Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013974.1 Corchorus capsularis cultivar CVL-1 contig13995, 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: 15983
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Found at i:3735 original size:14 final size:14
Alignment explanation
Indices: 3716--3745 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3706 CCATGGATTG
3716 TCCCTCTTTATACT
1 TCCCTCTTTATACT
3730 TCCCTCTTTATACT
1 TCCCTCTTTATACT
3744 TC
1 TC
3746 ATATTGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.37, G:0.00, T:0.50
Consensus pattern (14 bp):
TCCCTCTTTATACT
Found at i:5659 original size:34 final size:35
Alignment explanation
Indices: 5607--5680 Score: 123
Period size: 34 Copynumber: 2.1 Consensus size: 35
5597 TTTGGTTGCA
5607 TTTAAAATGGCCAAAGTAAATTAAAAGGGTATAGC
1 TTTAAAATGGCCAAAGTAAATTAAAAGGGTATAGC
* *
5642 TTTAAAA-GGCCATAGTAAATTAAAAGGGTGTAGC
1 TTTAAAATGGCCAAAGTAAATTAAAAGGGTATAGC
5676 TTTAA
1 TTTAA
5681 TGATCATTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
34 30 0.81
35 7 0.19
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.28
Consensus pattern (35 bp):
TTTAAAATGGCCAAAGTAAATTAAAAGGGTATAGC
Found at i:5666 original size:18 final size:18
Alignment explanation
Indices: 5608--5668 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
5598 TTGGTTGCAT
*
5608 TTAAAATGGCCAAAGTAAA
1 TTAAAA-GGCCATAGTAAA
**
5627 TTAAAAGGGTATAGCT---
1 TTAAAAGGCCATAG-TAAA
5643 TTAAAAGGCCATAGTAAA
1 TTAAAAGGCCATAGTAAA
5661 TTAAAAGG
1 TTAAAAGG
5669 GTGTAGCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
15 1 0.03
16 12 0.36
18 13 0.39
19 7 0.21
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.25
Consensus pattern (18 bp):
TTAAAAGGCCATAGTAAA
Found at i:9281 original size:40 final size:41
Alignment explanation
Indices: 9167--9298 Score: 146
Period size: 40 Copynumber: 3.3 Consensus size: 41
9157 AGAAAGGGAT
** * * * *
9167 TAATCAGTAATTTGATAATCAAGAGTCAAG-GTAAGAG-AT
1 TAATCAGTAAAATGGTAATTAAGAGTCAAGAGTAAAAGAAG
* *
9206 TAATCAGTGAAATCAGTAATTAAAGAGTCAA-AGTAAAAGAAG
1 TAATCAGTAAAAT-GGTAATT-AAGAGTCAAGAGTAAAAGAAG
9248 TAATCAGTAAAATGGTAATTAAGAGT-AAGAGTAAAAGAAG
1 TAATCAGTAAAATGGTAATTAAGAGTCAAGAGTAAAAGAAG
9288 TAATCAGTAAA
1 TAATCAGTAAA
9299 TCGGTAAAGA
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
39 12 0.15
40 32 0.41
41 21 0.27
42 13 0.17
ACGTcount: A:0.50, C:0.06, G:0.20, T:0.24
Consensus pattern (41 bp):
TAATCAGTAAAATGGTAATTAAGAGTCAAGAGTAAAAGAAG
Found at i:9305 original size:40 final size:42
Alignment explanation
Indices: 9182--9305 Score: 152
Period size: 40 Copynumber: 3.1 Consensus size: 42
9172 AGTAATTTGA
* * * * *
9182 TAATCAAGAGTCAAG-GTAAGAG-ATTAATCAGTGAAATCAG
1 TAATTAAGAGTCAAGAGTAAAAGAAGTAATCAGTAAAATCGG
9222 TAATTAAAGAGTCAA-AGTAAAAGAAGTAATCAGTAAAAT-GG
1 TAATT-AAGAGTCAAGAGTAAAAGAAGTAATCAGTAAAATCGG
9263 TAATTAAGAGT-AAGAGTAAAAGAAGTAATCAGT-AAATCGG
1 TAATTAAGAGTCAAGAGTAAAAGAAGTAATCAGTAAAATCGG
9303 TAA
1 TAA
9306 AGAGTAAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
39 6 0.08
40 34 0.46
41 21 0.28
42 13 0.18
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.23
