Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020702.1 Corchorus olitorius cultivar O-4 contig20735, 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: 29740
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:951 original size:36 final size:36
Alignment explanation
Indices: 904--973 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
894 TTCAATAACC
*
904 TTACATCTTTTGTGATTTTTG-TTATCATATTTCTTA
1 TTACATCTTTTGT-AATTTTGATTATCATATTTCTTA
*
940 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
974 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.61
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:2074 original size:42 final size:41
Alignment explanation
Indices: 2015--2093 Score: 122
Period size: 42 Copynumber: 1.9 Consensus size: 41
2005 AAACCTAAGA
* *
2015 ATTTAATTGATGTAAGTATTTCAGTTATTATAGTATTATAAC
1 ATTTAATTAATGTAAGTATTTCAATTATTATA-TATTATAAC
*
2057 ATTTAATTAATGTAAGTATTTTAATTATTATATATTA
1 ATTTAATTAATGTAAGTATTTCAATTATTATATATTA
2094 CATCGGAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 5 0.15
42 29 0.85
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.51
Consensus pattern (41 bp):
ATTTAATTAATGTAAGTATTTCAATTATTATATATTATAAC
Found at i:3557 original size:19 final size:18
Alignment explanation
Indices: 3533--3568 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3523 TGAAGACCAT
3533 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
3552 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
3569 TCTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:6346 original size:12 final size:12
Alignment explanation
Indices: 6326--6355 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
6316 AACAACAGAA
6326 GCAACAAGATCAG
1 GCAA-AAGATCAG
6339 GCAAAAGATCAG
1 GCAAAAGATCAG
6351 GCAAA
1 GCAAA
6356 TGCTTGTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.50, C:0.20, G:0.23, T:0.07
Consensus pattern (12 bp):
GCAAAAGATCAG
Found at i:10822 original size:77 final size:77
Alignment explanation
Indices: 10695--10893 Score: 362
Period size: 77 Copynumber: 2.6 Consensus size: 77
10685 ATTACCCTGG
*
10695 ACTTCCAAATTTCAATACTTGGAGAACTTGAAGTCTTCACCAAATTCCTTTCTCATTGGGGTGTT
1 ACTTCCAAATTTCAATACTTGGAGAACTTGAAGTCTTCACCAAATTCCTTTCTCATTGGGGTGTC
10760 TTGTGATCTTGT
66 TTGTGATCTTGT
*
10772 ACTTCCAAATTTCAATACTTGGAGAACTTGAAATCTTCACCAAATTCCTTTCTCATTGGGGTGTC
1 ACTTCCAAATTTCAATACTTGGAGAACTTGAAGTCTTCACCAAATTCCTTTCTCATTGGGGTGTC
10837 TTGTGATCTTGT
66 TTGTGATCTTGT
* *
10849 ACTTCCAAATTTCAGTTCTTGGAGAACTTGAAGTCTTCACCAAAT
1 ACTTCCAAATTTCAATACTTGGAGAACTTGAAGTCTTCACCAAAT
10894 ACATCATGTT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 117 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (77 bp):
ACTTCCAAATTTCAATACTTGGAGAACTTGAAGTCTTCACCAAATTCCTTTCTCATTGGGGTGTC
TTGTGATCTTGT
Found at i:11398 original size:23 final size:24
Alignment explanation
Indices: 11368--11413 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
11358 CATCTACCTT
*
11368 ATTGGGATGACATTGGG-GATATC
1 ATTGGGATGACATCGGGAGATATC
*
11391 ATTGGGATGGCATCGGGAGATAT
