Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014226.1 Corchorus capsularis cultivar CVL-1 contig14247, 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: 63112
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:325 original size:22 final size:22
Alignment explanation
Indices: 300--347 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
290 TTATTGCACC
*
300 ATTACAAGGTGTCATAGAAAAG
1 ATTACAAGGTGTAATAGAAAAG
322 ATTACAAGGTGTAATAGAAAAG
1 ATTACAAGGTGTAATAGAAAAG
344 ATTA
1 ATTA
348 TACATTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (22 bp):
ATTACAAGGTGTAATAGAAAAG
Found at i:7201 original size:12 final size:12
Alignment explanation
Indices: 7186--7241 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
7176 TATATAAACA
*
7186 ATAATATCAGAT
1 ATAATATAAGAT
*
7198 ATAATATAATAT
1 ATAATATAAGAT
*
7210 ATAATATAATAT
1 ATAATATAAGAT
* *
7222 AAAATATAAAAT
1 ATAATATAAGAT
*
7234 ATATTATA
1 ATAATATA
7242 TATTAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (12 bp):
ATAATATAAGAT
Found at i:7208 original size:17 final size:17
Alignment explanation
Indices: 7196--7244 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
7186 ATAATATCAG
7196 ATATAATATAATATATA
1 ATATAATATAATATATA
*
7213 ATATAATATAAAATATA
1 ATATAATATAATATATA
* *
7230 AAAT-ATATTATATAT
1 ATATAATATAATATAT
7245 TAATTTTCGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATATAATATATA
Found at i:9766 original size:211 final size:212
Alignment explanation
Indices: 9402--9827 Score: 791
Period size: 211 Copynumber: 2.0 Consensus size: 212
9392 AGAGAAATAT
9402 GACCTACCACTTGAATATATAAGTGAATCTAACTACCAACAATTGATCGGTTTATCGATTTAAAT
1 GACCTACCACTTGAATATATAAGTGAATCTAACTACCAACAATTGATCGGTTTATCGATTTAAAT
*
9467 GATTCAGATATCTATTTATATTTAGACTAATTATACAATACACCGTCAGTGGAGTTTAGCAGACT
66 GATTCAGATATCTATTTATATTTAGACAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACT
*
9532 ACACAAGCGGGTCCTGATGGGTGACATGTGTCCTTTAGGGACTAGATTGAAATATTTAAAACTTA
131 ACACAAGCGGGTCCTGATGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTA
9597 ATTAATT-AAAAAAATG
196 ATTAATTAAAAAAAATG
9613 GACCTACCACTTGAATATATAAGTGAATCTAACTACCAACAATTGATCGGTTTATCGATTTAAAT
1 GACCTACCACTTGAATATATAAGTGAATCTAACTACCAACAATTGATCGGTTTATCGATTTAAAT
* *
9678 GATTCTGATATCTATTTATATTTAGGCAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACT
66 GATTCAGATATCTATTTATATTTAGACAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACT
* *
9743 ACACAAGCGGGTCCTGATGGGTGACATGTGTTCTCTAGGGACTAGATTGAAATATTTAAGACTTA
131 ACACAAGCGGGTCCTGATGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTA
9808 ATTAATTAAAAAAAATG
196 ATTAATTAAAAAAAATG
9825 GAC
1 GAC
9828 ATGTGTCAAC
Statistics
Matches: 208, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
211 196 0.94
212 12 0.06
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (212 bp):
GACCTACCACTTGAATATATAAGTGAATCTAACTACCAACAATTGATCGGTTTATCGATTTAAAT
GATTCAGATATCTATTTATATTTAGACAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACT
ACACAAGCGGGTCCTGATGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTA
ATTAATTAAAAAAAATG
Found at i:19128 original size:2 final size:2
Alignment explanation
Indices: 19121--19166 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
19111 CTTATTTAGA
* *
19121 AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A- AT AA AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
19163 AT AT
1 AT AT
19167 GAAAAAGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:22661 original size:25 final size:25
Alignment explanation
