Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013468.1 Corchorus capsularis cultivar CVL-1 contig13489, 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: 12349
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Found at i:975 original size:42 final size:42
Alignment explanation
Indices: 918--1106 Score: 351
Period size: 42 Copynumber: 4.5 Consensus size: 42
908 AACGGAGTGC
918 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
*
960 TGAAATGCAGGTTTTGAATTTTGACTTTTGAAGAATGAACCG
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
*
1002 TGAAATGCAAGTTTTGAATTTTGACGTTTGAAGAATGAACCG
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
1044 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
1 TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
*
1086 TGAAATGCAGGTTTTGAATTT
1 TGAAATGCAAGTTTTGAATTT
1107 CGAACCATGA
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 142 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (42 bp):
TGAAATGCAAGTTTTGAATTTTGACTTTTGAAGAATGAACCG
Found at i:1111 original size:28 final size:28
Alignment explanation
Indices: 1080--1134 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1070 TTTGAAGAAT
* *
1080 GAACCGTGAAATGCAGGTTTTGAATTTC
1 GAACCATGAAATGCAGATTTTGAATTTC
* *
1108 GAACCATGAGATGCTGATTTTGAATTT
1 GAACCATGAAATGCAGATTTTGAATTT
1135 TGATTTTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.35
Consensus pattern (28 bp):
GAACCATGAAATGCAGATTTTGAATTTC
Found at i:1136 original size:35 final size:35
Alignment explanation
Indices: 1097--1180 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
1087 GAAATGCAGG
* * **
1097 TTTTGAATTTCGAACCATGAGATGCTGATTTTGAA
1 TTTTGATTTTCGAACCATGAAATGCAAATTTTGAA
* *
1132 TTTTGATTTTTGAATCATGAAATGCAAATTTTGAA
1 TTTTGATTTTCGAACCATGAAATGCAAATTTTGAA
*
1167 CTTTGATTTTCGAA
1 TTTTGATTTTCGAA
1181 GAATAGAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.44
Consensus pattern (35 bp):
TTTTGATTTTCGAACCATGAAATGCAAATTTTGAA
Found at i:1456 original size:37 final size:37
Alignment explanation
Indices: 1415--1777 Score: 248
Period size: 37 Copynumber: 9.8 Consensus size: 37
1405 TTGTTTTCGA
*
1415 ACACCTAAACAAGGATCATT-AACAAGATTTTGATGAG
1 ACACCTAAACAAGGATC-TTAAACAAGATTTTGATAAG
* * *
1452 ACACCTAAATAGGGA-CTTTAAATAAGGA-TTTGATAAG
1 ACACCTAAACAAGGATC-TTAAACAA-GATTTTGATAAG
* * * * * *
1489 AAACCTAAAC-AGGCATCTTGAAGAAGGTTTTGATGAC
1 ACACCTAAACAAGG-ATCTTAAACAAGATTTTGATAAG
* * *
1526 ACACCTAAAC-AGGTACCTTAAATAAAGATTTTGGTAAG
1 ACACCTAAACAAGG-ATCTTAAA-CAAGATTTTGATAAG
* * *
1564 AAACCTAAA-TAGGAATCTTGAACAAGATTTTGAT--G
1 ACACCTAAACAAGG-ATCTTAAACAAGATTTTGATAAG
* * *
1599 ACACCTAAACAGGGACCTTAAACAAGGA-TTTAATAAG
1 ACACCTAAACAAGGATCTTAAACAA-GATTTTGATAAG
* * *
1636 AAACCTAAAC-AGGAATCTTGAACAAGATTTTGATGAG
1 ACACCTAAACAAGG-ATCTTAAACAAGATTTTGATAAG
* *
1673 ACACCTAAACAGGGACCTTAAACAAGGA-TTTGATAAG
1 ACACCTAAACAAGGATCTTAAACAA-GATTTTGATAAG
* * *
1710 AAATCTAAAC-AGGTATCTTGAACAAGATTTTGATGAA-
1 ACACCTAAACAAGG-ATCTTAAACAAGATTTTGAT-AAG
* * *
1747 ACACCTAAACAGGGATTTTAAATAAGGATTT
1 ACACCTAAACAAGGATCTTAAACAA-GATTT
1778 GTCATGAAAA
Statistics
Matches: 250, Mismatches: 56, Indels: 39
0.72 0.16 0.11
Matches are distributed among these distances:
35 23 0.09
36 18 0.07
37 166 0.66
38 43 0.17
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.25