1 ATTGGGATGACATCGGGAGATAT
11414 TTTAAGCGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.26, C:0.09, G:0.37, T:0.28
Consensus pattern (24 bp):
ATTGGGATGACATCGGGAGATATC
Found at i:11654 original size:64 final size:64
Alignment explanation
Indices: 11553--11734 Score: 258
Period size: 64 Copynumber: 2.8 Consensus size: 64
11543 ACATAGGGTG
* * * * * *
11553 ACATTTGGAACGCATAAGGAGTTC-AGGGACGTCTCTTCTCGCCAAAGTGTTTCTATCAAAAGTC
1 ACATTGGGAACACATAGGGAGTTCGAGCG-CATCTCTTCTCGCCAAAGTGTTTCCATCAAAAGTC
**
11617 ACATTGGGAACACATAGGGAGTTCGAGCGTTTCTCTTCTCGCCAAAGTGTTTCCATCAAAAGTC
1 ACATTGGGAACACATAGGGAGTTCGAGCGCATCTCTTCTCGCCAAAGTGTTTCCATCAAAAGTC
* *
11681 ACATTGGGAACACATAGGGAGTTCGAGCGCATCTCTTCTTGCCAAAGTGCTTCC
1 ACATTGGGAACACATAGGGAGTTCGAGCGCATCTCTTCTCGCCAAAGTGTTTCC
11735 TCCCTATGTC
Statistics
Matches: 106, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
64 103 0.97
65 3 0.03
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (64 bp):
ACATTGGGAACACATAGGGAGTTCGAGCGCATCTCTTCTCGCCAAAGTGTTTCCATCAAAAGTC
Found at i:11898 original size:87 final size:87
Alignment explanation
Indices: 11748--11914 Score: 217
Period size: 87 Copynumber: 1.9 Consensus size: 87
11738 CTATGTCACT
* * * *
11748 CATTGGGAGAGTACTTGGCCATGTCTCTTCTCGCCTAAATGTTTCCACCTTATGTCACACATTGG
1 CATTGGGAGAGTACTTGGCCACGTCTCTTCTCGCCTAAACGCTTCCACCCTATGTCACACATTGG
*
11813 GACATAGGGTGACATAAGGTGA
66 GACATAAGGTGACATAAGGTGA
** * * * * *
11835 CATTGGGAGAGTGTTTGGCCGCGTTTCTTCTCGCCTAAGCGCTTCCTCCCTATGTCACTCATTGG
1 CATTGGGAGAGTACTTGGCCACGTCTCTTCTCGCCTAAACGCTTCCACCCTATGTCACACATTGG
*
11900 GATATAAGGTGACAT
66 GACATAAGGTGACAT
11915 TGGGAGAGAA
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (87 bp):
CATTGGGAGAGTACTTGGCCACGTCTCTTCTCGCCTAAACGCTTCCACCCTATGTCACACATTGG
GACATAAGGTGACATAAGGTGA
Found at i:12001 original size:140 final size:140
Alignment explanation
Indices: 11821--12082 Score: 416
Period size: 140 Copynumber: 1.9 Consensus size: 140
11811 GGGACATAGG
**
11821 GTGACATAAGGTGACATTGGGAGAGTGTTTGGCCGCGTTTCTTCTCGCCTAAGCGCTTCCTCCCT
1 GTGACATAAGGTGACACAGGGAGAGTGTTTGGCCGCGTTTCTTCTCGCCTAAGCGCTTCCTCCCT
*
11886 ATGTCACTCATTGGGATATAAGGTGACATTGGGAGAGAACTTAGCCACGTCTCTTCTTGCCTAAA
66 ATGTCACTCATTGGGATATAAAGTGACATTGGGAGAGAACTTAGCCACGTCTCTTCTTGCCTAAA
11951 TGTTTCCACT
131 TGTTTCCACT
* * *
11961 GTGACATAAGGTGACACAGGGAGAGTGTTTGGTCGTGTTTCTTCTCGCCTAAGTGCTTCCTCCCT
1 GTGACATAAGGTGACACAGGGAGAGTGTTTGGCCGCGTTTCTTCTCGCCTAAGCGCTTCCTCCCT
* * * * **
12026 GTGTCACTCATTGGGATATAAAGTGACATTTGGAGAGAGCTTGGCCGTGTCTCTTCT
66 ATGTCACTCATTGGGATATAAAGTGACATTGGGAGAGAACTTAGCCACGTCTCTTCT
12083 CGCCCAATTT
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
140 110 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (140 bp):
GTGACATAAGGTGACACAGGGAGAGTGTTTGGCCGCGTTTCTTCTCGCCTAAGCGCTTCCTCCCT
ATGTCACTCATTGGGATATAAAGTGACATTGGGAGAGAACTTAGCCACGTCTCTTCTTGCCTAAA
TGTTTCCACT
Found at i:12336 original size:77 final size:77
Alignment explanation
Indices: 12203--12529 Score: 487
Period size: 77 Copynumber: 4.2 Consensus size: 77
12193 TTTTCGCCTG
