Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013325.1 Corchorus capsularis cultivar CVL-1 contig13346, 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: 77966
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:112 original size:33 final size:32
Alignment explanation
Indices: 5--106 Score: 143
Period size: 32 Copynumber: 3.2 Consensus size: 32
1 GCCC
5 CCCCATGAGGGCGGCCTGCCGTGGCGAAGCCG
1 CCCCATGAGGGCGGCCTGCCGTGGCGAAGCCG
*
37 CCCCATGAGGGCGGCCTGCCGTAGCGAAGCCG
1 CCCCATGAGGGCGGCCTGCCGTGGCGAAGCCG
* * *
69 CCACAGTG-GGGCGGCCTGCCCATGGTGAAGCCG
1 CCCCA-TGAGGGCGGCCTG-CCGTGGCGAAGCCG
102 CCCCA
1 CCCCA
107 GTGGGGAGGC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
32 45 0.73
33 17 0.27
ACGTcount: A:0.15, C:0.38, G:0.37, T:0.10
Consensus pattern (32 bp):
CCCCATGAGGGCGGCCTGCCGTGGCGAAGCCG
Found at i:143 original size:33 final size:33
Alignment explanation
Indices: 97--184 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
87 CCCATGGTGA
* * *
97 AGCCGCCCCAGTGGGGAGGCTCCGCCGTGGTTG
1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGCTG
130 AGCCTCCCTAGTGGGGAAGG-TCCGCCGTGGCTG
1 AGCCTCCCTAGTGGGG-AGGCTCCGCCGTGGCTG
*
163 AACCGT-CCTAGTGGGGAGGCTC
1 AGCC-TCCCTAGTGGGGAGGCTC
185 AGTGTAAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
32 3 0.06
33 41 0.85
34 4 0.08
ACGTcount: A:0.12, C:0.31, G:0.40, T:0.17
Consensus pattern (33 bp):
AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGCTG
Found at i:10913 original size:19 final size:19
Alignment explanation
Indices: 10875--10927 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
10865 TACTATTTAG
*
10875 ATATTATACAGATGAGATT
1 ATATTATACAGATGAAATT
* *
10894 ATATTATATAGATTAAATT
1 ATATTATACAGATGAAATT
*
10913 AGATACTATACAGAT
1 --ATATTATACAGAT
10928 AAACTATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 16 0.59
21 11 0.41
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (19 bp):
ATATTATACAGATGAAATT
Found at i:12510 original size:3 final size:3
Alignment explanation
Indices: 12498--12529 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
12488 TTCCTTTCTT
*
12498 CTG CTC CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
12530 TCAGTCTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.38, G:0.28, T:0.34
Consensus pattern (3 bp):
CTG
Found at i:19025 original size:10 final size:10
Alignment explanation
Indices: 19010--19043 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
19000 CTCCTCCTAT
19010 ATAAATATAA
1 ATAAATATAA
19020 ATAAATATAA
1 ATAAATATAA
19030 ATTAAATTATAA
1 A-TAAA-TATAA
19042 AT
1 AT
19044 GGAAAAGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 11 0.50
11 5 0.23
12 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
ATAAATATAA
Found at i:26396 original size:6 final size:6
Alignment explanation
Indices: 26385--26426 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
26375 TGGAGGTACT
26385 GGTGCC GGTGCC GGTGCC GGTGCC GGTGCC GGTGCC GGTGCC
1 GGTGCC GGTGCC GGTGCC GGTGCC GGTGCC GGTGCC GGTGCC
26427 TCATGTTCGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.50, T:0.17
Consensus pattern (6 bp):
GGTGCC
Found at i:26799 original size:21 final size:21
Alignment explanation
Indices: 26775--26816 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
26765 TGATCATTAT
26775 TATA-ATA-TTATTATATATA
1 TATATATATTTATTATATATA
26794 TATATATATTTATTATATATA
1 TATATATATTTATTATATATA
26815 TA
1 TA
26817 AGATCTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.19
20 3 0.14
21 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATATATTTATTATATATA
Found at i:30513 original size:13 final size:13
Alignment explanation
Indices: 30495--30521 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30485 AATCTTGCTG
30495 AAACTTAAAGCCC
1 AAACTTAAAGCCC
30508 AAACTTAAAGCCC
1 AAACTTAAAGCCC
30521 A
1 A
30522 TTTTTCATAT
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:0.48, C:0.30, G:0.07, T:0.15
Consensus pattern (13 bp):