Consensus pattern (37 bp):
ACACCTAAACAAGGATCTTAAACAAGATTTTGATAAG
Found at i:1547 original size:74 final size:74
Alignment explanation
Indices: 1417--1778 Score: 507
Period size: 74 Copynumber: 4.9 Consensus size: 74
1407 GTTTTCGAAC
* *
1417 ACCTAAACAAGG-ATCATT-AACAAGATTTTGATGAGACACCTAAATAGGGACTTTAAATAAGGA
1 ACCTAAAC-AGGAATC-TTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA
1480 TTTGATAAGAA
64 TTTGATAAGAA
* * * * * *
1491 ACCTAAACAGGCATCTTGAAGAAGGTTTTGATGACACACCTAAACAGGTACCTTAAATAAAGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA-T
*
1556 TTGGTAAGAA
65 TTGATAAGAA
* *
1566 ACCTAAATAGGAATCTTGAACAAGATTTTGAT--GACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
*
1629 TAATAAGAA
66 TGATAAGAA
*
1638 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
1703 TGATAAGAA
66 TGATAAGAA
* * * **
1712 ATCTAAACAGGTATCTTGAACAAGATTTTGATGAAACACCTAAACAGGGATTTTAAATAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
1777 TG
66 TG
1779 TCATGAAAAA
Statistics
Matches: 257, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
72 40 0.16
73 30 0.12
74 149 0.58
75 38 0.15
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (74 bp):
ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
TGATAAGAA
Found at i:2826 original size:19 final size:18
Alignment explanation
Indices: 2799--2850 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
2789 TTCCTTTTGA
* *
2799 TTTTCTTTTCTTTTTCTCC
1 TTTTTTTTTCTTTTGCT-C
*
2818 TTTTTTTTTCTTTTGCTT
1 TTTTTTTTTCTTTTGCTC
2836 TCTTTTTTTTCTTTT
1 T-TTTTTTTTCTTTT
2851 AGATCGCTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTTTTCTTTTGCTC
Found at i:3535 original size:14 final size:14
Alignment explanation
Indices: 3503--3554 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
3493 ATTCAAAACC
*
3503 TTTTTGAAAACTCA-
1 TTTTTG-AAAGTCAT
3517 TTTTTGAAAGTCATT
1 TTTTTGAAAGTCA-T
3532 TTTTTGAAAG-CAT
1 TTTTTGAAAGTCAT
3545 TTTCTTGAAA
1 TTT-TTGAAA
3555 ATCTTTTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 10 0.29
14 14 0.41
15 10 0.29
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (14 bp):
TTTTTGAAAGTCAT
Found at i:3535 original size:15 final size:14
Alignment explanation
Indices: 3517--3554 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
3507 TGAAAACTCA
3517 TTTTTGAAAGTCATT
1 TTTTTGAAAG-CATT
3532 TTTTTGAAAGCATT
1 TTTTTGAAAGCATT
*
3546 TTCTTGAAA
1 TTTTTGAAA
3555 ATCTTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (14 bp):
TTTTTGAAAGCATT
Found at i:3643 original size:12 final size:10
Alignment explanation
Indices: 3626--3678 Score: 70
Period size: 10 Copynumber: 4.9 Consensus size: 10
3616 CACAATTCTT
3626 TTTTTTTTTA
1 TTTTTTTTTA
3636 CCTTTTTTTTTA
1 --TTTTTTTTTA
3648 TTTTTTTTTA
1 TTTTTTTTTA
3658 TTTTTTATTTA
1 TTTTTT-TTTA
3669 TTTATTTTTT
1 TTT-TTTTTT
3679 GGCAACTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
10 16 0.41
11 10 0.26
12 13 0.33
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:3652 original size:11 final size:11
Alignment explanation
Indices: 3625--3678 Score: 65
Period size: 12 Copynumber: 4.8 Consensus size: 11
3615 TCACAATTCT
3625 TTTTTTTTTTA
1 TTTTTTTTTTA
*
3636 CCTTTTTTTTTA
1 -TTTTTTTTTTA
3648 -TTTTTTTTTA
1 TTTTTTTTTTA
*
3658 TTTTTTATTTA
1 TTTTTTTTTTA
3669 TTTATTTTTT
1 TTT-TTTTTT
3679 GGCAACTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 10 0.27
