Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016107.1 Corchorus capsularis cultivar CVL-1 contig16128, 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: 41111
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2134 original size:2 final size:2
Alignment explanation
Indices: 2127--2158 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2117 GAGGCCTAGC
2127 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2159 TGTTGTAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4415 original size:19 final size:18
Alignment explanation
Indices: 4391--4426 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
4381 GTCAAAATCC
4391 TAACATATATATATATATA
1 TAACATATATA-ATATATA
4410 TAACATATATAATATAT
1 TAACATATATAATATAT
4427 GTATATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
TAACATATATAATATATA
Found at i:13738 original size:21 final size:21
Alignment explanation
Indices: 13714--13754 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13704 AATGACTCAT
13714 ATGCTATGAA-TGCTATGAATG
1 ATGCTATGAATTGCT-TGAATG
*
13735 ATGCTTTGAATTGCTTGAAT
1 ATGCTATGAATTGCTTGAAT
13755 TACTTGATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (21 bp):
ATGCTATGAATTGCTTGAATG
Found at i:28424 original size:56 final size:58
Alignment explanation
Indices: 28336--28458 Score: 157
Period size: 56 Copynumber: 2.1 Consensus size: 58
28326 GGCGATCATT
28336 CTTCAATTTACTTCAATGATCCAAGGGTGGTCTT-TCTTCAATTCTTC-A-T-TCAATG
1 CTTCAATTTACTTCAATGATCCAAGGGTGGTCTTGT-TTCAATTCTTCAATTATCAATG
* *
28391 CTTCAATTTATTTCAGAATGATCC-AGGGTGGTCTTGTTTTAATTCTTCAATTACTCAATG
1 CTTCAATTTACTTC--AATGATCCAAGGGTGGTCTTGTTTCAATTCTTCAATTA-TCAATG
28451 CTTCAATT
1 CTTCAATT
28459 CTTCGATTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
55 13 0.22
56 21 0.36
57 10 0.17
58 1 0.02
60 14 0.24
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (58 bp):
CTTCAATTTACTTCAATGATCCAAGGGTGGTCTTGTTTCAATTCTTCAATTATCAATG
Found at i:28467 original size:24 final size:24
Alignment explanation
Indices: 28431--28482 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
28421 GTCTTGTTTT
28431 AATTCTTCAATTACTCAATGCTTC
1 AATTCTTCAATTACTCAATGCTTC
* * *
28455 AATTCTTCGATTATTCAGTGCTTC
1 AATTCTTCAATTACTCAATGCTTC
28479 AATT
1 AATT
28483 TATTTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (24 bp):
AATTCTTCAATTACTCAATGCTTC
Found at i:28552 original size:35 final size:35
Alignment explanation
Indices: 28499--28735 Score: 231
Period size: 35 Copynumber: 6.7 Consensus size: 35
28489 AAAATGATCG
*
28499 AGGGTGGTCATTCTTCAGTTTATTTCAGTTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
* * * * * *
28534 AAGGTGGTCTTCCATCAGTTTATTTCAGGATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATTTCA-GTTGACCC
* * *
28570 AGGGTGGACATTCTTCAGTATATTTCAGTTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
* * * * * * * *
28605 TGGGTGGTCTTTCATCAGTTTGTGTCGGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATTTCAG-TTGACCC
* * *
28641 AGGGTTGTAGTTTCTTCAGTTTATTTCAGGTGACCC
1 AGGGTGGT-CTTTCTTCAGTTTATTTCAGTTGACCC
*
28677 AGGGTGGTCTTTCTTCAGTTTATGTCAGTTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
*
28712 AGGGTGGTCCTTTTTTCAGTTTAT
1 AGGGTGGT-CTTTCTTCAGTTTAT
28736 GTCGGAATGA
Statistics
Matches: 156, Mismatches: 42, Indels: 7
0.76 0.20 0.03
Matches are distributed among these distances:
35 80 0.51
36 61 0.39
37 15 0.10
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (35 bp):
AGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCC
Found at i:28569 original size:71 final size:71
Alignment explanation
Indices: 28492--28735 Score: 296