Consensus pattern (42 bp):
TAATTAAGAGTCAAGAGTAAAAGAAGTAATCAGTAAAATCGG
Found at i:9398 original size:22 final size:22
Alignment explanation
Indices: 9370--9598 Score: 125
Period size: 22 Copynumber: 10.1 Consensus size: 22
9360 AAAGTGATAA
9370 TAATCAGTAAAAGGTAAAATGG
1 TAATCAGTAAAAGGTAAAATGG
* *
9392 TAATCAGTAAGA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATGG
*
9413 TAATCAGT-AAAGAGTAAAATCG
1 TAATCAGTAAAAG-GTAAAATGG
** *
9435 TAAAAAGTAATAATCAGTAAAA-GG
1 TAATCAGTAA-AA--GGTAAAATGG
* *
9459 TAAAAT-GGTAATCAGTAAGAGCAAAATGG
1 T--AATCAGT-A--A--AAG-GTAAAATGG
*
9488 TAATCAGTAAAAAGTAAAA-GG
1 TAATCAGTAAAAGGTAAAATGG
* *
9509 TAATCAGTAAGA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATGG
*
9530 TAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATGG
*
9552 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAAGGTAA-AATGG
* *
9574 TCATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATGG
9596 TAA
1 TAA
9599 AAAAGTAATC
Statistics
Matches: 158, Mismatches: 27, Indels: 44
0.69 0.12 0.19
Matches are distributed among these distances:
20 9 0.06
21 44 0.28
22 63 0.40
23 8 0.05
24 4 0.03
25 9 0.06
26 3 0.02
27 4 0.03
28 8 0.05
29 6 0.04
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (22 bp):
TAATCAGTAAAAGGTAAAATGG
Found at i:9454 original size:17 final size:17
Alignment explanation
Indices: 9413--9461 Score: 66
Period size: 15 Copynumber: 3.0 Consensus size: 17
9403 AGCAAAATGG
*
9413 TAATCAGTAAAGAGTAA
1 TAATCAGTAAAAAGTAA
9430 -AATC-GTAAAAAGTAA
1 TAATCAGTAAAAAGTAA
*
9445 TAATCAGTAAAAGGTAA
1 TAATCAGTAAAAAGTAA
9462 AATGGTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 10 0.36
16 8 0.29
17 10 0.36
ACGTcount: A:0.55, C:0.06, G:0.16, T:0.22
Consensus pattern (17 bp):
TAATCAGTAAAAAGTAA
Found at i:9477 original size:75 final size:77
Alignment explanation
Indices: 9333--9743 Score: 322
Period size: 75 Copynumber: 5.4 Consensus size: 77
9323 AAAGTAAGAA
9333 GGTAATCAGTAAAGAGTAAAATAGTAAAAAGTGATAATAATCAGTAAAAGGTAAAATGGTAATCA
1 GGTAATCAGTAAAGAGTAAAATAGTAAAAAG-GATAATAATCAGTAAAAGGTAAAATGGTAATCA
9398 GTAAGAGCAAAAT
65 GTAAGAGCAAAAT
*
9411 GGTAATCAGTAAAGAGTAAAATCGTAAAAA-G-TAATAATCAGTAAAAGGTAAAATGGTAATCAG
1 GGTAATCAGTAAAGAGTAAAATAGTAAAAAGGATAATAATCAGTAAAAGGTAAAATGGTAATCAG
9474 TAAGAGCAAAAT
66 TAAGAGCAAAAT
* * * * *
9486 GGTAATCAGTAAAAAGTAAAA-GGTAATCAGTAA-GAGCAA-AAT-GGTAATCA-GT-AAA-GAG
1 GGTAATCAGTAAAGAGTAAAATAGTAA--A--AAGGA-TAATAATCAGTAA-AAGGTAAAATG-G
* *
9544 TAAAAT-AGTAATCAGTAAAAAGT
59 T--AATCAGTAA-GAG-CAAAA-T
* * *
9567 AAGAAGGTCATCAGTAAAGAGTAAAATAGT-AAAA--A-AGTAATCAGTAAAAGGTAAAATAGTA
1 -----GGTAATCAGTAAAGAGTAAAATAGTAAAAAGGATAATAATCAGTAAAAGGTAAAATGGTA
9628 ATCAGTAAGAGCAAAAAT
61 ATCAGTAAGAGC-AAAAT
* * * ** *
9646 GGTTATTAG-AAAGAGTAAAATAGT-AAAA--A-AGTAATCAGTGTAAGGTAAAATAGTAATCAG
1 GGTAATCAGTAAAGAGTAAAATAGTAAAAAGGATAATAATCAGTAAAAGGTAAAATGGTAATCAG
*
9706 TAAGAGCTAAAT
66 TAAGAGCAAAAT
* * *
9718 GGTTATTAG-AAAGAGTAAGATAGTAA
1 GGTAATCAGTAAAGAGTAAAATAGTAA
9744 TCTGTAAAGA
Statistics
Matches: 283, Mismatches: 23, Indels: 59
0.78 0.06 0.16
Matches are distributed among these distances:
