Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012788.1 Corchorus capsularis cultivar CVL-1 contig12809, 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: 52013
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:2033 original size:2 final size:2
Alignment explanation
Indices: 2026--2052 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2016 AGTTGTACAT
2026 TA TA 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 T
2053 TTTTGACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10645 original size:27 final size:27
Alignment explanation
Indices: 10589--10662 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
10579 GTAGATTAAG
*
10589 AATGACCAAAATATCCCCTAAATGCAAA
1 AATGACCAAAAT-GCCCCTAAATGCAAA
* **
10617 AATGACCAAAATGCCCCTAGATGTGAA
1 AATGACCAAAATGCCCCTAAATGCAAA
10644 AATGACCAAAATGCCCCTA
1 AATGACCAAAATGCCCCTA
10663 TGTGACCCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 30 0.71
28 12 0.29
ACGTcount: A:0.45, C:0.26, G:0.12, T:0.18
Consensus pattern (27 bp):
AATGACCAAAATGCCCCTAAATGCAAA
Found at i:11024 original size:23 final size:23
Alignment explanation
Indices: 10998--11041 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
10988 TATAGCAATA
10998 ATAATAAATATATAATAATTACC
1 ATAATAAATATATAATAATTACC
* * *
11021 ATAATTAGTATATATTAATTA
1 ATAATAAATATATAATAATTA
11042 ACTATGACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAATAAATATATAATAATTACC
Found at i:12651 original size:5 final size:5
Alignment explanation
Indices: 12641--12678 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
12631 AGCATTTTAA
* *
12641 AATAT AATAT AATAT AATAT AATAT AACAT TATAT AAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT
12679 TTTGGTTCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:13043 original size:180 final size:180
Alignment explanation
Indices: 12734--13075 Score: 465
Period size: 180 Copynumber: 1.9 Consensus size: 180
12724 AGGTTGTTCC
*
12734 ATGATCTACAACTTTCATGAAAGACTCGAAAACTAAATTTAGTGTTTCAAGTATCAAAAAAACTT
1 ATGATCTACAACTTTCATGAAAGACTCGAAAACTAAATTTAATGTTTCAAGTATCAAAAAAACTT
* * * * * * *
12799 CCGAATAATTAGTTGTTTCGATTAACGGGAATGGACGATCCACTTAATATAACATTACTTTTGCT
66 CCAAAAAATTAATTGTTTCGATTAACGAGAACGAACGATCCACTTAATATAACATAACTTTTGCT
**
12864 CCAGATGTCTTATTGAGCTGATTCAAATGTCTTATAAAAGATTATTTTAT
131 CCAGATGTCCGATTGAGCTGATTCAAATGTCTTATAAAAGATTATTTTAT
* *
12914 ATGATCTACAACTTTCATGCAAGACTC-AAAAGCTAAATTTAATGTTTCAAGTAT-AAAAAATGC
1 ATGATCTACAACTTTCATGAAAGACTCGAAAA-CTAAATTTAATGTTTCAAGTATCAAAAAA-AC
* * * * *
12977 TTCCAAAAAATTAATT-TTTCCGGTTAGCGAGAACGAACGGTCCACTTAATATTACATAATTTTT
64 TTCCAAAAAATTAATTGTTT-CGATTAACGAGAACGAACGATCCACTTAATATAACATAACTTTT
* *
13041 GCTCCAGATGTCCGATTGAGGTGATTCAAGTGTCT
128 GCTCCAGATGTCCGATTGAGCTGATTCAAATGTCT
13076 GCTAAAAGGT
Statistics
Matches: 140, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
179 13 0.09
180 127 0.91
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (180 bp):
ATGATCTACAACTTTCATGAAAGACTCGAAAACTAAATTTAATGTTTCAAGTATCAAAAAAACTT
CCAAAAAATTAATTGTTTCGATTAACGAGAACGAACGATCCACTTAATATAACATAACTTTTGCT
CCAGATGTCCGATTGAGCTGATTCAAATGTCTTATAAAAGATTATTTTAT
Found at i:13166 original size:178 final size:180
Alignment explanation
