Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011892.1 Corchorus olitorius cultivar O-4 contig11925, 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: 5947
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Found at i:115 original size:10 final size:10
Alignment explanation
Indices: 102--142 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
92 CCCCAATATA
102 CATAAAAATC
1 CATAAAAATC
**
112 CATAAAAAGA
1 CATAAAAATC
*
122 CATAAACATC
1 CATAAAAATC
132 CATAAAAATC
1 CATAAAAATC
142 C
1 C
143 CAAAATATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.59, C:0.22, G:0.02, T:0.17
Consensus pattern (10 bp):
CATAAAAATC
Found at i:124 original size:20 final size:20
Alignment explanation
Indices: 101--139 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
91 ACCCCAATAT
101 ACATAAAAATCCATAAAAAG
1 ACATAAAAATCCATAAAAAG
*
121 ACATAAACATCCATAAAAA
1 ACATAAAAATCCATAAAAA
140 TCCCAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.18, G:0.03, T:0.15
Consensus pattern (20 bp):
ACATAAAAATCCATAAAAAG
Found at i:2194 original size:27 final size:27
Alignment explanation
Indices: 2164--2231 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
2154 AGGACCAGCG
2164 GCAGCCTC-CCTCTCCCTATACATCCGA
1 GCAGCCTCACC-CTCCCTATACATCCGA
* *
2191 GCAGCCTCAGCCTCCCTATACATCTGA
1 GCAGCCTCACCCTCCCTATACATCCGA
*
2218 GCAGCCTCAGCCTC
1 GCAGCCTCACCCTC
2232 TTTATCCCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.46, G:0.15, T:0.21
Consensus pattern (27 bp):
GCAGCCTCACCCTCCCTATACATCCGA
Found at i:2240 original size:33 final size:27
Alignment explanation
Indices: 2175--2231 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
2165 CAGCCTCCCT
2175 CTCCCTATACATCCGAGCAGCCTCAGC
1 CTCCCTATACATCCGAGCAGCCTCAGC
*
2202 CTCCCTATACATCTGAGCAGCCTCAGC
1 CTCCCTATACATCCGAGCAGCCTCAGC
2229 CTC
1 CTC
2232 TTTATCCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.44, G:0.14, T:0.21
Consensus pattern (27 bp):
CTCCCTATACATCCGAGCAGCCTCAGC
Found at i:2519 original size:26 final size:25
Alignment explanation
Indices: 2490--2566 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
2480 TAATTAATTT
*
2490 TAATTAAATTTCATAAACTAATTAAC
1 TAATTAAA-TTAATAAACTAATTAAC
2516 TAATTACAATTAATAAACTAA-T---
1 TAATTA-AATTAATAAACTAATTAAC
*
2538 T-A-TCAATTAATAAACTAATTAAC
1 TAATTAAATTAATAAACTAATTAAC
2561 TAATTA
1 TAATTA
2567 CAAAAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 15
0.69 0.05 0.25
Matches are distributed among these distances:
19 14 0.34
20 2 0.05
21 1 0.02
22 1 0.02
23 1 0.02
24 1 0.02
25 2 0.05
26 17 0.41
27 2 0.05
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (25 bp):
TAATTAAATTAATAAACTAATTAAC
Found at i:2546 original size:19 final size:18
Alignment explanation
Indices: 2508--2558 Score: 84
Period size: 19 Copynumber: 2.8 Consensus size: 18
2498 TTTCATAAAC
*
2508 TAATTAACTAATTACAAT
1 TAATAAACTAATTACAAT
2526 TAATAAACTAATTATCAAT
1 TAATAAACTAATTA-CAAT
2545 TAATAAACTAATTA
1 TAATAAACTAATTA
2559 ACTAATTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAAACTAATTACAAT
Found at i:2564 original size:27 final size:26
Alignment explanation
Indices: 2526--2579 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
2516 TAATTACAAT
**
2526 TAATAAACTAATTATCAATTAATAAAC
1 TAATAAACTAATTA-CAAAAAATAAAC
*
2553 TAATTAACTAATTACAAAAAATAAAC
1 TAATAAACTAATTACAAAAAATAAAC
2579 T
1 T
