Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006408.1 Corchorus capsularis cultivar CVL-1 contig06429, 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: 66204
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:112 original size:26 final size:26
Alignment explanation
Indices: 78--145 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
68 TACTTAGTTT
* *
78 ATTATTTTATGTTTAATTAATATCTA
1 ATTAGTTTATGATTAATTAATATCTA
* *
104 ATTAGTTTACT-ATTAATTAGTATTTA
1 ATTAGTTTA-TGATTAATTAATATCTA
130 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
146 AATGAAGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 34 0.94
27 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAATATCTA
Found at i:145 original size:15 final size:14
Alignment explanation
Indices: 97--145 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
87 TGTTTAATTA
97 ATATCTAATTAGTTT
1 ATAT-TAATTAGTTT
112 ACTATTAATTAG--T
1 A-TATTAATTAGTTT
125 AT-TTAATTAGTTT
1 ATATTAATTAGTTT
138 ATGATTAA
1 AT-ATTAA
146 AATGAAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
11 8 0.28
12 1 0.03
13 5 0.17
15 12 0.41
16 3 0.10
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (14 bp):
ATATTAATTAGTTT
Found at i:378 original size:16 final size:17
Alignment explanation
Indices: 352--384 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
342 TTTTTATTTG
352 TTAATATATAATATATA
1 TTAATATATAATATATA
*
369 TTAA-ATATAATTTATA
1 TTAATATATAATATATA
385 CATACACCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATATATAATATATA
Found at i:530 original size:14 final size:13
Alignment explanation
Indices: 494--532 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
484 ATTTTATATT
*
494 TATAATTATATTTA
1 TATAATTA-ATTAA
508 TATAATTAATTAA
1 TATAATTAATTAA
521 TATAATTTAATT
1 TATAA-TTAATT
533 CTTAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATAATTAATTAA
Found at i:6827 original size:2 final size:2
Alignment explanation
Indices: 6820--6851 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6810 TCTTTCCTTT
6820 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6852 AAATCTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:12039 original size:37 final size:37
Alignment explanation
Indices: 11989--12062 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
11979 GCATATGTTC
11989 GGTGTATTTAGGGGTAGAATGATGATTTATGCATTAT
1 GGTGTATTTAGGGGTAGAATGATGATTTATGCATTAT
12026 GGTGTATTTAGGGGTAGAATGATGATTTATGCATTAT
1 GGTGTATTTAGGGGTAGAATGATGATTTATGCATTAT
12063 TATCCCATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.03, G:0.30, T:0.41
Consensus pattern (37 bp):
GGTGTATTTAGGGGTAGAATGATGATTTATGCATTAT
Found at i:19468 original size:29 final size:29
Alignment explanation
Indices: 19415--19470 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
19405 AGTATATATG
* * *
19415 GACAATTTGCATCGTAAACTTTAATTTTA
1 GACAATTTGCACCCTAAACTATAATTTTA
*
19444 GACAATTTGCACCCTATACTATAATTT
1 GACAATTTGCACCCTAAACTATAATTT
19471 ACGGAGAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (29 bp):
GACAATTTGCACCCTAAACTATAATTTTA
Found at i:22341 original size:21 final size:21
Alignment explanation
Indices: 22312--22351 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
22302 TGTGAGCAAA
*
22312 CCTTTAGTATGTTT-CTAATTT
1 CCTTGAGTA-GTTTACTAATTT
22333 CCTTGAGTAGTTTACTAAT
1 CCTTGAGTAGTTTACTAAT
22352 GAATTGACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (21 bp):
CCTTGAGTAGTTTACTAATTT
Found at i:27555 original size:16 final size:16
Alignment explanation
Indices: 27531--27561 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27521 TTCAGAAATT
*
27531 AATATATTATTAAAAA
1 AATAAATTATTAAAAA
27547 AATAAATTATTAAAA
1 AATAAATTATTAAAA
27562 GAAACTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAAATTATTAAAAA
Found at i:27855 original size:20 final size:21
Alignment explanation
Indices: 27817--27856 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
27807 ATGCTGAATT
27817 TCAACTAATGTCAGATGTCAC
1 TCAACTAATGTCAGATGTCAC
27838 TCAACTAATGTC-GATGTCA
1 TCAACTAATGTCAGATGTCA
27857 TGATGGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (21 bp):
TCAACTAATGTCAGATGTCAC
Found at i:28615 original size:107 final size:104