Indices: 22612--22662 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
22602 TTAGTTGAAT
*
22612 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
22637 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
22663 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Found at i:29015 original size:13 final size:13
Alignment explanation
Indices: 28997--29023 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28987 TTTCAGTGAG
28997 ACTTGTAGGAGAT
1 ACTTGTAGGAGAT
29010 ACTTGTAGGAGAT
1 ACTTGTAGGAGAT
29023 A
1 A
29024 AAGTGTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (13 bp):
ACTTGTAGGAGAT
Found at i:32942 original size:14 final size:14
Alignment explanation
Indices: 32923--32953 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
32913 AAAACATAAA
32923 TCTTGGAAGAGTTT
1 TCTTGGAAGAGTTT
*
32937 TCTTGGGAGAGTTT
1 TCTTGGAAGAGTTT
32951 TCT
1 TCT
32954 CTTATATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.10, G:0.29, T:0.45
Consensus pattern (14 bp):
TCTTGGAAGAGTTT
Found at i:40566 original size:2 final size:2
Alignment explanation
Indices: 40559--40584 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40549 CATTTTCTAC
40559 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
40585 CACTAGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41784 original size:37 final size:37
Alignment explanation
Indices: 41677--41766 Score: 144
Period size: 37 Copynumber: 2.4 Consensus size: 37
41667 AAAGAAAAAA
* *
41677 AAAAAGCATAATTAAACACAACGTTGGAAACAAAGAC
1 AAAAGGCAAAATTAAACACAACGTTGGAAACAAAGAC
* *
41714 AAAATGCAAAATTAAACACAACGTTGGAAACAAAGAT
1 AAAAGGCAAAATTAAACACAACGTTGGAAACAAAGAC
41751 AAAAGGCAAAATTAAA
1 AAAAGGCAAAATTAAA
41767 TAGGATGTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.14
Consensus pattern (37 bp):
AAAAGGCAAAATTAAACACAACGTTGGAAACAAAGAC
Found at i:42076 original size:29 final size:31
Alignment explanation
Indices: 42038--42104 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
42028 ATGGCAATTT
* *
42038 AGAAATATATTTTTAA-AAAAAGGGTATAATC
1 AGAAATATA-TTTAAAGAAAAAGGGTACAATC
*
42069 AGAAATATATTTAAAGAAAAATGGTACAATC
1 AGAAATATATTTAAAGAAAAAGGGTACAATC
42100 AGAAA
1 AGAAA
42105 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.27
Consensus pattern (31 bp):
AGAAATATATTTAAAGAAAAAGGGTACAATC
Found at i:42122 original size:133 final size:134
Alignment explanation
Indices: 41858--42123 Score: 435
Period size: 134 Copynumber: 2.0 Consensus size: 134
41848 AATTTATGGT
* **
41858 AAAAAAATAATGGAATAATTAAAATATTATTTATTAAAGGCAATTTAGAAATATATTTTTTTAAA
1 AAAAAAATAATGGAATAATTAAAATATTATTTAGTAAAGGCAATTTAGAAATATATTTTTAAAAA
* * *
41923 AAGGGTATAATCTGAAATATGTTTTAAAAAAAAAGGGTACAATCGGAAAACATAAAGTTTCACCT
66 AAGGGTATAATCAGAAATATGATTTAAAAAAAAAGGGTACAATCAGAAAACATAAAGTTTCACCT
41988 TATA
131 TATA
*
41992 AAAAAAATAATGGAATAATTAAAATATTATTTAGTAATGGCAATTTAGAAATATATTTTTAAAAA
1 AAAAAAATAATGGAATAATTAAAATATTATTTAGTAAAGGCAATTTAGAAATATATTTTTAAAAA
* * *
42057 AAGGGTATAATCAGAAATAT-ATTTAAAGAAAAATGGTACAATCAGAAAACATAAAGTTTCCCCT
66 AAGGGTATAATCAGAAATATGATTTAAAAAAAAAGGGTACAATCAGAAAACATAAAGTTTCACCT
42121 TAT
131 TAT
42124 TTGTACTTTT
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
133 42 0.34
134 80 0.66
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (134 bp):
AAAAAAATAATGGAATAATTAAAATATTATTTAGTAAAGGCAATTTAGAAATATATTTTTAAAAA
AAGGGTATAATCAGAAATATGATTTAAAAAAAAAGGGTACAATCAGAAAACATAAAGTTTCACCT
TATA
Found at i:43342 original size:34 final size:35
Alignment explanation
Indices: 43292--43362 Score: 85
Period size: 37 Copynumber: 2.1 Consensus size: 35
