern (60 bp):
AAAAATGGTATTAAGAAAAAGAGTCAAAAATGGTATCAAGTAAAGTATGGTATTAAGGTC
Found at i:2729 original size:21 final size:21
Alignment explanation
Indices: 2705--2748 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2695 AAAAACTGGA
*
2705 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCAATTT
*
2726 TTGCTATTCACCGCCCAATTT
1 TTGCTAATCACCGCCCAATTT
2747 TT
1 TT
2749 CACGCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.20, C:0.32, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAATCACCGCCCAATTT
Found at i:3010 original size:34 final size:32
Alignment explanation
Indices: 2935--3027 Score: 123
Period size: 32 Copynumber: 2.8 Consensus size: 32
2925 TGACCCGTGC
**
2935 TGGGCAGGCCGCCCCAAGAGGGCGGCTTACCA
1 TGGGCAGGCCGCCCCACTAGGGCGGCTTACCA
*
2967 TGGGCAGGCCGCCCCACTTGGGCGGCTTCACCA
1 TGGGCAGGCCGCCCCACTAGGGCGGCTT-ACCA
* *
3000 TTGGGCAGGCCGCCTCACTGGGGCGGCT
1 -TGGGCAGGCCGCCCCACTAGGGCGGCT
3028 CGGCTATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 25 0.46
33 4 0.07
34 25 0.46
ACGTcount: A:0.13, C:0.35, G:0.38, T:0.14
Consensus pattern (32 bp):
TGGGCAGGCCGCCCCACTAGGGCGGCTTACCA
Found at i:3214 original size:32 final size:32
Alignment explanation
Indices: 3166--3299 Score: 162
Period size: 32 Copynumber: 4.2 Consensus size: 32
3156 AAAAAAAAAA
* *
3166 CCTGCCTTGACGAAGCCGCCCCACCGGGGCGG
1 CCTGCCGTGGCGAAGCCGCCCCACCGGGGCGG
* * * *
3198 CCTACCGTGGCAAAGCCACCCCA-TGAGGGCGG
1 CCTGCCGTGGCGAAGCCGCCCCACCG-GGGCGG
* *
3230 CCTGCCTTGGCGAAGCCGCCCCACCCGGGCGG
1 CCTGCCGTGGCGAAGCCGCCCCACCGGGGCGG
**
3262 CCTGCCGTGGCGAAGCCGCCCCAGTGGGGCGG
1 CCTGCCGTGGCGAAGCCGCCCCACCGGGGCGG
3294 CCTGCC
1 CCTGCC
3300 CATGGTGAAG
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
31 1 0.01
32 83 0.99
ACGTcount: A:0.13, C:0.43, G:0.35, T:0.10
Consensus pattern (32 bp):
CCTGCCGTGGCGAAGCCGCCCCACCGGGGCGG
Found at i:3270 original size:64 final size:64
Alignment explanation
Indices: 3166--3299 Score: 207
Period size: 64 Copynumber: 2.1 Consensus size: 64
3156 AAAAAAAAAA
*
3166 CCTGCCTTGACGAAGCCGCCCCACCGGGGCGGCCTACCGTGGCAAAGCCACCCCA-TGAGGGCGG
1 CCTGCCTTGACGAAGCCGCCCCACCCGGGCGGCCTACCGTGGCAAAGCCACCCCAGTG-GGGCGG
* * * *
3230 CCTGCCTTGGCGAAGCCGCCCCACCCGGGCGGCCTGCCGTGGCGAAGCCGCCCCAGTGGGGCGG
1 CCTGCCTTGACGAAGCCGCCCCACCCGGGCGGCCTACCGTGGCAAAGCCACCCCAGTGGGGCGG
3294 CCTGCC
1 CCTGCC
3300 CATGGTGAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
64 62 0.97
65 2 0.03
ACGTcount: A:0.13, C:0.43, G:0.35, T:0.10
Consensus pattern (64 bp):
CCTGCCTTGACGAAGCCGCCCCACCCGGGCGGCCTACCGTGGCAAAGCCACCCCAGTGGGGCGG
Found at i:3323 original size:33 final size:32
Alignment explanation
Indices: 3166--3323 Score: 122
Period size: 32 Copynumber: 4.9 Consensus size: 32
3156 AAAAAAAAAA
* * * **
3166 CCTGCCTTGACGAAGCCGCCCCACCGGGGCGG
1 CCTGCCATGGCGAAGCCGACCCAGTGGGGCGG
* * *
3198 CCTACCGTGGCAAAGCC-ACCCCA-TGAGGGCGG
1 CCTGCCATGGCGAAGCCGA-CCCAGTG-GGGCGG
* * ***
3230 CCTGCCTTGGCGAAGCCGCCCCACCCGGGCGG
1 CCTGCCATGGCGAAGCCGACCCAGTGGGGCGG
* *
3262 CCTGCCGTGGCGAAGCCGCCCCAGTGGGGCGG
1 CCTGCCATGGCGAAGCCGACCCAGTGGGGCGG
* *
3294 CCTGCCCATGGTGAAGTCGACCCAGTGGGG
1 CCTG-CCATGGCGAAGCCGACCCAGTGGGG
3324 AGGCTCCGCC
Statistics
Matches: 101, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
31 1 0.01
32 79 0.78
33 21 0.21
ACGTcount: A:0.14, C:0.39, G:0.36, T:0.11
Consensus pattern (32 bp):
CCTGCCATGGCGAAGCCGACCCAGTGGGGCGG
Found at i:3409 original size:15 final size:15
Alignment explanation
Indices: 3368--3409 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
3358 GGCTCAGTGT
*
3368 AAAAGTGTAAAAAGGGT
1 AAAAGTGT--AAAGGGC
3385 AAAA-TGTAAAGGGC
1 AAAAGTGTAAAGGGC
3399 AAAAGTGTAAA
1 AAAAGTGTAAA
3410 AAGTGGGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.43
15 6 0.26
16 3 0.13
17 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17
Consensus pattern (15 bp):
AAAAGTGTAAAGGGC
Found at i:3485 original size:27 final size:27
Alignment explanation
Indices: 3437--3493 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
3427 GCAACCCCAC
*
3437 AAAAAAATGGTATCAAGTAAAA-GAGTA
1 AAAAAAATGGTATAAAGTAAAATGA-TA
3464 AAAAAAATGGTA-AAAGTAAAAATGATA
1 AAAAAAATGGTATAAAGT-AAAATGATA
3491 AAA
1 AAA
3494 GTAGCAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
27 21 0.78
28 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.16, T:0.18
Consensus pattern (27 bp):
AAAAAAATGGTATAAAGTAAAATGATA
Found at i:3486 original size:15 final size:15
Alignment explanation
Indices: 3466--3496 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3456 AAAGAGTAAA
*
3466 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
3481 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
3496 A
1 A
3497 GCAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Found at i:4108 original size:2 final size:2
Alignment explanation
Indices: 4101--4129 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4091 ATTCATAACA
4101 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 A
4130 CACTAGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16261 original size:12 final size:13
Alignment explanation
Indices: 16220--16264 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
16210 AATTATTGTT
*
16220 TGCTTTATTGATC
1 TGCTTTATTAATC
*
16233 TGCTTTATTAATT
1 TGCTTTATTAATC
16246 TGCTTTA-TAATC
1 TGCTTTATTAATC
16258 TGCTTTA
1 TGCTTTA
16265 GATTTAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:16272 original size:6 final size:6
Alignment explanation
Indices: 16261--16287 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16251 TATAATCTGC
16261 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
16288 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Done.