AAACTTAAAGCCC
Found at i:31082 original size:2 final size:2
Alignment explanation
Indices: 31070--31110 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
31060 ATGCAAACTT
*
31070 TA TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TC TA TA -A TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31111 TTTAAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:31383 original size:79 final size:79
Alignment explanation
Indices: 31252--31410 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
31242 ATGCGTGTGG
31252 GTTTTGTGCTGCTTTGTTAGTTTGTATTTAATTGCTCATGGATATCATCAACAAGAAGGAACCAA
1 GTTTTGTGCTGCTTTGTTAGTTTGTATTTAATTGCTCATGGATATCATCAACAAGAAGGAACCAA
*
31317 TGTTATGGGAAGGA
66 TGTTATGAGAAGGA
31331 GTTTTGTGCTGCTTTGTTAGTTTGTATTTAATTGCTCATGGATATCATCAACAAGAAGGAACCAA
1 GTTTTGTGCTGCTTTGTTAGTTTGTATTTAATTGCTCATGGATATCATCAACAAGAAGGAACCAA
31396 TGTTATGAGAAGGA
66 TGTTATGAGAAGGA
31410 G
1 G
31411 CTTGCTTAAT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.36
Consensus pattern (79 bp):
GTTTTGTGCTGCTTTGTTAGTTTGTATTTAATTGCTCATGGATATCATCAACAAGAAGGAACCAA
TGTTATGAGAAGGA
Found at i:46128 original size:2 final size:2
Alignment explanation
Indices: 46121--46153 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
46111 TTATAAACTT
46121 TA TA TA TA TA TA TA TA TA TA TA T- TA TA GTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
46154 TAAAATAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47097 original size:42 final size:44
Alignment explanation
Indices: 47042--47134 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 44
47032 AGTGCATTAC
* *
47042 CTAA-ATTATACTC-T-ATCTCTAAATAATTCATCAAAATAAAG
1 CTAATATTATACTCTTCAGCTCTAAATAATTCATCAAAATAAAA
* * *
47083 CTAATATTCTACTCTTCCAGCTCTAGATAATTCATTAAAATAAAA
1 CTAATATTATACTCTT-CAGCTCTAAATAATTCATCAAAATAAAA
47128 CTAATAT
1 CTAATAT
47135 ATTAATTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.19
43 1 0.02
45 30 0.70
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.35
Consensus pattern (44 bp):
CTAATATTATACTCTTCAGCTCTAAATAATTCATCAAAATAAAA
Found at i:49319 original size:23 final size:23
Alignment explanation
Indices: 49270--49319 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
49260 GAACTTACTT
* ** *
49270 AAATACCTATGATGTGTAAGGTT
1 AAATACCTATGATGTCTAAAATA
49293 AAATACCTATGATGTCTAAAATA
1 AAATACCTATGATGTCTAAAATA
49316 AAAT
1 AAAT
49320 TAAAAGAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (23 bp):
AAATACCTATGATGTCTAAAATA
Found at i:49469 original size:29 final size:27
Alignment explanation
Indices: 49409--49492 Score: 100
Period size: 25 Copynumber: 3.0 Consensus size: 27
49399 ATATGATTTA
49409 TAAAAATTAATTATT-ATTTATTATA-
1 TAAAAATTAATTATTCATTTATTATAT
49434 TAAAAATTAATTATTCATCTTATATATAT
1 TAAAAATTAATTATTCAT-TTAT-TATAT
* *
49463 TACAAATTATAATATGTCATTTATTATAT
1 TAAAAATTA-ATTAT-TCATTTATTATAT
49492 T
1 T
49493 TATATATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
25 15 0.29
26 2 0.04
27 4 0.08
28 4 0.08
29 14 0.27
30 8 0.16
31 4 0.08
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (27 bp):
TAAAAATTAATTATTCATTTATTATAT
Found at i:52939 original size:2 final size:2
Alignment explanation
Indices: 52934--52964 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52924 ACACACACAC
52934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52965 GTGGAAACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54416 original size:17 final size:18
Alignment explanation
Indices: 54390--54424 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
54380 TTAGTCAAAA
54390 AATTCAAAAA-TGGAATT
1 AATTCAAAAATTGGAATT
*
54407 AATTCCAAAATTGGAATT
1 AATTCAAAAATTGGAATT
54425 GGAATTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (18 bp):
AATTCAAAAATTGGAATT
Found at i:54421 original size:18 final size:17
Alignment explanation
Indices: 54390--54424 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54380 TTAGTCAAAA
54390 AATTCAAAAATGGAATT
