Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015415.1 Corchorus capsularis cultivar CVL-1 contig15436, 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: 7737
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:182 original size:12 final size:13
Alignment explanation
Indices: 157--190 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
147 ATAATTATTG
157 TTTGCTTTATTAA
1 TTTGCTTTATTAA
170 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
182 TTTGTTTTA
1 TTTGCTTTA
191 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.65
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:198 original size:6 final size:6
Alignment explanation
Indices: 187--213 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
177 TATAATTTGT
187 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
214 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
Found at i:584 original size:13 final size:13
Alignment explanation
Indices: 566--600 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
556 ATAATTATTG
566 TTTGCTTTATTAA
1 TTTGCTTTATTAA
579 TTTGCTTTATTAA
1 TTTGCTTTATTAA
592 TTTGCTTTA
1 TTTGCTTTA
601 GATTTAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.63
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:608 original size:6 final size:6
Alignment explanation
Indices: 597--623 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
587 ATTAATTTGC
597 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
624 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
Found at i:1098 original size:9 final size:8
Alignment explanation
Indices: 1063--1097 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
1053 ATTTAATTAA
1063 TTTTCC-T
1 TTTTCCTT
*
1070 TTTTCCGT
1 TTTTCCTT
1078 TTTTCCTT
1 TTTTCCTT
1086 TTTTCCTT
1 TTTTCCTT
1094 TTTT
1 TTTT
1098 TAAAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (8 bp):
TTTTCCTT
Found at i:6688 original size:10 final size:10
Alignment explanation
Indices: 6673--6697 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6663 GTCCCTGCAC
6673 AATTCCAGAA
1 AATTCCAGAA
6683 AATTCCAGAA
1 AATTCCAGAA
6693 AATTC
1 AATTC
6698 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:6991 original size:22 final size:22
Alignment explanation
Indices: 6941--7093 Score: 159
Period size: 22 Copynumber: 7.0 Consensus size: 22
6931 TAATCAATAG
*
6941 GAGTAAGATAGTAATCAGT-AA
1 GAGTAAAATAGTAATCAGTAAA
* **
6962 GAGCAAAACGGTAATCAGTAAA
1 GAGTAAAATAGTAATCAGTAAA
**
6984 GAGTAAAATAACAATCAGTAAA
1 GAGTAAAATAGTAATCAGTAAA
* * *
7006 AAGTAAGAA-GGTAATCAGTAGA
1 GAGTAA-AATAGTAATCAGTAAA
7028 GAGTAAAATAGTAATCAGTAAA
1 GAGTAAAATAGTAATCAGTAAA
* * *
7050 AAGTAAGAA-GGTAATGAGTAAA
1 GAGTAA-AATAGTAATCAGTAAA
7072 GAGTAAAATAGTAATCAGTAAA
1 GAGTAAAATAGTAATCAGTAAA
7094 AGGTAATAAG
Statistics
Matches: 104, Mismatches: 23, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
21 19 0.18
22 81 0.78
23 4 0.04
ACGTcount: A:0.53, C:0.06, G:0.22, T:0.20
Consensus pattern (22 bp):
GAGTAAAATAGTAATCAGTAAA
Found at i:7019 original size:15 final size:15
Alignment explanation
Indices: 7001--7063 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
6991 ATAACAATCA
7001 GTAAAAAGTAAGAAG
1 GTAAAAAGTAAGAAG
**
7016 GTAATCAGT-AG-AG
1 GTAAAAAGTAAGAAG
**
7029 AGTAAAATAGTAATCA-
1 -GTAAAA-AGTAAGAAG
7045 GTAAAAAGTAAGAAG
1 GTAAAAAGTAAGAAG
7060 GTAA
1 GTAA
7064 TGAGTAAAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
13 2 0.06
14 12 0.33
15 20 0.56
16 1 0.03
17 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.24, T:0.19
Consensus pattern (15 bp):
GTAAAAAGTAAGAAG
Found at i:7031 original size:44 final size:43
Alignment explanation
Indices: 6922--7200 Score: 253
Period size: 44 Copynumber: 6.7 Consensus size: 43
6912 AATAGTAATC
* * * *
6922 AGTAAAAGGTAATCAAT-AGGAGTAAGATAGTAATCAGT-AAG
