Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015534.1 Corchorus capsularis cultivar CVL-1 contig15555, 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: 41634
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2488 original size:59 final size:60
Alignment explanation
Indices: 2415--2567 Score: 263
Period size: 59 Copynumber: 2.5 Consensus size: 60
2405 TTAAAAACGG
2415 AAATTTTTTTTTTTTAGAAAAATCGGAAAAACGCAAAAAAC-TGTTTTTTATCGACGCAA
1 AAATTTTTTTTTTTTAGAAAAATCGGAAAAACGCAAAAAACTTGTTTTTTATCGACGCAA
*
2474 AAATTTTTTTTTTTTAGAAAAATCGGAAAAACGCAAAAAACTTTTTTTTTATCGACGCAA
1 AAATTTTTTTTTTTTAGAAAAATCGGAAAAACGCAAAAAACTTGTTTTTTATCGACGCAA
*
2534 AAATCTTTTTTTTTTTAGAAAAAAACGGAAAAAC
1 AAAT-TTTTTTTTTTTAG-AAAAATCGGAAAAAC
2568 AAAAACAAAT
Statistics
Matches: 89, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
59 41 0.46
60 21 0.24
61 13 0.15
62 14 0.16
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (60 bp):
AAATTTTTTTTTTTTAGAAAAATCGGAAAAACGCAAAAAACTTGTTTTTTATCGACGCAA
Found at i:3836 original size:10 final size:10
Alignment explanation
Indices: 3821--3846 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3811 GAGGACTCTA
3821 GAATTTTCTG
1 GAATTTTCTG
3831 GAATTTTCTG
1 GAATTTTCTG
3841 GAATTT
1 GAATTT
3847 GGCAGCAACT
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:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:5157 original size:23 final size:22
Alignment explanation
Indices: 5131--5182 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 22
5121 TTGGGCTTGG
5131 TCTTTTTAT-TAGTATGTGGGTTT
1 TCTTTTTATATA-TAT-TGGGTTT
5154 TCTTTTTTATATATATTGGGTTT
1 TC-TTTTTATATATATTGGGTTT
5177 TACTTT
1 T-CTTT
5183 GTTTGCTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
23 13 0.50
24 11 0.42
25 2 0.08
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.63
Consensus pattern (22 bp):
TCTTTTTATATATATTGGGTTT
Found at i:5182 original size:24 final size:24
Alignment explanation
Indices: 5133--5182 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
5123 GGGCTTGGTC
5133 TTTTTATTAGTATGTGGGTTTTCT
1 TTTTTATTAGTATGTGGGTTTTCT
5157 TTTTTATATA-TAT-TGGGTTTTACT
1 TTTTTAT-TAGTATGTGGGTTTT-CT
5181 TT
1 TT
5183 GTTTGCTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 8 0.33
24 14 0.58
25 2 0.08
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (24 bp):
TTTTTATTAGTATGTGGGTTTTCT
Found at i:5836 original size:17 final size:17
Alignment explanation
Indices: 5790--5871 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 17
5780 CAGTAATAAG
5790 CAACTTAATTCAGGTAAT
1 CAACTTAATTCA-GTAAT
* * *
5808 TAA-GTAAGTCAGTAAT
1 CAACTTAATTCAGTAAT
*
5824 CAACTTAATTCAGGGTGAT
1 CAACTTAATTCA--GTAAT
* * *
5843 TAA-GTAATTTAGTAAT
1 CAACTTAATTCAGTAAT
5859 CAACTTAATTCAG
1 CAACTTAATTCAG
5872 GGTAATTAAG
Statistics
Matches: 46, Mismatches: 14, Indels: 9
0.67 0.20 0.13
Matches are distributed among these distances:
16 13 0.28
17 19 0.41
18 8 0.17
19 6 0.13
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (17 bp):
CAACTTAATTCAGTAAT
Found at i:5857 original size:35 final size:35
Alignment explanation
Indices: 5790--6445 Score: 740