1 AATTCAAAAATGGAATT
*
54407 AATTCCAAAATTGGAATT
1 AATT-CAAAAATGGAATT
54425 GGAATTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (17 bp):
AATTCAAAAATGGAATT
Found at i:62674 original size:3 final size:3
Alignment explanation
Indices: 62666--62699 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
62656 TCAACAAATT
62666 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
62700 ATCACACCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:63005 original size:21 final size:21
Alignment explanation
Indices: 62979--63024 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
62969 CTCTACCAAA
*
62979 CTAATGAATGATCAATGTGAT
1 CTAATGAATGATCAATATGAT
63000 CTAATGAATGATCAATATGAT
1 CTAATGAATGATCAATATGAT
63021 CTAA
1 CTAA
63025 AATAACATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (21 bp):
CTAATGAATGATCAATATGAT
Found at i:64748 original size:29 final size:28
Alignment explanation
Indices: 64716--64778 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
64706 AATAAGCCTC
* *
64716 TATTTTCATATTGA-ACCTAAATAAACTCT
1 TATTTTCAAATT-ATACC-AAATAAACCCT
*
64745 TATTTTTAAATTATACCAAATAAACCCT
1 TATTTTCAAATTATACCAAATAAACCCT
64773 TATTTT
1 TATTTT
64779 TTCACTATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 17 0.57
29 13 0.43
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (28 bp):
TATTTTCAAATTATACCAAATAAACCCT
Found at i:65810 original size:5 final size:5
Alignment explanation
Indices: 65797--65830 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
65787 ATTCATATTT
*
65797 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
65831 TGACTCAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:71034 original size:17 final size:17
Alignment explanation
Indices: 71012--71069 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
71002 TTTAGTTTTC
71012 TTTTTTAAATGGATAGT
1 TTTTTTAAATGGATAGT
*
71029 TTTTTT-AATTGAGT-GTT
1 TTTTTTAAATGGA-TAG-T
*
71046 TTTTTTAAATGGGTAGT
1 TTTTTTAAATGGATAGT
71063 TTATTTT
1 TT-TTTT
71070 TAGTTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
16 6 0.18
17 18 0.55
18 9 0.27
ACGTcount: A:0.22, C:0.00, G:0.17, T:0.60
Consensus pattern (17 bp):
TTTTTTAAATGGATAGT
Found at i:71083 original size:34 final size:32
Alignment explanation
Indices: 70992--71087 Score: 97
Period size: 34 Copynumber: 2.9 Consensus size: 32
70982 ATAATTAGAA
*
70992 GGTAGTTTA-TTTTAGTTTTCTTTTTTAAATG
1 GGTAGTTTATTTTTAGTTTTTTTTTTTAAATG
* * *
71023 GATAGTTTTTTTAATTGAG-TGTTTTTTTTAAATG
1 GGTAGTTTATTT--TT-AGTTTTTTTTTTTAAATG
*
71057 GGTAGTTTATTTTTAGTTTTAATTTTTTAAA
1 GGTAGTTTATTTTTAGTTTT-TTTTTTTAAA
71088 AACTAAGTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
31 9 0.18
32 6 0.12
33 9 0.18
34 25 0.49
35 2 0.04
ACGTcount: A:0.23, C:0.01, G:0.16, T:0.60
Consensus pattern (32 bp):
GGTAGTTTATTTTTAGTTTTTTTTTTTAAATG
Found at i:72978 original size:45 final size:45
Alignment explanation
Indices: 72928--73030 Score: 188
Period size: 45 Copynumber: 2.3 Consensus size: 45
72918 AGTGGAAAGC
72928 ACAATTCATGGGGAGATAACAGGCCTAGGGATTGGAATACTGGCA
1 ACAATTCATGGGGAGATAACAGGCCTAGGGATTGGAATACTGGCA
* *
72973 ACAATTCATGGGGAGATAACAGGTCTAGGGATTGGTATACTGGCA
1 ACAATTCATGGGGAGATAACAGGCCTAGGGATTGGAATACTGGCA
73018 ACAATTCATGGGG
1 ACAATTCATGGGG
73031 CCATAGCTGT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (45 bp):
ACAATTCATGGGGAGATAACAGGCCTAGGGATTGGAATACTGGCA
Found at i:77767 original size:60 final size:60
Alignment explanation
Indices: 77674--77792 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
77664 ATATAGACTT
*
77674 ATAGTAGCATTTAAAAGGAGGCTAATGTGTACTTTGCCTCTGTTATGCTAAAACGTGCAG
1 ATAGTAGCATTTAAAAGGAGGCTAATATGTACTTTGCCTCTGTTATGCTAAAACGTGCAG
77734 ATAGTAGCATTTAAAAGGAGGCTAATATGTACTTTGCCTCTGTTATGCTAAAACGTGCA
1 ATAGTAGCATTTAAAAGGAGGCTAATATGTACTTTGCCTCTGTTATGCTAAAACGTGCA
77793 AGACAGAGTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (60 bp):
ATAGTAGCATTTAAAAGGAGGCTAATATGTACTTTGCCTCTGTTATGCTAAAACGTGCAG
Done.