Period size: 71 Copynumber: 3.4 Consensus size: 71
28482 TTATTTCAAA
* *
28492 ATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAGTTGACCCAAGGTGGTCTTCCATCAGTTTAT
1 ATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCATCAGTTTAT
*
28557 TTCAGG
66 GTCAGG
* * * *
28563 ATGATCGAGGGTGGACATTCTTCAGTATATTTCAGTTGACCCTGGGTGGTCTTTCATCAGTTTGT
1 ATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCATCAGTTTAT
28628 GTC-GG
66 GTCAGG
* * *
28633 AATGATCGAGGGTTGT-AGTTTCTTCAGTTTATTTCAGGTGACCCAGGGTGGTCTTTCTTCAGTT
1 -ATGATCGAGGGTGGTCA--TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCATCAGTT
28697 TATGTCA-G
63 TATGTCAGG
* * * * *
28705 TTGACCCAGGGTGGTCCTTTTTTCAGTTTAT
1 ATGATCGAGGGTGGT-CATTCTTCAGTTTAT
28736 GTCGGAATGA
Statistics
Matches: 147, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
70 3 0.02
71 97 0.66
72 47 0.32
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (71 bp):
ATGATCGAGGGTGGTCATTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCATCAGTTTAT
GTCAGG
Found at i:28670 original size:108 final size:108
Alignment explanation
Indices: 28548--28753 Score: 306
Period size: 108 Copynumber: 1.9 Consensus size: 108
28538 TGGTCTTCCA
* * * *
28548 TCAGTTTATTTCAGGATGATCGAGGGTGGACATTCTTCAGTATATTTCAGTTGACCCTGGGTGGT
1 TCAGTTTATTTCAGG-TGACCCAGGGTGGACATTCTTCAGTATATGTCAGTTGACCCAGGGTGGT
*
28613 -CTTTCATCAGTTTGTGTCGGAATGATCGAGGGTTGTAGTTTCT
65 CCTTTCATCAGTTTATGTCGGAATGATCGAGGGTTGTAGTTTCT
* * *
28656 TCAGTTTATTTCAGGTGACCCAGGGTGGTCTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTC
1 TCAGTTTATTTCAGGTGACCCAGGGTGGACATTCTTCAGTATATGTCAGTTGACCCAGGGTGGTC
**
28721 CTTTTTTCAGTTTATGTCGGAATGATCGAGGGT
66 CTTTCATCAGTTTATGTCGGAATGATCGAGGGT
28754 GGTCGTTCTT
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
107 42 0.48
108 45 0.52
ACGTcount: A:0.17, C:0.16, G:0.28, T:0.39
Consensus pattern (108 bp):
TCAGTTTATTTCAGGTGACCCAGGGTGGACATTCTTCAGTATATGTCAGTTGACCCAGGGTGGTC
CTTTCATCAGTTTATGTCGGAATGATCGAGGGTTGTAGTTTCT
Found at i:28764 original size:107 final size:108
Alignment explanation
Indices: 28548--28765 Score: 305
Period size: 107 Copynumber: 2.0 Consensus size: 108
28538 TGGTCTTCCA
* * * *
28548 TCAGTTTATTTCAGGATGATCGAGGGTGGACATTCTTCAGTATATTTCAGTTGACCCTGGGTGGT
1 TCAGTTTATTTCAGGATGACCCAGGGTGGACATTCTTCAGTATATGTCAGTTGACCCAGGGTGGT
* *
28613 CTTTCATCAGTTTGTGTCGGAATGATCGAGGGTTGTAGTTTCT
66 CTTTCATCAGTTTATGTCGGAATGATCGAGGGTGGTAGTTTCT
* * *
28656 TCAGTTTATTTCAGG-TGACCCAGGGTGGTCTTTCTTCAGTTTATGTCAGTTGACCCAGGGTGGT
1 TCAGTTTATTTCAGGATGACCCAGGGTGGACATTCTTCAGTATATGTCAGTTGACCCAGGGTGGT
** *
28720 CCTTTTTTCAGTTTATGTCGGAATGATCGAGGGTGGTCG-TTCT
66 -CTTTCATCAGTTTATGTCGGAATGATCGAGGGTGGTAGTTTCT
28763 TCA
1 TCA
28766 ATTCAGTTTG
Statistics
Matches: 97, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
107 49 0.51
108 48 0.49
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (108 bp):
TCAGTTTATTTCAGGATGACCCAGGGTGGACATTCTTCAGTATATGTCAGTTGACCCAGGGTGGT
CTTTCATCAGTTTATGTCGGAATGATCGAGGGTGGTAGTTTCT
Found at i:28801 original size:108 final size:107
Alignment explanation
Indices: 28580--28801 Score: 261
Period size: 108 Copynumber: 2.1 Consensus size: 107
28570 AGGGTGGACA
* * *
28580 TTCTTCAGTATATTTCAGTTGACCCTGGGTGGTCTTTCATCAGTTTGTGTCGGAATGATCGAGGG
1 TTCTTCAGTATATGTCAGTTGACCCAGGGTGGTCTTTCATCAGTTTATGTCGGAATGATCGAGGG
* * * * * *
28645 TTGTAGTTTCTTCAGTTTATTTCAGGTGACCCAGGGTGGTCT
66 TGGTAGTTTCTTCAATTCATTTCAGATGAACCACGGTGGTCT
* **
28687 TTCTTCAGTTTATGTCAGTTGACCCAGGGTGGTCCTTTTTTCAGTTTATGTCGGAATGATCGAGG
1 TTCTTCAGTATATGTCAGTTGACCCAGGGTGGT-CTTTCATCAGTTTATGTCGGAATGATCGAGG
* *
28752 GTGGTCG-TTCTTCAATTCAGTTTGTA-ATGAACCACGGTGGT-T