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAA
* **
6963 AGCAAAACGGTAATCAGTAAAGAGTAAAATAACAATCAGTAAAA
1 AGTAAAA-GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAA
*
7007 AGTAAGAAGGTAATCAGTAGAGAGTAAAATAGTAATCAGTAAAA
1 AGTAA-AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAA
*
7051 AGTAAGAAGGTAATGAGTAAAGAGTAAAATAGTAATC-------
1 AGTAA-AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAA
* * *
7088 AGTAAAAGGTAATAAGT-AAGAGTAAAATAGTAATCAAT-AAG
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAA
* * * *
7129 AGCAAAATGGTAATTAG-CAAGAGTAAAATAGTAATTAG-AAAA
1 AGTAAAA-GGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAA
7171 GAGTAAAATGGTAATCAGTTAAA-AGTAAAA
1 -AGTAAAA-GGTAATCAG-TAAAGAGTAAAA
7201 AAAGAGAGTC
Statistics
Matches: 200, Mismatches: 22, Indels: 29
0.80 0.09 0.12
Matches are distributed among these distances:
35 18 0.09
36 11 0.05
37 5 0.03
41 12 0.06
42 37 0.19
43 32 0.16
44 81 0.41
45 4 0.02
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (43 bp):
AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAA
Found at i:7091 original size:15 final size:15
Alignment explanation
Indices: 7029--7094 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
7019 ATCAGTAGAG
7029 AGTAAAATAGTAATC
1 AGTAAAATAGTAATC
**
7044 AGTAAAA-AGTAAGA
1 AGTAAAATAGTAATC
**
7058 AGGT--AATGAGTAAAG
1 A-GTAAAAT-AGTAATC
7073 AGTAAAATAGTAATC
1 AGTAAAATAGTAATC
7088 AGTAAAA
1 AGTAAAA
7095 GGTAATAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
13 2 0.05
14 8 0.20
15 27 0.68
16 3 0.08
ACGTcount: A:0.56, C:0.03, G:0.20, T:0.21
Consensus pattern (15 bp):
AGTAAAATAGTAATC
Found at i:7116 original size:35 final size:37
Alignment explanation
Indices: 7051--7129 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 37
7041 ATCAGTAAAA
*
7051 AGTAAGAAGGTAATGAGTAAAGAGTAAAATAGTAATC
1 AGTAAGAAGGTAATAAGTAAAGAGTAAAATAGTAATC
7088 AGTAA-AAGGTAATAAGT-AAGAGTAAAATAGTAATC
1 AGTAAGAAGGTAATAAGTAAAGAGTAAAATAGTAATC
*
7123 AATAAGA
1 AGTAAGA
7130 GCAAAATGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
35 22 0.56
36 12 0.31
37 5 0.13
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.22
Consensus pattern (37 bp):
AGTAAGAAGGTAATAAGTAAAGAGTAAAATAGTAATC
Found at i:7255 original size:166 final size:166
Alignment explanation
Indices: 6903--7202 Score: 430
Period size: 166 Copynumber: 1.8 Consensus size: 166
6893 AGAAAAAGTA
* * *
6903 AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAATAGGAGTAAGATAGTAATCAGTAAGAGCAA
1 AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAATAAGAGTAAAATAGTAATCAATAAGAGCAA
*
6968 AACGGTAATCAGTAAAGAGTAAAATAACAATCAGTAAAAAGTAAGAAGGTAATCAGTAGAGAGTA
66 AACGGTAATCAGTAAAGAGTAAAATAACAATCAGTAAAAAGTAAGAAGGTAATCAGTAGAAAGTA
*
7033 AAATAGTAATCAGTAAAAAGTAAGAAGGTAATGAGT
131 AAAAAGTAATCAGTAAAAAGTAAGAAGGTAATGAGT
7069 AAAGAGTAAAATAGTAATCAGTAAAAGGTAAT-AAGTAAGAGTAAAATAGTAATCAATAAGAGCA
1 AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAA-TAAGAGTAAAATAGTAATCAATAAGAGCA
* * * ** *
7133 AAATGGTAATTAG-CAAGAGTAAAATAGTAATTAG-AAAAGAGTAA-AATGGTAATCAGTTA-AA
65 AAACGGTAATCAGTAAAGAGTAAAATAACAATCAGTAAAA-AGTAAGAA-GGTAATCAG-TAGAA
7194 AGTAAAAAA
127 AGTAAAAAA
7203 AGAGAGTCAG
Statistics
Matches: 119, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
164 6 0.05
165 42 0.35
166 71 0.60
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (166 bp):
AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAATAAGAGTAAAATAGTAATCAATAAGAGCAA
AACGGTAATCAGTAAAGAGTAAAATAACAATCAGTAAAAAGTAAGAAGGTAATCAGTAGAAAGTA
AAAAAGTAATCAGTAAAAAGTAAGAAGGTAATGAGT
Found at i:7316 original size:15 final size:15
Alignment explanation
Indices: 7296--7343 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
7286 TAATAAACAC
7296 TAAAAAGTAAAAAGG
1 TAAAAAGTAAAAAGG
*
7311 TAAAAAG-AAAAGGG
1 TAAAAAGTAAAAAGG