Indices: 12733--13156 Score: 444
Period size: 180 Copynumber: 2.4 Consensus size: 180
12723 AAGGTTGTTC
* * * *
12733 CATGATCTACAACTTTCATGAAAGACTCGAAAA-CTAAATTTAGTGTTTCAAGTATCAAAAAA-A
1 CATGATCTACAACTTTCATGCAAGACTC-AAAAGCTAAATTTAATGTTTCAAATA-CAAAAAATG
* * * * * * * * * *
12796 CTTCCGAATAATTAGTTGTTT-CGATTAACGGGAATGGACGATCCACTTAATATAACATTACTTT
64 CTTCCAAAAAATTAATT-TTTCCGGTTAGCGAGAACGAACGGTCCACTTAATATAACATAACTTT
** * *
12860 TGCTCCAGATGTCTTATTGAGCTGATTCAAATGTCTTATAAAAGATTATTTTA
128 TGCTCCAGATGTCCGATTGAGCTGATTCAAATGTCTGATAAAAGATTAGTTTA
* * *
12913 TATGATCTACAACTTTCATGCAAGACTCAAAAGCTAAATTTAATGTTTCAAGTATAAAAAATGCT
1 CATGATCTACAACTTTCATGCAAGACTCAAAAGCTAAATTTAATGTTTCAAATACAAAAAATGCT
* *
12978 TCCAAAAAATTAATTTTTCCGGTTAGCGAGAACGAACGGTCCACTTAATATTACATAATTTTTGC
66 TCCAAAAAATTAATTTTTCCGGTTAGCGAGAACGAACGGTCCACTTAATATAACATAACTTTTGC
* * * *
13043 TCCAGATGTCCGATTGAGGTGATTCAAGTGTCTGCTAAAAGGTT-GTTT-
131 TCCAGATGTCCGATTGAGCTGATTCAAATGTCTGATAAAAGATTAGTTTA
* ** * * ** ** * *
13091 CGTGATCTTTAACTTTCATGTAGGACTTGAAAGCTAAATTTTTTTTTTCAAATACCAAAAATGCT
1 CATGATCTACAACTTTCATGCAAGACTCAAAAGCTAAATTTAATGTTTCAAATACAAAAAATGCT
13156 T
66 T
13157 TTGAAAAATT
Statistics
Matches: 202, Mismatches: 39, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
178 52 0.26
179 16 0.08
180 134 0.66
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (180 bp):
CATGATCTACAACTTTCATGCAAGACTCAAAAGCTAAATTTAATGTTTCAAATACAAAAAATGCT
TCCAAAAAATTAATTTTTCCGGTTAGCGAGAACGAACGGTCCACTTAATATAACATAACTTTTGC
TCCAGATGTCCGATTGAGCTGATTCAAATGTCTGATAAAAGATTAGTTTA
Found at i:16883 original size:9 final size:10
Alignment explanation
Indices: 16859--16884 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
16849 CCAAAACTAT
16859 ATTTTTTGTA
1 ATTTTTTGTA
16869 ATTTTTTGTA
1 ATTTTTTGTA
16879 ATTTTT
1 ATTTTT
16885 CTTATTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (10 bp):
ATTTTTTGTA
Found at i:20699 original size:48 final size:48
Alignment explanation
Indices: 20639--20735 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
20629 CAACGTTAAT
* * *
20639 TTAATACTAAAATATTATGAGATTAGTGCAAATCATAACACTTATGAA
1 TTAATACAAAAATATTATGAGATTAGAGCAAATCATAACACTCATGAA
*
20687 TTAATACAAAAATATTATGAGATTAGAGCAAATCATAGCACTCATGAA
1 TTAATACAAAAATATTATGAGATTAGAGCAAATCATAACACTCATGAA
20735 T
1 T
20736 CAAAATAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (48 bp):
TTAATACAAAAATATTATGAGATTAGAGCAAATCATAACACTCATGAA
Found at i:21056 original size:30 final size:31
Alignment explanation
Indices: 20988--21060 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 31
20978 TAGCGTTTAG
*
20988 ACGTTTTGCCCCCCGAACTTAAATCTTGGAT
1 ACGTTTTGCCCCCTGAACTTAAATCTTGGAT
* *
21019 A--TTTTGCCCCCTGAACTTCAATTTTGGA-
1 ACGTTTTGCCCCCTGAACTTAAATCTTGGAT
21047 ACGTTTTGCCCCCT
1 ACGTTTTGCCCCCT
21061 CAACCTAACG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 1 0.03
29 24 0.65
30 11 0.30
31 1 0.03
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.36
Consensus pattern (31 bp):
ACGTTTTGCCCCCTGAACTTAAATCTTGGAT
Found at i:22559 original size:2 final size:2
Alignment explanation
Indices: 22540--22579 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
22530 AGTTTAGACT
* *