* * * **
12203 ATTTTATACTTGGAAATTTAGACTTCCAAATTTCATTTATTTGGACCCTATGACACTCATCCGAA
1 ATTTTACACTTGGAAATTTATATTTCCAAATTTCATTTATTTGCTCCCTATGACACTCATCCGAA
12268 CATAGGGTAACA
66 CATAGGGTAACA
* *
12280 A-TTTACACTTGGAAAATTTACACATT-CAAATTTCATTTATTTGCTCCCTATGACACTCATCCG
1 ATTTTACACTTGG-AAATTTATA-TTTCCAAATTTCATTTATTTGCTCCCTATGACACTCATCCG
* *
12343 GACATAGGGTGACA
64 AACATAGGGTAACA
* * * *
12357 ATTTTACACTTTGAAACTTATATTTCCAAATTTCGTTTATTTGCTCCCTATGACACTCATCCGGA
1 ATTTTACACTTGGAAATTTATATTTCCAAATTTCATTTATTTGCTCCCTATGACACTCATCCGAA
*
12422 CATAGGGTGACA
66 CATAGGGTAACA
12434 ATTTTACACTTGGAAATTTATATTTCCAAATTTCATTTATTTGCTCCCTATGACACTCATCCGAA
1 ATTTTACACTTGGAAATTTATATTTCCAAATTTCATTTATTTGCTCCCTATGACACTCATCCGAA
12499 CATAGGGTAACA
66 CATAGGGTAACA
*
12511 ATTTTACACTTCGAAATTT
1 ATTTTACACTTGGAAATTT
12530 CGTTTATTTG
Statistics
Matches: 228, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
76 12 0.05
77 204 0.89
78 12 0.05
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (77 bp):
ATTTTACACTTGGAAATTTATATTTCCAAATTTCATTTATTTGCTCCCTATGACACTCATCCGAA
CATAGGGTAACA
Found at i:12483 original size:154 final size:149
Alignment explanation
Indices: 12203--12625 Score: 526
Period size: 154 Copynumber: 2.8 Consensus size: 149
12193 TTTTCGCCTG
* * ** *
12203 ATTTTATACTTGGAAATTTAGACTTCCAAATTTCATTTATTTGGACCCTATGACACTCATCCGAA
1 ATTTTA-ACTT-GAAACTTA-A-TTCCAAATTTCGTTTATTTGCTCCCTATGACACTCATCCGGA
*
12268 CATAGGGTAACAATTTACACTTGGAAAATTTACACATT-CAAATTTCATTTATTTGCTCCCTATG
62 CATAGGGTGACAATTTACACTTGG-AAATTTACA-ATTCCAAATTTCATTTATTTGCTCCCTATG
* *
12332 ACACTCATCCGGACATAGGGTGACA
125 ACACTCATCCGAACATAGGGTAACA
12357 ATTTTACACTTTGAAACTTATATTTCCAAATTTCGTTTATTTGCTCCCTATGACACTCATCCGGA
1 ATTTTA-AC-TTGAAACTTA-A-TTCCAAATTTCGTTTATTTGCTCCCTATGACACTCATCCGGA
* *
12422 CATAGGGTGACAATTTTACACTTGGAAATTTATATTTCCAAATTTCATTTATTTGCTCCCTATGA
62 CATAGGGTGACAA-TTTACACTTGGAAATTTACAATTCCAAATTTCATTTATTTGCTCCCTATGA
12487 CACTCATCCGAACATAGGGTAACA
126 CACTCATCCGAACATAGGGTAACA
* *
12511 ATTTT-AC-----AC----TTCGAAATTTCGTTTATTTGCTCCCTATGACACTCATTCGGACATA
1 ATTTTAACTTGAAACTTAATTCCAAATTTCGTTTATTTGCTCCCTATGACACTCATCCGGACATA
* * *
12566 AGGTGACAATTTACACTTGGAAATTTACACTTCCAAATTTCATTTAATTTCCTCCCTATG
66 GGGTGACAATTTACACTTGGAAATTTACAATTCCAAATTTCATTT-ATTTGCTCCCTATG
12626 TCACATATAA
Statistics
Matches: 246, Mismatches: 19, Indels: 22
0.86 0.07 0.08
Matches are distributed among these distances:
139 34 0.14
140 65 0.26
146 2 0.01
152 2 0.01
153 2 0.01
154 128 0.52
155 13 0.05
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Consensus pattern (149 bp):
ATTTTAACTTGAAACTTAATTCCAAATTTCGTTTATTTGCTCCCTATGACACTCATCCGGACATA
GGGTGACAATTTACACTTGGAAATTTACAATTCCAAATTTCATTTATTTGCTCCCTATGACACTC
ATCCGAACATAGGGTAACA
Found at i:12565 original size:63 final size:62
Alignment explanation
Indices: 12461--12591 Score: 199
Period size: 63 Copynumber: 2.1 Consensus size: 62
12451 TTATATTTCC
*
12461 AAATTTCATTTATTTGCTCCCTATGACACTCATCCGAACATAGGGTAACAATTTTACACTTCG
1 AAATTTCATTTATTTGCTCCCTATGACACTCATCCGAACATAAGGTAACAA-TTTACACTTCG
* * * * *