65 GTGGTAGTTTCTTCAATTCA-TTT-CAGATGAACCACGGTGGTCT
28794 TTCCTTCA
1 TT-CTTCA
28802 ATTATTTATC
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
107 43 0.44
108 53 0.55
109 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.40
Consensus pattern (107 bp):
TTCTTCAGTATATGTCAGTTGACCCAGGGTGGTCTTTCATCAGTTTATGTCGGAATGATCGAGGG
TGGTAGTTTCTTCAATTCATTTCAGATGAACCACGGTGGTCT
Found at i:31814 original size:18 final size:17
Alignment explanation
Indices: 31791--31826 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
31781 CTCAACCTAA
31791 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
31809 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
31826 A
1 A
31827 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:34214 original size:16 final size:16
Alignment explanation
Indices: 34189--34231 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
34179 AGGAATAGGC
34189 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
*
34205 AATCATTCAAAGCAA-
1 AATCAATCAAAGCAAT
34220 AA-CAATGCAAAG
1 AATCAAT-CAAAG
34232 AAAAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 7 0.29
16 14 0.58
ACGTcount: A:0.56, C:0.19, G:0.09, T:0.16
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:36890 original size:22 final size:21
Alignment explanation
Indices: 36865--36911 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
36855 TTTATAACGC
* *
36865 AAACCCTAATTTTTTTTTTGAA
1 AAACCC-AATGTTTTTTTAGAA
*
36887 AAACGCAATGTTTTTTTAGAA
1 AAACCCAATGTTTTTTTAGAA
36908 AAAC
1 AAAC
36912 GCAAAAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (21 bp):
AAACCCAATGTTTTTTTAGAA
Found at i:36902 original size:21 final size:21
Alignment explanation
Indices: 36876--36915 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
36866 AACCCTAATT
*
36876 TTTTTTTTGAAAAACGCAATG
1 TTTTTTTAGAAAAACGCAATG
36897 TTTTTTTAGAAAAACGCAA
1 TTTTTTTAGAAAAACGCAA
36916 AAAGAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (21 bp):
TTTTTTTAGAAAAACGCAATG
Found at i:37176 original size:20 final size:21
Alignment explanation
Indices: 37151--37198 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
37141 TAAGATTATC
* *
37151 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAGCAAAGTA
37171 AATTAAAAACAAAGCAAAGTA
1 AATTAAAAACAAAGCAAAGTA
37192 AATTAAA
1 AATTAAA
37199 TATAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAAGTA
Found at i:37951 original size:18 final size:17
Alignment explanation
Indices: 37928--37963 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
37918 CTCAACCTAA
37928 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
37946 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
37963 A
1 A
37964 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:40927 original size:15 final size:15
Alignment explanation
Indices: 40907--40937 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40897 ATGCCATGTG
40907 GGACTTAGTTGCCAT
1 GGACTTAGTTGCCAT
*
40922 GGACTTGGTTGCCAT
1 GGACTTAGTTGCCAT
40937 G
1 G
40938 AGCCATGGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.19, G:0.32, T:0.32
Consensus pattern (15 bp):
GGACTTAGTTGCCAT
Found at i:40942 original size:22 final size:23
Alignment explanation
Indices: 40917--40962 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
40907 GGACTTAGTT
40917 GCCAT-GGACTTGGTTGCCATGA
1 GCCATGGGACTTGGTTGCCATGA
40939 GCCATGGGGACTTGGTTGCCATGA
1 GCCAT-GGGACTTGGTTGCCATGA
40963 TATGGCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.23
24 17 0.77
ACGTcount: A:0.17, C:0.22, G:0.35, T:0.26
Consensus pattern (23 bp):
GCCATGGGACTTGGTTGCCATGA
Done.