22540 TA TA TA -A TA TA AA GA TA 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 TA TA TA TA T
22580 CCATCTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:25007 original size:16 final size:15
Alignment explanation
Indices: 24986--25016 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
24976 GGAGATAAAC
24986 AAAGACAAAAGAAAAG
1 AAAGACAAAA-AAAAG
25002 AAAGACAAAAAAAAG
1 AAAGACAAAAAAAAG
25017 TCAATACTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAGACAAAAAAAAG
Found at i:25166 original size:148 final size:146
Alignment explanation
Indices: 24980--25254 Score: 406
Period size: 148 Copynumber: 1.9 Consensus size: 146
24970 GTGCAGGGAG
*
24980 ATAAACAAAGACAAAAGAAAAGAAAGACAAAAAAAAGTCAATACTGAATGAAACAACAAACATAA
1 ATAAACAAAGACAAAAGAAAAGAAAGACAAAAAAAAGTCAATACTCAATGAAACAACAAACATAA
* * * * *
25045 GAATGAGAATGAGAGCAGTTTAAATGTTGCATTCAAATTATCATGAACCATATTGGGGAAACACA
66 GAATGAAAATGAGAGCAGTTGAAATCTTGCATTCAAATCAACATGAACCATATTGGGGAAACACA
25110 TTATCAACAGGAACAA
131 TTATCAACAGGAACAA
* * ** *
25126 ATAAACAAAGGCAGAAAAGAAAAGAAAGGCCCAAAGAAGTCAATACTCAATGAAACAACAAACAT
1 ATAAACAAA-G-ACAAAAGAAAAGAAAGACAAAAAAAAGTCAATACTCAATGAAACAACAAACAT
* * *
25191 AATAATGAAAATGAGAGCAGTTGAAATCTTGCTTTGAAATCAACATGAACCATATTGGGGAAAC
64 AAGAATGAAAATGAGAGCAGTTGAAATCTTGCATTCAAATCAACATGAACCATATTGGGGAAAC
25255 GAAGAAAAAA
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
146 9 0.08
147 1 0.01
148 103 0.91
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (146 bp):
ATAAACAAAGACAAAAGAAAAGAAAGACAAAAAAAAGTCAATACTCAATGAAACAACAAACATAA
GAATGAAAATGAGAGCAGTTGAAATCTTGCATTCAAATCAACATGAACCATATTGGGGAAACACA
TTATCAACAGGAACAA
Found at i:28066 original size:21 final size:21
Alignment explanation
Indices: 28040--28088 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
28030 GCACTCGAGT
* *
28040 ACATGGGGTGCGAGGCAAACC
1 ACATGGGGTGCCAAGCAAACC
*
28061 ACATGGGGTGCCAAGCATACC
1 ACATGGGGTGCCAAGCAAACC
28082 ACATGGG
1 ACATGGG
28089 CGCCCAGCGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.35, T:0.12
Consensus pattern (21 bp):
ACATGGGGTGCCAAGCAAACC
Found at i:32341 original size:121 final size:121
Alignment explanation
Indices: 32197--32559 Score: 428
Period size: 121 Copynumber: 3.0 Consensus size: 121
32187 CTCAAACTTG
* * *
32197 TCAAATTCATTTAAGGATTCACTTAAATCTTAAAAGAATTATGAAAGTTTCCCAAAGCTTATTTA
1 TCAAATTCAATTAAGGATTCACTTAAATCTTAAAAGAATTATGAAA-ATTACC-AAGCTTATTTA
* * * *
32262 CCT-AAGGTTATAATCATTTAATTAAACCTTAAGTTTT-AGGTCACTCAACCTCAATT
64 ACTAAAGGTTATAATCACTTAATTAAACCTTAAGTTTTAAGGTCACTTAACCTTAATT
* * * * *
32318 TCAAATTCAATTAAAGATTCACTTAAATCTT-AATGAATTACGAAAATTGCCAA-CTTTTATTAA
1 TCAAATTCAATTAAGGATTCACTTAAATCTTAAAAGAATTATGAAAATTACCAAGCTTAT-TTAA
* * * ** *
32381 CTAAAGGTTATAATTACTTAATTAAACCTAAAGTTTTAAGGTCACTTAATCTTGGTA
65 CTAAAGGTTATAATCACTTAATTAAACCTTAAGTTTTAAGGTCACTTAACCTTAATT
* * * * * *
32438 TCATATTTAATTAAGGATTTACTTAAATCTTAAAAGAATTATGAAAATTACCAAGGTTGTTAAAC
1 TCAAATTCAATTAAGGATTCACTTAAATCTTAAAAGAATTATGAAAATTACCAAGCTTATTTAAC
* * *
32503 TAAAGGTTTTAATCACTTAATTAAAGCTTAAGTTTTAAGGACACTTAACCTTAATT
66 TAAAGGTTATAATCACTTAATTAAACCTTAAGTTTTAAGGTCACTTAACCTTAATT
32559 T
1 T
32560 TTTAAATCTA
Statistics
Matches: 201, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