**
7325 TAATCAGT-AAAAGG
1 TAAAAAGTAAAAAGG
7339 TAAAA
1 TAAAA
7344 TGGTAATTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.62, C:0.02, G:0.21, T:0.15
Consensus pattern (15 bp):
TAAAAAGTAAAAAGG
Found at i:7343 original size:22 final size:21
Alignment explanation
Indices: 7310--7375 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
7300 AAGTAAAAAG
7310 GTAAAAAGAAAAGGGTAATCA
1 GTAAAAAGAAAAGGGTAATCA
* * *
7331 GTAAAAGGTAAAATGGTAATTA
1 GTAAAAAG-AAAAGGGTAATCA
* * *
7353 GTAAAGAGCAATATGGTAATCA
1 GTAAAAAG-AAAAGGGTAATCA
7375 G
1 G
7376 AGTAAAGGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 7 0.19
22 29 0.81
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.21
Consensus pattern (21 bp):
GTAAAAAGAAAAGGGTAATCA
Found at i:7430 original size:26 final size:26
Alignment explanation
Indices: 7399--7484 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
7389 GAAATCAGTA
7399 AATCAGTAATTAAGTGAAAAGAGATT
1 AATCAGTAATTAAGTGAAAAGAGATT
* ** *
7425 AATCAGAGTCAAGGTAA-TGATAATCAG-TA
1 AATC--AGT-AA-TTAAGTGA-AAAGAGATT
*
7454 AATCAGTAATTAAGTGAAAAGAAATT
1 AATCAGTAATTAAGTGAAAAGAGATT
7480 AATCA
1 AATCA
7485 AAGTCAAGGT
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 6 0.14
26 15 0.34
27 3 0.07
28 3 0.07
29 10 0.23
30 7 0.16
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (26 bp):
AATCAGTAATTAAGTGAAAAGAGATT
Found at i:7582 original size:55 final size:55
Alignment explanation
Indices: 7369--7568 Score: 285
Period size: 55 Copynumber: 3.6 Consensus size: 55
7359 AGCAATATGG
* * * *
7369 TAATCAGAGTAAAGGTAATAGAAATCAGTAAATCAGTAATTAAGTGAAAAGAGAT
1 TAATCAAAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
* * *
7424 TAATCAGAGTCAAGGTAAT-GATAATCAGTAAATCAGTAATTAAGTGAAAAGAAAT
1 TAATCAAAGTCAAGGTAATAG-TAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
* *
7479 TAATCAAAGTCAAGGTAATGGTAATCAGTAAATCAGCAATTAAGTAAAAAGAGAT
1 TAATCAAAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
* *
7534 TAATCAAAGTCGAGGTAATAGTAATAAGTAAATCA
1 TAATCAAAGTCAAGGTAATAGTAATCAGTAAATCA
7569 ATGATCACGT
Statistics
Matches: 133, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
54 1 0.01
55 131 0.98
56 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.24
Consensus pattern (55 bp):
TAATCAAAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
Found at i:7625 original size:70 final size:71
Alignment explanation
Indices: 7534--7686 Score: 220
Period size: 70 Copynumber: 2.2 Consensus size: 71
7524 AAAAAGAGAT
* * *
7534 TAATCAA-AGTCGAGGTAATAGTAATAAGTAAATCAATGATCACGT-AAAAGATAGTAATCAGTA
1 TAATCAAGAGTCCAGATAATAGTAATAAGTAAATCAATAATCACGTAAAAAGATAGTAATCAGTA
7597 AATTGA
66 AATTGA
* * *
7603 TAATCAAGAGTCCAGATAATAGTAATCAGTAAATCAGTAATCAGGTAAAAAGATAGTAATCAGTA
1 TAATCAAGAGTCCAGATAATAGTAATAAGTAAATCAATAATCACGTAAAAAGATAGTAATCAGTA
7668 AATTGA
66 AATTGA
*
7674 TAACTAAAGAGTC
1 TAA-TCAAGAGTC
7687 AAGGTAAGAG
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
69 7 0.09
70 32 0.43
71 27 0.36
72 8 0.11
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (71 bp):
TAATCAAGAGTCCAGATAATAGTAATAAGTAAATCAATAATCACGTAAAAAGATAGTAATCAGTA
AATTGA
Found at i:7631 original size:37 final size:37
Alignment explanation
Indices: 7579--7688 Score: 122
Period size: 37 Copynumber: 3.0 Consensus size: 37
7569 ATGATCACGT
7579 AAAAGATAGTAATCAGTAAATTGATAATCAAGAGTCCA
1 AAAAGATAGTAATCAGTAAATTGATAATCAAGAGT-CA
* * *
7617 GATA-ATAGTAATCAGTAAA-TCAGTAATC-AG-GT-A
1 AAAAGATAGTAATCAGTAAATTGA-TAATCAAGAGTCA
*
7650 AAAAGATAGTAATCAGTAAATTGATAACTAAAGAGTCA
1 AAAAGATAGTAATCAGTAAATTGATAA-TCAAGAGTCA
7688 A
1 A
7689 GGTAAGAGAT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
33 3 0.05
34 18 0.31
35 5 0.09
36 6 0.10
37 22 0.38
38 4 0.07
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (37 bp):
AAAAGATAGTAATCAGTAAATTGATAATCAAGAGTCA
Done.