Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010146.1 Corchorus capsularis cultivar CVL-1 contig10167, 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: 10324
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Found at i:855 original size:27 final size:28
Alignment explanation
Indices: 825--893 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
815 AAGTGAACTT
*
825 AAAATGATCAAAATACCCCCT-AA-ATGCA
1 AAAATGACCAAAAT-CCCCCTGAACATG-A
*
853 AAAATGACCAAAATGCCCCTGAACATG-
1 AAAATGACCAAAATCCCCCTGAACATGA
880 AAAATGACCAAAAT
1 AAAATGACCAAAAT
894 GCCCTTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 19 0.51
28 15 0.41
29 3 0.08
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATCCCCCTGAACATGA
Found at i:1381 original size:47 final size:47
Alignment explanation
Indices: 1215--1447 Score: 313
Period size: 47 Copynumber: 4.9 Consensus size: 47
1205 AAAGCCCGTT
* * *** *
1215 GACCAACTCTGGTCACTAAATTGCGTACTCGCATGGAAGCGAGAGAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGA-AAA
*
1263 GACCATCTTTGGTCACTAAATTGAAAACCCGCGTGGAAGCGAGAAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAG-AAAA
* * * *
1311 GACCATCTTTGGCCACTAGATTGAAAACTCGCATGGAAGCGAGAAAC
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
*
1358 GACCATCTTTGGTCACCAAATTGAAAACTCGCGTGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
* * *
1405 GACAATATTTGGTCACTAAATTGAAAATTCGCGTGGAAGCGAG
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAG
1448 TTTGGCTTAT
Statistics
Matches: 163, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
47 84 0.52
48 78 0.48
49 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (47 bp):
GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAAAA
Found at i:1391 original size:95 final size:95
Alignment explanation
Indices: 1241--1447 Score: 317
Period size: 95 Copynumber: 2.2 Consensus size: 95
1231 TAAATTGCGT
*
1241 ACTCGCATGGAAGCGAGAGAAAGACCATCTTTGGTCACTAAATTGAAAACCCGCGTGGAAGCGAG
1 ACTCGCATGGAAGCGAGAGAAAGACCATCTTTGGTCACCAAATTGAAAACCCGCGTGGAAGCGAG
* * *
1306 AAAAAGACCATCTTTGGCCACTAGATTGAAA
66 -AAAAGACAATATTTGGCCACTAAATTGAAA
* *
1337 ACTCGCATGGAAGCGAGA-AACGACCATCTTTGGTCACCAAATTGAAAACTCGCGTGGAAGCGAG
1 ACTCGCATGGAAGCGAGAGAAAGACCATCTTTGGTCACCAAATTGAAAACCCGCGTGGAAGCGAG
*
1401 AAAAGACAATATTTGGTCACTAAATTGAAA
66 AAAAGACAATATTTGGCCACTAAATTGAAA
* *
1431 ATTCGCGTGGAAGCGAG
1 ACTCGCATGGAAGCGAG
1448 TTTGGCTTAT
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 41 0.40
95 43 0.42
96 18 0.18
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (95 bp):
ACTCGCATGGAAGCGAGAGAAAGACCATCTTTGGTCACCAAATTGAAAACCCGCGTGGAAGCGAG
AAAAGACAATATTTGGCCACTAAATTGAAA
Found at i:1605 original size:69 final size:70
Alignment explanation
Indices: 1505--1724 Score: 259
Period size: 69 Copynumber: 3.2 Consensus size: 70
1495 ATCTGAGTCG
* * * *
1505 TGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTGAAACT-ATCTCGCGTGGAAGCGAGT
1 TGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTGAAACTGA-CTCGTGTGGAAACAAGT
1569 TTGGCT
65 TTGGCT
* * * * * * * *
1575 TATGGAAAAGCCTCT-ATTGCCTGGATGGAACCGAAGCTGGATCTGACTCGTGTGGAAACCAGTT
1 TGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAAACAAGTT
1639 TAGG-T
66 T-GGCT
** *
1644 TGTGGAAAAGCCCCTGAATGCTTGGGCGGAACCAAGGCT-AAACTGACTCGTGTGGAAACAAGTT
1 TGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAAACAAGTT
1708 TGGCT
66 TGGCT
1713 TGTGGAAAAGCC
1 TGTGGAAAAGCC
1725 GGAGCATTCG
Statistics
Matches: 124, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
68 2 0.02
69 89 0.72
70 33 0.27
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (70 bp):
TGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAAACAAGTT
TGGCT
Found at i:2000 original size:29 final size:29
Alignment explanation
Indices: 1967--2027 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
1957 TTGCCCCGGA
1967 TCTGAATTGAATAGTATGCTTTGAAAGAT
1 TCTGAATTGAATAGTATGCTTTGAAAGAT
*
1996 TCTGACTTGAATAGTATGCTTTGAAAGAT
1 TCTGAATTGAATAGTATGCTTTGAAAGAT
2025 TCT
1 TCT
2028 TTTACTGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (29 bp):
TCTGAATTGAATAGTATGCTTTGAAAGAT
Found at i:2339 original size:50 final size:50
Alignment explanation
Indices: 2275--2381 Score: 155
Period size: 50 Copynumber: 2.2 Consensus size: 50
2265 TAAAATGCCC
** *
2275 TTTGAAAAGTGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTAT
1 TTTGAAAAGTGAATTTTGATAATGGACTCACAAATGGAATGCAATCTCAT
*
2325 TTTGAAAA-TCGAATTTTGATAATGGACTCACAAATGGAATGCCATCTCAT
1 TTTGAAAAGT-GAATTTTGATAATGGACTCACAAATGGAATGCAATCTCAT
2375 TTT-AAAA
1 TTTGAAAA
2382 CTTCTTGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
49 5 0.10
50 47 0.90
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (50 bp):
TTTGAAAAGTGAATTTTGATAATGGACTCACAAATGGAATGCAATCTCAT
Found at i:3064 original size:20 final size:21
Alignment explanation
Indices: 3010--3064 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
3000 TCACTCTTCC
3010 TTTCACTTTTATC-TTCAATT
1 TTTCACTTTTATCTTTCAATT
3030 TTTC-CTTTTCA-CTTTCAA-T
1 TTTCACTTTT-ATCTTTCAATT
*
3049 TTTCACTTTTTTCTTT
1 TTTCACTTTTATCTTT
3065 TCTTTTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTCACTTTTATCTTTCAATT
Found at i:3064 original size:27 final size:26
Alignment explanation
Indices: 3006--3066 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
2996 AACTTCACTC
*
3006 TTCC-TTTCACTTTTATCTTCAATTT
1 TTCCTTTTCACTTTAATCTTCAATTT
* *
3031 TTCCTTTTCACTTTCAATTTTCACTTT
1 TTCCTTTTCACTTT-AATCTTCAATTT
*
3058 TTTCTTTTC
1 TTCCTTTTC
3067 TTTTTCTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 4 0.13
26 9 0.30
27 17 0.57
ACGTcount: A:0.13, C:0.25, G:0.00, T:0.62
Consensus pattern (26 bp):
TTCCTTTTCACTTTAATCTTCAATTT
Found at i:3072 original size:11 final size:11
Alignment explanation
Indices: 3056--3100 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
3046 AATTTTCACT
3056 TTTTTCTTTTC
1 TTTTTCTTTTC
3067 TTTTTC-TTTC
1 TTTTTCTTTTC
*
3077 TTTTTTCTTTTT
1 -TTTTTCTTTTC
3089 TTTTTCTCTTTC
1 TTTTTCT-TTTC
3101 CTTCCCTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 4 0.14
11 19 0.66
12 6 0.21
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:3079 original size:22 final size:22
Alignment explanation
Indices: 3054--3095 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3044 TCAATTTTCA
3054 CTTTTTTCTTTTCTTTTTCTTT
1 CTTTTTTCTTTTCTTTTTCTTT
*
3076 CTTTTTTCTTTTTTTTTTCT
1 CTTTTTTCTTTTCTTTTTCT
3096 CTTTCCTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
CTTTTTTCTTTTCTTTTTCTTT
Found at i:3092 original size:10 final size:10
Alignment explanation
Indices: 3055--3092 Score: 58
Period size: 11 Copynumber: 3.6 Consensus size: 10
3045 CAATTTTCAC
3055 TTTTTTCTTT
1 TTTTTTCTTT
3065 TCTTTTTCTTT
1 T-TTTTTCTTT
3076 CTTTTTTCTTT
1 -TTTTTTCTTT
3087 TTTTTT
1 TTTTTT
3093 TCTCTTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.27
11 18 0.69
12 1 0.04
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:3493 original size:46 final size:45
Alignment explanation
Indices: 3442--3558 Score: 175
Period size: 44 Copynumber: 2.6 Consensus size: 45
3432 ACCACTTTGG
* *
3442 AAAACCATGACTCTTTTTGAAAAAGCATTTTATCAAAATCTTTTAA
1 AAAACCATGACTCTTTTTGAAAAACCATTTTATCAAAACCTTTT-A
* *
3488 AAAACCATGACTCTTTTT-TAAAACCATTTTATCAAAACCTTTTG
1 AAAACCATGACTCTTTTTGAAAAACCATTTTATCAAAACCTTTTA
3532 AAAACCATGACTCTTTTTG-AAAACCAT
1 AAAACCATGACTCTTTTTGAAAAACCAT
3559 CATTGCTTCT
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
44 26 0.39
45 22 0.33
46 18 0.27
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (45 bp):
AAAACCATGACTCTTTTTGAAAAACCATTTTATCAAAACCTTTTA
Found at i:3646 original size:10 final size:10
Alignment explanation
Indices: 3573--3642 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 10
3563 GCTTCTGCTC
3573 TTTTTCTTTT
1 TTTTTCTTTT
*
3583 TTTTTCCTGTT
1 TTTTT-CTTTT
*
3594 TTATTCTTCTT
1 TTTTTCTT-TT
*
3605 CTTTCTCTTTT
1 -TTTTTCTTTT
*
3616 TCTCTTCTTTT
1 T-TTTTCTTTT
*
3627 TTCTTCTTCTT
1 TTTTTCTT-TT
3638 TTTTT
1 TTTTT
3643 TTCTGGGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
10 15 0.32
11 26 0.55
12 6 0.13
ACGTcount: A:0.01, C:0.20, G:0.01, T:0.77
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:3646 original size:13 final size:13
Alignment explanation
Indices: 3576--3646 Score: 61
Period size: 13 Copynumber: 5.1 Consensus size: 13
3566 TCTGCTCTTT
3576 TTCTTTTTTTTTC
1 TTCTTTTTTTTTC
* * *
3589 CTGTTTTATTCTTC
1 TTCTTTT-TTTTTC
3603 TTCTTTCTCTTTTTCTC
1 TTC-TT-T-TTTTT-TC
*
3620 TTCTTTTTTCTTC
1 TTCTTTTTTTTTC
3633 TTCTTTTTTTTTC
1 TTCTTTTTTTTTC
3646 T
1 T
3647 GGGAAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
13 20 0.44
14 10 0.22
15 3 0.07
16 6 0.13
17 6 0.13
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.76
Consensus pattern (13 bp):
TTCTTTTTTTTTC
Done.