11 12 0.32
12 15 0.41
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:3654 original size:22 final size:21
Alignment explanation
Indices: 3626--3678 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 21
3616 CACAATTCTT
3626 TTTTTTTTTACCTTTTTT-TTTA
1 TTTTTTTTTA--TTTTTTATTTA
3648 TTTTTTTTTATTTTTTATTTA
1 TTTTTTTTTATTTTTTATTTA
3669 TTTATTTTTT
1 TTT-TTTTTT
3679 GGCAACTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.21
21 7 0.24
22 16 0.55
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTTTTTTATTTTTTATTTA
Found at i:5823 original size:35 final size:34
Alignment explanation
Indices: 5777--6180 Score: 409
Period size: 35 Copynumber: 11.7 Consensus size: 34
5767 TTCTTACTAA
* *
5777 ACTTAATTTCCCTGAATTAAGTTACTTATTGAACT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGAACT
* *
5812 ACTTAACTT-CCCTAAATTAAGTTGATTA-TTAACT
1 ACTTAA-TTACCCTGAATTAAGTT-ATTACTGAACT
*
5846 CACTTAATTACCCTGAATTAAGCTGATT-CTTG-ACT
1 -ACTTAATTACCCTGAATTAAG-TTATTAC-TGAACT
*
5881 CACTTAATTACCCTGAATTAAGTTAATTACTGAATT
1 -ACTTAATTACCCTGAATTAAGTT-ATTACTGAACT
*
5917 ACTTAATTACCCTGAATTAAGTTGATTCCTG-ACT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGAACT
5951 CACTTAATTACCCTGAATTAAGTTGATTACTG-ACTT
1 -ACTTAATTACCCTGAATTAAGTT-ATTACTGAAC-T
* **
5987 ACTTAATTACACTGAATTAAGTTGATTACTGAGTT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGAACT
* *
6022 ACTTAATTACCCTGAATTAAGTTACTAACTGACCT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGAACT
* *
6057 ACTTAATTACCCTAAATT-AG--AGT--TGAACT
1 ACTTAATTACCCTGAATTAAGTTATTACTGAACT
* *
6086 ACTTAATTACCCTGAATTAAGTTACTAGCTGAATT
1 ACTTAATTACCCTGAATTAAGTTATTA-CTGAACT
*
6121 ACTTAATTACCCTGAATTAAGTTGATTATTG-ACT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGAACT
6155 CACTTAATTACCCTGAATTAGAGTTA
1 -ACTTAATTACCCTGAATTA-AGTTA
6181 CTTATTGCTG
Statistics
Matches: 318, Mismatches: 28, Indels: 46
0.81 0.07 0.12
Matches are distributed among these distances:
29 22 0.07
30 2 0.01
32 3 0.01
34 15 0.05
35 260 0.82
36 16 0.05
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (34 bp):
ACTTAATTACCCTGAATTAAGTTATTACTGAACT
Found at i:5895 original size:105 final size:103
Alignment explanation
Indices: 5777--6174 Score: 494
Period size: 105 Copynumber: 3.9 Consensus size: 103
5767 TTCTTACTAA
* * * * *
5777 ACTTAATTTCCCTGAATTAAGTTACTTATTGAACTACTTAACTT-CCCTAAATTAAGTTGATTAT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGAATTACTTAA-TTACCCTGAATTAAGTTGATTAC
*
5841 TAACTCACTTAATTACCCTGAATTAAGCTGATTCTTGACT
65 TGACTCACTTAATTACCCTGAATTAAG-TGATTCTTGACT
* *
5881 CACTTAATTACCCTGAATTAAGTTAATTACTGAATTACTTAATTACCCTGAATTAAGTTGATTCC
1 -ACTTAATTACCCTGAATTAAGTTACTTACTGAATTACTTAATTACCCTGAATTAAGTTGATTAC
5946 TGACTCACTTAATTACCCTGAATTAAGTTGATTAC-TGACTT
65 TGACTCACTTAATTACCCTGAATTAAG-TGATT-CTTGAC-T
* * *
5987 ACTTAATTACACTGAATTAAGTTGA-TTACTGAGTTACTTAATTACCCTGAATTAAGTT-ACTAA
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTGAATTACTTAATTACCCTGAATTAAGTTGA-TTA
* *
6050 CTGAC-CTACTTAATTACCCTAAATT-A--GA--GTTGAACT
64 CTGACTC-ACTTAATTACCCTGAATTAAGTGATTCTTG-ACT
*
6086 ACTTAATTACCCTGAATTAAGTTAC-TAGCTGAATTACTTAATTACCCTGAATTAAGTTGATTAT
1 ACTTAATTACCCTGAATTAAGTTACTTA-CTGAATTACTTAATTACCCTGAATTAAGTTGATTAC
6150 TGACTCACTTAATTACCCTGAATTA
65 TGACTCACTTAATTACCCTGAATTA
6175 GAGTTACTTA