2580 CATTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (26 bp):
TAATAAACTAATTACAAAAAATAAAC
Found at i:3595 original size:101 final size:103
Alignment explanation
Indices: 3361--3617 Score: 362
Period size: 107 Copynumber: 2.5 Consensus size: 103
3351 TATTATAGAA
*
3361 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAAATTAAAATTTTATTTTTAT
1 TTTTAGAAATAAAATATAAAA-TAATTTCACTAAGTTTAGCCCCAAATT--AATTTTATTTTTAT
*
3426 TTTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGGG
63 TTTAAGGGTAAATTCCAAAATTAATAA-TTATTGTTATAGGG
* * *
3468 TTTTAGAAATAAAATACGAAACTAATTTCACTAATTTTAGCCCCAAATTAA-TTT-TTTTTATTT
1 TTTTAGAAATAAAATA-TAAAATAATTTCACTAAGTTTAGCCCCAAATTAATTTTATTTTTATTT
*
3531 TAAGGGTAAATTCCATAATTAATAA-TATTGTTATAGGG
65 TAAGGGTAAATTCCAAAATTAATAATTATTGTTATAGGG
*
3569 TTTTAGAAATAAAATATATAAATAA-TTCACTAAGTTTAG-TCCAAATTAA
1 TTTTAGAAATAAAATATA-AAATAATTTCACTAAGTTTAGCCCCAAATTAA
3618 AATTAAAATT
Statistics
Matches: 138, Mismatches: 10, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
99 9 0.07
100 14 0.10
101 34 0.25
103 32 0.23
104 3 0.02
105 2 0.01
107 41 0.30
108 3 0.02
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (103 bp):
TTTTAGAAATAAAATATAAAATAATTTCACTAAGTTTAGCCCCAAATTAATTTTATTTTTATTTT
AAGGGTAAATTCCAAAATTAATAATTATTGTTATAGGG
Found at i:3630 original size:103 final size:102
Alignment explanation
Indices: 3361--3638 Score: 366
Period size: 103 Copynumber: 2.7 Consensus size: 102
3351 TATTATAGAA
3361 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAAATTAAAATTTTATTTTTAT
1 TTTTAGAAATAAAATATAAAA-TAATTTCACTAAGTTTAGCCC-AAATTAAAA--TTATTTTTAT
*
3426 TTTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGGG
62 TTTAAGGGTAAATTCCAAAATTAATAA-TTATTGTTATAGGG
* * * *
3468 TTTTAGAAATAAAATACGAAACTAATTTCACTAATTTTAGCCCCAAATT--AATTTTTTTTATTT
1 TTTTAGAAATAAAATA-TAAAATAATTTCACTAAGTTTAG-CCCAAATTAAAATTATTTTTATTT
*
3531 TAAGGGTAAATTCCATAATTAATAA-TATTGTTATAGGG
64 TAAGGGTAAATTCCAAAATTAATAATTATTGTTATAGGG
* *
3569 TTTTAGAAATAAAATATATAAATAA-TTCACTAAGTTTAGTCCAAATTAAAATTAAAATTTTATT
1 TTTTAGAAATAAAATATA-AAATAATTTCACTAAGTTTAGCCCAAATTAAAATT--ATTTTTATT
3633 TTAAGG
63 TTAAGG
3639 ATTAGAAAAA
Statistics
Matches: 152, Mismatches: 12, Indels: 18
0.84 0.07 0.10
Matches are distributed among these distances:
99 7 0.05
100 14 0.09
101 38 0.25
103 47 0.31
105 2 0.01
107 38 0.25
108 6 0.04
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (102 bp):
TTTTAGAAATAAAATATAAAATAATTTCACTAAGTTTAGCCCAAATTAAAATTATTTTTATTTTA
AGGGTAAATTCCAAAATTAATAATTATTGTTATAGGG
Found at i:5678 original size:16 final size:16
Alignment explanation
Indices: 5659--5701 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
5649 TCCGAACCCG
*
5659 CCCGAACCCGAAATTA
1 CCCGAACCCGAAAATA
*
5675 CCCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
5691 CCCGAACCCGA
1 CCCGAACCCGA
5702 CCCGAGACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.35, C:0.42, G:0.16, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:5717 original size:17 final size:17
Alignment explanation
Indices: 5692--5746 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
5682 CCGAAAATAC
*
5692 CCGAACCCGACCCGAGA
1 CCGAGCCCGACCCGAGA
5709 CCGAGCCCGACCCGAGA
1 CCGAGCCCGACCCGAGA
* *
5726 CCGAGCCCGACTCGAGC
1 CCGAGCCCGACCCGAGA
5743 CCGA
1 CCGA
5747 ACCTGAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.24, C:0.47, G:0.27, T:0.02
Consensus pattern (17 bp):
CCGAGCCCGACCCGAGA
Done.