72 27 0.10
73 57 0.20
74 11 0.04
75 64 0.23
76 3 0.01
77 5 0.02
78 43 0.15
79 11 0.04
80 19 0.07
81 13 0.05
82 7 0.02
84 1 0.00
86 20 0.07
87 2 0.01
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.22
Consensus pattern (77 bp):
GGTAATCAGTAAAGAGTAAAATAGTAAAAAGGATAATAATCAGTAAAAGGTAAAATGGTAATCAG
TAAGAGCAAAAT
Found at i:9512 original size:117 final size:118
Alignment explanation
Indices: 9370--9720 Score: 423
Period size: 117 Copynumber: 3.0 Consensus size: 118
9360 AAAGTGATAA
*
9370 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGTAAAATCG
1 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGTAAAATAG
*
9435 TAAAAAGTAATAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGG
66 TAAAAAGTAATAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGCAAAATGG
*
9488 TAATCAGTAAAAAGTAAAA-GGTAATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGTAAAATAG
** * ** * * **
9552 TAATCAGTAA-AA--AGTAAGAAGGT--CATCAGTAAAGAGTAAAATAGTAAAAAAG
66 TAAAAAGTAATAATCAGTAA-AAGGTAAAAT-AGTAATCAGT--AAGAGCAAAATGG
* * *
9604 TAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGCAAAAATGGTTATTAG-AAAGAGTAAAATA
1 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGC-AAAATGGTAATCAGTAAAGAGTAAAATA
* ** *
9668 GTAAAAA--AGTAATCAGTGTAAGGTAAAATAGTAATCAGTAAGAGCTAAATGG
65 GTAAAAAGTAATAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGCAAAATGG
9720 T
1 T
9721 TATTAGAAAG
Statistics
Matches: 193, Mismatches: 29, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
113 2 0.01
114 12 0.06
115 6 0.03
116 40 0.21
117 90 0.47
118 41 0.21
119 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.22
Consensus pattern (118 bp):
TAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGTAAAATAG
TAAAAAGTAATAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGCAAAATGG
Found at i:9610 original size:30 final size:29
Alignment explanation
Indices: 9557--9628 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
9547 AATAGTAATC
* * *
9557 AGTAAAA-AGTAAGAAGGTCATCAGTAAA
1 AGTAAAATAGTAAAAAAGTAATCAGTAAA
9585 GAGTAAAATAGTAAAAAAGTAATCAGTAAA
1 -AGTAAAATAGTAAAAAAGTAATCAGTAAA
9615 AGGTAAAATAGTAA
1 A-GTAAAATAGTAA
9629 TCAGTAAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.21
30 30 0.79
ACGTcount: A:0.57, C:0.04, G:0.19, T:0.19
Consensus pattern (29 bp):
AGTAAAATAGTAAAAAAGTAATCAGTAAA
Found at i:9618 original size:44 final size:43
Alignment explanation
Indices: 9445--9620 Score: 135
Period size: 42 Copynumber: 4.1 Consensus size: 43
9435 TAAAAAGTAA
* ** * *
9445 TAATCAGTAAA-AGGTAAAATGGTAATCAGT-AAGAGCAAAATGG
1 TAATCAGTAAAGA-GTAAAATAGTAAAAAGTAAAAAGTAAAA-GG
* * ** * *
9488 TAATCAGTAAAAAGTAAAA-GGTAATCAGT-AAGAGCAAAATGG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAAAGTAAAA-GG
**
9530 TAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAAAGTAA-AAGG
* **
9574 TCATCAGTAAAGAGTAAAATAGTAAAAAAGTAATCAGTAAAAGG
1 TAATCAGTAAAGAGTAAAATAGT-AAAAAGTAAAAAGTAAAAGG
9618 TAA
1 TAA
9621 AATAGTAATC
Statistics
Matches: 118, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
42 41 0.35
43 26 0.22
44 37 0.31
45 14 0.12
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.20