Statistics
Matches: 260, Mismatches: 20, Indels: 31
0.84 0.06 0.10
Matches are distributed among these distances:
98 3 0.01
99 77 0.30
100 4 0.02
101 2 0.01
104 5 0.02
105 166 0.64
106 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (103 bp):
ACTTAATTACCCTGAATTAAGTTACTTACTGAATTACTTAATTACCCTGAATTAAGTTGATTACT
GACTCACTTAATTACCCTGAATTAAGTGATTCTTGACT
Found at i:6799 original size:52 final size:52
Alignment explanation
Indices: 6692--6875 Score: 185
Period size: 53 Copynumber: 3.5 Consensus size: 52
6682 CACATTATTC
* * *
6692 AAAGATTTAATCTTTTACTTAAAAGATT-TAATCTTTATTTACAAAAATTACTTA
1 AAAGA-TTAATCTTTTAATTAAAAAATTACAATCTTTATTTAC--AAATTACTTA
* * * *
6746 AAAG-TTCAATCTTTTAA-TCAAAGATTACATTTTTTATTTACAAACTTACTTA
1 AAAGATT-AATCTTTTAATTAAAAAATTACAATCTTTATTTACAAA-TTACTTA
* * * *
6798 AAAGCTTAATCTTTCAATTAAAAAATTTCAATCTTTATTCACAAATTACTTA
1 AAAGATTAATCTTTTAATTAAAAAATTACAATCTTTATTTACAAATTACTTA
*
6850 AAAGATTTAATCTTTTACTTAAAAAA
1 AAAGA-TTAATCTTTTAATTAAAAAA
6876 AATCAATCTT
Statistics
Matches: 109, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
51 3 0.03
52 41 0.38
53 61 0.56
54 4 0.04
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (52 bp):
AAAGATTAATCTTTTAATTAAAAAATTACAATCTTTATTTACAAATTACTTA
Found at i:6867 original size:21 final size:21
Alignment explanation
Indices: 6843--6906 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 21
6833 TATTCACAAA
* * *
6843 TTACTTAAAAGATTTAATCTT
1 TTACTTAAAAAAATCAATCTT
6864 TTACTTAAAAAAAATCAATCTT
1 TTACTT-AAAAAAATCAATCTT
6886 TTACTT-AAAAAATCAATCTT
1 TTACTTAAAAAAATCAATCTT
6906 T
1 T
6907 ATATATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
20 15 0.38
21 6 0.15
22 18 0.46
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (21 bp):
TTACTTAAAAAAATCAATCTT
Found at i:6882 original size:53 final size:52
Alignment explanation
Indices: 6675--6886 Score: 171
Period size: 53 Copynumber: 4.1 Consensus size: 52
6665 AGATTTCATT
* * * * * *
6675 TTTATTC-CACATTA-TTCAAAGATTTAATCTTTTACTT-AAAAGATTTAATC
1 TTTATTCACAAATTACTTAAAAG-TTTAATCTTTTAATTAAAAAAAATCAATC
* * * * ** * *
6725 TTTATTTACAAAAATTACTTAAAAGTTCAATCTTTTAATCAAAGATTA-CATTT
1 TTTA-TT-CACAAATTACTTAAAAGTTTAATCTTTTAATTAAAAAAAATCAATC
* * * **
6778 TTTATTTACAAACTTACTTAAAAGCTTAATCTTTCAATTAAAAAATTTCAATC
1 TTTATTCACAAA-TTACTTAAAAGTTTAATCTTTTAATTAAAAAAAATCAATC
*
6831 TTTATTCACAAATTACTTAAAAGATTTAATCTTTTACTTAAAAAAAATCAATC
1 TTTATTCACAAATTACTTAAAAG-TTTAATCTTTTAATTAAAAAAAATCAATC
6884 TTT
1 TTT
6887 TACTTAAAAA
Statistics
Matches: 124, Mismatches: 30, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
50 4 0.03
51 6 0.05
52 41 0.33
53 64 0.52
54 9 0.07
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.43
Consensus pattern (52 bp):
TTTATTCACAAATTACTTAAAAGTTTAATCTTTTAATTAAAAAAAATCAATC
Found at i:6897 original size:20 final size:20
Alignment explanation
Indices: 6843--6906 Score: 83
Period size: 20 Copynumber: 3.0 Consensus size: 20
6833 TATTCACAAA
* *
6843 TTACTTAAAAGATTTAATCTT
1 TTACTTAAAA-AATCAATCTT
6864 TTACTTAAAAAAAATCAATCTT
1 TTACTT--AAAAAATCAATCTT
6886 TTACTTAAAAAATCAATCTT
1 TTACTTAAAAAATCAATCTT
6906 T
1 T
6907 ATATATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 15 0.38
21 6 0.15
22 14 0.36
23 4 0.10
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (20 bp):
TTACTTAAAAAATCAATCTT
Done.