117 4 0.02
118 7 0.03
119 35 0.17
120 52 0.26
121 100 0.50
122 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (121 bp):
TCAAATTCAATTAAGGATTCACTTAAATCTTAAAAGAATTATGAAAATTACCAAGCTTATTTAAC
TAAAGGTTATAATCACTTAATTAAACCTTAAGTTTTAAGGTCACTTAACCTTAATT
Found at i:40513 original size:13 final size:13
Alignment explanation
Indices: 40491--40530 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
40481 GAGAGAATAT
40491 TATCAACAGAAGA
1 TATCAACAGAAGA
*
40504 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
40517 TTTCAACTGAAGA
1 TATCAACAGAAGA
40530 T
1 T
40531 TATCTAGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:40976 original size:41 final size:41
Alignment explanation
Indices: 40916--41057 Score: 196
Period size: 41 Copynumber: 3.5 Consensus size: 41
40906 AATATTGAAT
* * *
40916 ATTACCTTTGACACCAGAAGTTGTCACTTTGATAAATTAAA
1 ATTACCTATGACACTAGAAGTTGTCACTTTGGTAAATTAAA
* *
40957 ATTA-CTGCTGACACTAGAAGTTGTCACCTTGGTAAATTAAA
1 ATTACCT-ATGACACTAGAAGTTGTCACTTTGGTAAATTAAA
40998 ATTACCTATGACACTAGAAGTTGTCACTTTGGTAAATTAAA
1 ATTACCTATGACACTAGAAGTTGTCACTTTGGTAAATTAAA
* * *
41039 ATTATCTTTGACACCAGAA
1 ATTACCTATGACACTAGAA
41058 ATGTTATTCC
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
40 2 0.02
41 86 0.96
42 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (41 bp):
ATTACCTATGACACTAGAAGTTGTCACTTTGGTAAATTAAA
Found at i:42363 original size:2 final size:2
Alignment explanation
Indices: 42348--42384 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
42338 TATTCAAATA
*
42348 AT AT AT AGT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42385 TACTTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 31 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48188 original size:23 final size:23
Alignment explanation
Indices: 48146--48194 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
48136 GCAAATCAGC
* *
48146 TTTTTCCCCTCCATTATGTATCTT
1 TTTTTCCCATCAATTATGTA-CTT
48170 TTTTTCCCATCAATT-TGTACTT
1 TTTTTCCCATCAATTATGTACTT
48192 TTT
1 TTT
48195 AAATCAAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 6 0.26
23 4 0.17
24 13 0.57
ACGTcount: A:0.14, C:0.24, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTTCCCATCAATTATGTACTT
Found at i:49401 original size:28 final size:30
Alignment explanation
Indices: 49370--49426 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
49360 GAAAAGTTCA
49370 GGCACTAATTTGA-CCTTTT-CATAGTTTG
1 GGCACTAATTTGACCCTTTTACATAGTTTG
*
49398 GGCACTTATTTGACCCTTTTAGCATAGTT
1 GGCACTAATTTGACCCTTTTA-CATAGTT
49427 CAGGGCCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 12 0.48
29 6 0.24
31 7 0.28
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (30 bp):
GGCACTAATTTGACCCTTTTACATAGTTTG
Found at i:50448 original size:31 final size:31
Alignment explanation
Indices: 50405--50469 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
50395 AACTGAACTA
*
50405 ACTCAAACATCCAAGATCTAAAGATCTGTAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
*
50436 ACTCAAATATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
50467 ACT
1 ACT
50470 GATAACCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.23
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGATCTGGAG
Done.