43282 TTTTTTTTTA
* *
43292 TTTTTTTCAAAAAG-AAAAGAAG-AA-AATGATTT
1 TTTTTTTAAAAAAGAAAAAAAAGAAACAATGATTT
43324 TTTTTTTGAAAAACAGAAAAAAAAGAAACAATGATTT
1 TTTTTTT-AAAAA-AGAAAAAAAAGAAACAATGATTT
43361 TT
1 TT
43363 CATTAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 2 0.06
35 7 0.22
36 2 0.06
37 10 0.31
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34
Consensus pattern (35 bp):
TTTTTTTAAAAAAGAAAAAAAAGAAACAATGATTT
Found at i:45938 original size:26 final size:26
Alignment explanation
Indices: 45908--45958 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
45898 ATGTATGCTT
*
45908 TTGTATTGGTCACTCTGTAATGCTGC
1 TTGTATTGGTCACTCCGTAATGCTGC
45934 TTGTATTGGTCACTCCGTAATGCTG
1 TTGTATTGGTCACTCCGTAATGCTG
45959 TTTGAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.41
Consensus pattern (26 bp):
TTGTATTGGTCACTCCGTAATGCTGC
Found at i:49130 original size:6 final size:6
Alignment explanation
Indices: 49112--49152 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
49102 TGTAGTCGAG
*
49112 GAGGAA GAAGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGA
49153 GGATGATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:53629 original size:11 final size:12
Alignment explanation
Indices: 53613--53642 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
53603 AGTTACTGAC
53613 CCTTTTGGTT-T
1 CCTTTTGGTTCT
53624 CCTTTTGGTTCT
1 CCTTTTGGTTCT
53636 CCTTTTG
1 CCTTTTG
53643 CGATTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.00, C:0.23, G:0.17, T:0.60
Consensus pattern (12 bp):
CCTTTTGGTTCT
Found at i:54648 original size:21 final size:23
Alignment explanation
Indices: 54624--54669 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
54614 AATCACTTAA
54624 TTATCAATAAAAT-TAT-TTTTT
1 TTATCAATAAAATGTATGTTTTT
* *
54645 TTATTATTAAAATGTATGTTTTT
1 TTATCAATAAAATGTATGTTTTT
54668 TT
1 TT
54670 TTAAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 3 0.14
23 7 0.33
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (23 bp):
TTATCAATAAAATGTATGTTTTT
Found at i:59295 original size:65 final size:64
Alignment explanation
Indices: 59188--59326 Score: 206
Period size: 65 Copynumber: 2.2 Consensus size: 64
59178 CCAAACCAAA
* *
59188 AAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTACAAAGGACGGCTTAAGCAAAAGTTAGAGC
1 AAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTACAAAGGACAGCTTAAGCAAAACTTAGAGC
* ** *
59252 AAAGAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGTAAAGGACAGCTTAGGCAAAACTTAGAGC
1 AAA-AAAAAAAAAAGCTCGCTAAGTTGAAAATCCTACAAAGGACAGCTTAAGCAAAACTTAGAGC
*
59317 ACAAAAAAAA
1 AAAAAAAAAA
59327 TGAACTACGT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 10 0.15
65 57 0.85
ACGTcount: A:0.51, C:0.15, G:0.19, T:0.15
Consensus pattern (64 bp):
AAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTACAAAGGACAGCTTAAGCAAAACTTAGAGC
Found at i:60091 original size:16 final size:16
Alignment explanation
Indices: 60070--60104 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
60060 ACAATTCAGA
60070 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
60086 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
60102 AAG
1 AAG
60105 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:63042 original size:3 final size:3
Alignment explanation
Indices: 63036--63104 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
63026 CTTATTATAT
63036 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
63084 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
63105 GTATATAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.