Consensus pattern (43 bp):
TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAAAGTAAAAGG
Found at i:9644 original size:22 final size:21
Alignment explanation
Indices: 9597--9671 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 21
9587 GTAAAATAGT
*
9597 AAAAA-AGTAATCAGTAAAAGG
1 AAAAATAGTAATCAGTAAGA-G
*
9618 TAAAATAGTAATCAGTAAGAG
1 AAAAATAGTAATCAGTAAGAG
* * * *
9639 CAAAAATGGTTATTAGAAAGAG
1 -AAAAATAGTAATCAGTAAGAG
*
9661 TAAAATAGTAA
1 AAAAATAGTAA
9672 AAAAGTAATC
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 13 0.31
22 29 0.69
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.21
Consensus pattern (21 bp):
AAAAATAGTAATCAGTAAGAG
Found at i:9691 original size:73 final size:72
Alignment explanation
Indices: 9529--9743 Score: 299
Period size: 73 Copynumber: 2.9 Consensus size: 72
9519 GAGCAAAATG
* * * * *
9529 GTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAA-GGTCATCAGTAAAGAGTAAAA
1 GTAATCAGTAAAG-GTAAAATAGTAATCAGT-AAGAGCAAAAATGGTTATTAG-AAAGAGTAAAA
9593 TAGTAAAAAA
63 TAGTAAAAAA
9603 GTAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGCAAAAATGGTTATTAGAAAGAGTAAAATA
1 GTAATCAGT-AAAGGTAAAATAGTAATCAGTAAGAGCAAAAATGGTTATTAGAAAGAGTAAAATA
9668 GTAAAAAA
65 GTAAAAAA
* * *
9676 GTAATCAGTGTAAGGTAAAATAGTAATCAGTAAGAGC-TAAATGGTTATTAGAAAGAGTAAGATA
1 GTAATCAGT-AAAGGTAAAATAGTAATCAGTAAGAGCAAAAATGGTTATTAGAAAGAGTAAAATA
9740 GTAA
65 GTAA
9744 TCTGTAAAGA
Statistics
Matches: 130, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
72 29 0.22
73 64 0.49
74 33 0.25
75 4 0.03
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (72 bp):
GTAATCAGTAAAGGTAAAATAGTAATCAGTAAGAGCAAAAATGGTTATTAGAAAGAGTAAAATAG
TAAAAAA
Found at i:9716 original size:22 final size:21
Alignment explanation
Indices: 9667--9755 Score: 65
Period size: 21 Copynumber: 4.1 Consensus size: 21
9657 AGAGTAAAAT
*
9667 AGTAAAAAAGTAATCAGTGTAAG
1 AGTAAAATAGTAATCA--GTAAG
9690 -GTAAAATAGTAATCAGTAAG
1 AGTAAAATAGTAATCAGTAAG
* * * *
9710 AGCT-AAATGGTTATTAGAAAG
1 AG-TAAAATAGTAATCAGTAAG
* *
9731 AGTAAGATAGTAATCTGTAAAG
1 AGTAAAATAGTAATCAGT-AAG
9753 AGT
1 AGT
9756 GAAAGGTGAT
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
20 6 0.12
21 24 0.47
22 21 0.41
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.26
Consensus pattern (21 bp):
AGTAAAATAGTAATCAGTAAG
Found at i:11107 original size:17 final size:19
Alignment explanation
Indices: 11080--11117 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
11070 TACTAACTAA
*
11080 TTTCTTTTGTTGTTT-GCT
1 TTTCTTTTGTTCTTTCGCT
11098 TTTC-TTTGTTCTTTCGCT
1 TTTCTTTTGTTCTTTCGCT
11116 TT
1 TT
11118 GCATTTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.00, C:0.16, G:0.13, T:0.71
Consensus pattern (19 bp):
TTTCTTTTGTTCTTTCGCT
Found at i:13717 original size:13 final size:13
Alignment explanation
Indices: 13699--13731 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
13689 ATGAATGATG
*
13699 ATAATAATAAATA
1 ATAATAATAAAAA
13712 ATAATAATAAAAA
1 ATAATAATAAAAA
13725 ATAATAA
1 ATAATAA
13732 CGATTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
ATAATAATAAAAA
Done.