Alignment explanation
Indices: 28447--28686 Score: 356
Period size: 107 Copynumber: 2.3 Consensus size: 104
28437 TAGCCTTAAT
* * * *
28447 TTCACTAAGTTTAGCCCCAAATGAAGATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTAATA
1 TTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAAGGTAAATTCCAAAATTAATA
*
28512 ATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAACTAA
66 A--TATTGTTATAGGGTTTTAAAAATAAAATACAAAACTAA
*
28553 TGTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAAGGTAAATTCCATAATTAAT
1 T-TCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAAGGTAAATTCCAAAATTAAT
* * *
28618 AATATTGTTATAGGGTTTTAAAAATAAAATATATAATTAA
65 AATATTGTTATAGGGTTTTAAAAATAAAATACAAAACTAA
28658 TTCACTAAGTTTTAG-CCCAAATTAAAATT
1 TTCACTAAG-TTTAGCCCCAAATTAAAATT
28687 AAAATTTAAT
Statistics
Matches: 123, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
104 22 0.18
105 40 0.33
106 1 0.01
107 60 0.49
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (104 bp):
TTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAAGGTAAATTCCAAAATTAATA
ATATTGTTATAGGGTTTTAAAAATAAAATACAAAACTAA
Found at i:28914 original size:30 final size:29
Alignment explanation
Indices: 28878--28945 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
28868 AAGGAGTTTT
* * *
28878 TTTACCAAAGTACAGCATTTTGAAAACTTA
1 TTTACCAAAATACAACACTTT-AAAACTTA
*
28908 TTTACCAAAATATAACACTTTAAAACTTA
1 TTTACCAAAATACAACACTTTAAAACTTA
*
28937 TTTCCCAAA
1 TTTACCAAA
28946 TTAATTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.43, C:0.19, G:0.04, T:0.34
Consensus pattern (29 bp):
TTTACCAAAATACAACACTTTAAAACTTA
Found at i:29676 original size:29 final size:29
Alignment explanation
Indices: 29628--29683 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
29618 GATGTGGTAA
29628 AAAAGTAGTATAGTTTGGGAAATAAGTTT
1 AAAAGTAGTATAGTTTGGGAAATAAGTTT
* *
29657 AAAAGTATTATA-TTTAGGGAATTAAGT
1 AAAAGTAGTATAGTTT-GGGAAATAAGT
29684 ATTATATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (29 bp):
AAAAGTAGTATAGTTTGGGAAATAAGTTT
Found at i:29757 original size:16 final size:16
Alignment explanation
Indices: 29732--29764 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29722 AACCAAAATG
29732 AGAAAAAAGAAAAGAA
1 AGAAAAAAGAAAAGAA
*
29748 AGAAAGAAGAAAAGAA
1 AGAAAAAAGAAAAGAA
29764 A
1 A
29765 ACAAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AGAAAAAAGAAAAGAA
Found at i:32137 original size:109 final size:109
Alignment explanation
Indices: 31978--32241 Score: 431
Period size: 109 Copynumber: 2.4 Consensus size: 109
31968 TAAATTAAAA
** * *
31978 TGGTAAAAATAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTA
1 TGGTAAAAATAAAGTAATTATA-AAGATATTAG-ATTTAATTAAATTAAAATAGAGTTTTTAGTA
32042 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
64 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
*
32088 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATTAAAATAGAGTTTTTAGTGGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATTAAAATAGAGTTTTTAGTAGA
*
32153 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* *
32197 TGGTAAAAATAAAGTAATTATAAAGATATTAAATTTAATTTAATT
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATT
32242 GAATAAAAAT
Statistics
Matches: 145, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
109 124 0.86
110 21 0.14
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATTAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:45733 original size:6 final size:6
Alignment explanation
Indices: 45692--45731 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
45682 TTTCCCCTTC
* *
45692 TGTTTC TGTTTT TGTTTT TGTTTT TGTTTT TGTTGT TGTT
1 TGTTTT TGTTTT TGTTTT TGTTTT TGTTTT TGTTTT TGTT
45732 GTAAGTTCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.20, T:0.78
Consensus pattern (6 bp):
TGTTTT
Found at i:49831 original size:15 final size:15
Alignment explanation
Indices: 49822--49862 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
49812 AAAAAGCTCA
49822 AACCCGAAAAATCAG
1 AACCCGAAAAATCAG
**
49837 AACCCGAAAAATTTG
1 AACCCGAAAAATCAG
*
49852 AAACCGAAAAA
1 AACCCGAAAAA
49863 ACCCGAACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.56, C:0.22, G:0.12, T:0.10