12524 AAATTTCGTTTATTTGCTCCCTATGACACTCATTCGGACATAAGGTGACAATTTACACTTGG
1 AAATTTCATTTATTTGCTCCCTATGACACTCATCCGAACATAAGGTAACAATTTACACTTCG
12586 AAATTT
1 AAATTT
12592 ACACTTCCAA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
62 16 0.26
63 46 0.74
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (62 bp):
AAATTTCATTTATTTGCTCCCTATGACACTCATCCGAACATAAGGTAACAATTTACACTTCG
Found at i:15169 original size:118 final size:119
Alignment explanation
Indices: 14960--15238 Score: 506
Period size: 118 Copynumber: 2.4 Consensus size: 119
14950 GCCCTGCTTG
*
14960 TTTTATTTAATTTCCTCCCTGTGTCACACATAAGGACATAGGGACATAGGGAGATTGGGTGAGAA
1 TTTTATTTAATTTCCTCCCTATGTCACACATAAGGACATAGGGACATAGGGAGATTGGGTGAGAA
*
15025 CTTGGCCACATCTCTTCTCATCCAATTTCATACTTGGAAACTTATACTTCCAAA
66 CTTGGCCACATCTCTTCTCACCCAATTTCATACTTGGAAACTTATACTTCCAAA
*
15079 TTTTATTTAATTTCCTTCCTATGTCACACATAAGGACATAGGGA-ATAGGGAGATTGGGTGAGAA
1 TTTTATTTAATTTCCTCCCTATGTCACACATAAGGACATAGGGACATAGGGAGATTGGGTGAGAA
* *
15143 CTTGGCCACATCTCTTTTCACCCAATTTCATACTTGGAAATTTATACTTCCAAA
66 CTTGGCCACATCTCTTCTCACCCAATTTCATACTTGGAAACTTATACTTCCAAA
15197 TTTTATTTAATTTCCTCCCTATGTCACACATAAGGACATAGG
1 TTTTATTTAATTTCCTCCCTATGTCACACATAAGGACATAGG
15239 CGCCTAATTT
Statistics
Matches: 154, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
118 112 0.73
119 42 0.27
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (119 bp):
TTTTATTTAATTTCCTCCCTATGTCACACATAAGGACATAGGGACATAGGGAGATTGGGTGAGAA
CTTGGCCACATCTCTTCTCACCCAATTTCATACTTGGAAACTTATACTTCCAAA
Found at i:16327 original size:2 final size:2
Alignment explanation
Indices: 16322--16346 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16312 CTCTGTATTT
16322 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
16347 AAGTGTCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:23119 original size:21 final size:21
Alignment explanation
Indices: 23089--23128 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23079 TGAAATCGAT
* *
23089 TTGCTTAAGTCGATTTCTCCC
1 TTGCTCAAGTCGACTTCTCCC
23110 TTGCTCAAGTCGACTTCTC
1 TTGCTCAAGTCGACTTCTC
23129 TCTTAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.30, G:0.15, T:0.40
Consensus pattern (21 bp):
TTGCTCAAGTCGACTTCTCCC
Found at i:23138 original size:21 final size:21
Alignment explanation
Indices: 23095--23139 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
23085 CGATTTGCTT
* **
23095 AAGTCGATTTCTCCCTTGCTC
1 AAGTCGACTTCTCCCTTAATC
*
23116 AAGTCGACTTCTCTCTTAATC
1 AAGTCGACTTCTCCCTTAATC
23137 AAG
1 AAG
23140 ACTATCGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.36
Consensus pattern (21 bp):
AAGTCGACTTCTCCCTTAATC
Found at i:23664 original size:11 final size:11
Alignment explanation
Indices: 23636--23674 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
23626 TGGTGCATGG
*
23636 CATGACCGGGC
1 CATGTCCGGGC
* *
23647 TATGTCCTGGC
1 CATGTCCGGGC
23658 CATGTCCGGGC
1 CATGTCCGGGC
23669 CATGTC
1 CATGTC
23675 TTTGCGCCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.13, C:0.33, G:0.31, T:0.23
Consensus pattern (11 bp):
CATGTCCGGGC
Done.