Consensus pattern (15 bp):
AACCCGAAAAATCAG
Found at i:49923 original size:20 final size:20
Alignment explanation
Indices: 49895--49933 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
49885 ACCTGAATTC
*
49895 AATACTAATATTTGAAAATA
1 AATAATAATATTTGAAAATA
*
49915 AATAATAATTTTTGAAAAT
1 AATAATAATATTTGAAAAT
49934 TTCATCTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
AATAATAATATTTGAAAATA
Found at i:50102 original size:16 final size:16
Alignment explanation
Indices: 50083--50170 Score: 72
Period size: 16 Copynumber: 5.5 Consensus size: 16
50073 CCTGAACCTG
*
50083 AATTAACCTGACCCAA
1 AATTAACCCGACCCAA
* *
50099 AATTGACCCGAATCC-A
1 AATTAACCCG-ACCCAA
* *
50115 AATCAACCCGACCTAA
1 AATTAACCCGACCCAA
*
50131 ATTTAACCCGAACCC-A
1 AATTAACCCG-ACCCAA
*
50147 AATCAACCCGACCCAA
1 AATTAACCCGACCCAA
*
50163 ATTTAACC
1 AATTAACC
50171 TGAACCCGAT
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
15 6 0.11
16 42 0.78
17 6 0.11
ACGTcount: A:0.41, C:0.35, G:0.07, T:0.17
Consensus pattern (16 bp):
AATTAACCCGACCCAA
Found at i:50140 original size:32 final size:32
Alignment explanation
Indices: 50087--50177 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 32
50077 AACCTGAATT
* * * *
50087 AACCTGACCCAAAATTGACCCGAATCCAAATC
1 AACCCGACCCAAATTTAACCCGAACCCAAATC
*
50119 AACCCGACCTAAATTTAACCCGAACCCAAATC
1 AACCCGACCCAAATTTAACCCGAACCCAAATC
*
50151 AACCCGACCCAAATTTAACCTGAACCC
1 AACCCGACCCAAATTTAACCCGAACCC
50178 GATTTAAGCC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.40, C:0.37, G:0.08, T:0.15
Consensus pattern (32 bp):
AACCCGACCCAAATTTAACCCGAACCCAAATC
Found at i:51049 original size:63 final size:63
Alignment explanation
Indices: 50967--51085 Score: 229
Period size: 63 Copynumber: 1.9 Consensus size: 63
50957 CATGTGTCCT
50967 TAGGGACTAGGTTGAAATATTTAAAATTTAATTAATTCAGAAAATGGACATGTGTCTACTGTC
1 TAGGGACTAGGTTGAAATATTTAAAATTTAATTAATTCAGAAAATGGACATGTGTCTACTGTC
*
51030 TAGGGACTAGGTTGAAATATTTAAAATTTAATTAATTCAGAAAATGGATATGTGTC
1 TAGGGACTAGGTTGAAATATTTAAAATTTAATTAATTCAGAAAATGGACATGTGTC
51086 AACTCCACCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (63 bp):
TAGGGACTAGGTTGAAATATTTAAAATTTAATTAATTCAGAAAATGGACATGTGTCTACTGTC
Found at i:56043 original size:25 final size:25
Alignment explanation
Indices: 56009--56063 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
55999 AAAAGTTCGA
56009 TGATTGTGATGAAAGTTGTATGAGT
1 TGATTGTGATGAAAGTTGTATGAGT
*
56034 TGATTGTGATGAAATTTGTATGAGT
1 TGATTGTGATGAAAGTTGTATGAGT
56059 TGATT
1 TGATT
56064 AGAAGCACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (25 bp):
TGATTGTGATGAAAGTTGTATGAGT
Found at i:57074 original size:22 final size:22
Alignment explanation
Indices: 57049--57093 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
57039 TGGACTAGCA
* *
57049 CGGCACGACACGACTCATGTGT
1 CGGCACAACACGACCCATGTGT
*
57071 CGGCACAACAGGACCCATGTGT
1 CGGCACAACACGACCCATGTGT
57093 C
1 C
57094 TATTTAGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.33, G:0.27, T:0.16
Consensus pattern (22 bp):
CGGCACAACACGACCCATGTGT
Found at i:57901 original size:21 final size:21
Alignment explanation
Indices: 57877--57943 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
57867 ATGTTTTGAG
57877 CAAGAATATTCCAATCGATTC
1 CAAGAATATTCCAATCGATTC
** * *
57898 CAAGCTTCTTACAATCGATTC
1 CAAGAATATTCCAATCGATTC
* * *
57919 TAGGAATATTCCAACCGATTC
1 CAAGAATATTCCAATCGATTC
57940 CAAG
1 CAAG
57944 TTATGCACAT
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.28
Consensus pattern (21 bp):
CAAGAATATTCCAATCGATTC
Found at i:65677 original size:12 final size:12
Alignment explanation
Indices: 65645--65683 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
65635 ATGGAATTAA
65645 ATATCCGTCGAT
1 ATATCCGTCGAT
65657 A-A--C-TCGAT
1 ATATCCGTCGAT
65665 ATATCCGTCGAT
1 ATATCCGTCGAT
65677 ATATCCG
1 ATATCCG
65684 ATATCTGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:66157 original size:3 final size:3
Alignment explanation
Indices: 66145--66190 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
66135 GCTCACGGAA
66145 GAT G-T GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
66191 GGGAAATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
GAT
Done.