Period size: 35 Copynumber: 18.7 Consensus size: 35
5780 CAGTAATAAG
5790 CAACTTAATTCA-GGTAATTAAGTAAGTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* * *
5824 CAACTTAATTCAGGGTGATTAAGTAATTTAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* *
5859 CAACTTAATTCAGGGTAATTAAGTGAGTCGGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* * * * *
5894 CAACTTAATTCAGGGTAATTGAGCAGGTCGGTTAGT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAG-TAAT
* * * *
5930 -AACTTAATTCAGGGTAGTTAAGCAGGTCAGTTAGT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAG-TAAT
* *
5965 -AACTTAATTCGGGGTAATTAAGTAATTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* **
5999 CGACTTAATTCAGGGTAATTAAGCGAGTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
*
6034 AAGCAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
1 ---CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* **
6072 CGACTTAATTCAGGGTAATTAAGCGAGTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
*
6107 AAGCAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
1 ---CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
** *
6145 CAACTTAATTCAGGGTAATTAAGCGAGCCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
*
6180 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
*
6215 CAACTTAATTCAGGGTAATTAAGTAGGTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
*
6250 CAACTTAATTCAGGGTAATTAAGTGAGTCAGTGAAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGT-AAT
*
6286 -AACTTAATTCAGGGTAATTAAGTCAGT-A--AAT
1 CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
** *
6317 -AGTTTAATTCAGGGTAATTGAGTGAA-TCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGT-AAGTCAGTAAT
* * * * * *
6351 CAACTTTAATTCAGGATAATTAAGTGAGTTAATGAG
1 CAAC-TTAATTCAGGGTAATTAAGTAAGTCAGTAAT
* *
6387 AAACTTAATTCAGGGTAATTAAGT-AGTTCAATAAGT
1 CAACTTAATTCAGGGTAATTAAGTAAG-TCAGTAA-T
6423 -AACTTAATTCAGGGTAATTAAGT
1 CAACTTAATTCAGGGTAATTAAGT
6446 TTAGTAAGCA
Statistics
Matches: 533, Mismatches: 70, Indels: 37
0.83 0.11 0.06
Matches are distributed among these distances:
31 24 0.05
32 2 0.00
34 21 0.04
35 393 0.74
36 31 0.06
38 62 0.12
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (35 bp):
CAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
Found at i:17369 original size:17 final size:18
Alignment explanation
Indices: 17342--17379 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
17332 CCCTCCTCAT
17342 GGTACCTAGGTAACATGA
1 GGTACCTAGGTAACATGA
*
17360 GGTA-CTAGGTAGCATGA
1 GGTACCTAGGTAACATGA
17377 GGT
1 GGT
17380 GCTGGATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (18 bp):
GGTACCTAGGTAACATGA
Found at i:18038 original size:156 final size:155
Alignment explanation
Indices: 17739--18030 Score: 335
Period size: 156 Copynumber: 1.9 Consensus size: 155
17729 CACCTCAAAC
** *
17739 TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGTGCTGAAATTTTTCCA
1 TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAAAAGTGCTG-AATTTTTCCA
* * * * * *
17804 AGGGACTTAGACTATCTCCATGAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTCCCCTTGAT
65 AGAGACTTAGACTATCTCCATAAGACTATGGAAAAAATTATAAGTAAAACCAAACTCCCCTAGAT
* *
17869 GGTGAACTAGGTTTCTTTCCCTGAGT
130 AGAGAACTAGGTTTCTTTCCCTGAGT
17895 TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAACAAG-GCTG-A-TTTTCCA
1 TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAA-AAGTGCTGAATTTTTCCA
* * * *
17957 CCAGTAGACTTAGATTATC-CCTATAA-AGCTATGGGAAAAATTATAAGTAAAATCAAACT-CTC
65 --AG-AGACTTAGACTATCTCC-ATAAGA-CTATGGAAAAAATTATAAGTAAAACCAAACTCCCC
18019 TAGCATAGAGAA
125 TAG-ATAGAGAA
18031 GTTGGTTTGA
Statistics
Matches: 114, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
153 7 0.06
154 1 0.01
155 9 0.08
156 95 0.83
157 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (155 bp):
TGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAAAAGTGCTGAATTTTTCCAA
GAGACTTAGACTATCTCCATAAGACTATGGAAAAAATTATAAGTAAAACCAAACTCCCCTAGATA
GAGAACTAGGTTTCTTTCCCTGAGT
Found at i:19978 original size:19 final size:19
Alignment explanation
Indices: 19949--19992 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
19939 ATTCGGACTC
19949 AAACT-AACTG-ACTCAAAA
1 AAACTGAACTGAACTC-AAA
19967 AAACTGAACTGAACTCAAA
1 AAACTGAACTGAACTCAAA
19986 AAACTGA
1 AAACTGA
19993 CTAAACCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 15 0.62
20 4 0.17
ACGTcount: A:0.55, C:0.20, G:0.09, T:0.16
Consensus pattern (19 bp):
AAACTGAACTGAACTCAAA
Found at i:21635 original size:408 final size:407
Alignment explanation
Indices: 20871--21679 Score: 1413
Period size: 408 Copynumber: 2.0 Consensus size: 407
20861 GAAGGGGAAG
* *
20871 GAAACAGAGAGAATAATTTGGGAGAGAAGTTAATTCTTTTCTTGTTATATTGTCAAGCCACAACG
1 GAAACAGAGAGAATAATTTGGGAGAGAAGTTAATTCTTTTCTTGTTACATTGCCAAGCCACAACG
*
20936 TGGTATTTAAACAGATATGTTCACAAGTTGCTTCCTAAAATCAAGCCACTACTAAGAGACATGTT
66 TGGTATTTAAACAGATATGTTCACAAGTTGCTTCCTAAAATCAAGCCACTACTAAGAGACAAGTT
*
21001 AAAACCAACTACAAAGAGAAATAACTGAATTAAACAACTAAATGGAAGTTAACTAGTTATAAGAG
131 AAAACCAACTACAAAGAGAAATAACTGAATTAAACAACTAAATGGAAATTAACTAGTTATAAGAG
* * *
21066 TATAGTCTGAATGGAAATTAACTTCTTGTCACGGCAGTTGAGTTTGTATCATTACTCCTCTTCTA
196 -ATACTCTAAATCGAAATTAACTTCTTGTCACGGCAGTTGAGTTTGTATCATTACTCCTCTTCTA
* * *
21131 TGGCAACCTTACCCTCATGGTTGAAGATAGGATAGGTGTAGAGCACAATTATTGGTATCAAGTTC
260 TGGCAACCTTACCCTCAAGGTTGAAGATAGGATAGGTGGAGAGCACAACTATTGGTATCAAGTTC
*
21196 TTTGGTTCCCCTAGCCGAAACCCAATGAAAACATCCAAAGGAAGTTGCATTGTAGCTGGTCGTAT
325 TTTGGTTCCCCTAGCCGAAACCCAATGAAAACATCCAAAGGAAGTTGCATTGTAGCCGGTCGTAT
21261 CTCTTCCACCACATATTC
390 CTCTTCCACCACATATTC
*
21279 GAAACAGAGAGAATAATTTGGGAGAGAAGTTAATTCTTTTCTTGTTACATTGCCAAGTCACAACG
1 GAAACAGAGAGAATAATTTGGGAGAGAAGTTAATTCTTTTCTTGTTACATTGCCAAGCCACAACG
21344 TGGTATTTAAACAGATATGTTCACAAGTTGCTTCCTAAAATCAAGCCACTACTAAGAGACAAGTT
66 TGGTATTTAAACAGATATGTTCACAAGTTGCTTCCTAAAATCAAGCCACTACTAAGAGACAAGTT
21409 AAAACCAACTACAAAGAGAAATAACTGAATTAAACAACTAAATGGAAATTAACTAGTTATAAGAG
131 AAAACCAACTACAAAGAGAAATAACTGAATTAAACAACTAAATGGAAATTAACTAGTTATAAGAG
*
21474 -TACTCTAAATCGAAATTAACTTCTTGTCATGGCAGTTGAGTTTGTATCATTACTCTCCTCTTCT
196 ATACTCTAAATCGAAATTAACTTCTTGTCACGGCAGTTGAGTTTGTATCATTA--CTCCTCTTCT
* * *
21538 ATGGCAACCTTGCCCTCAAGGTTGAAGGTAGGTTAGGTGGAGAGCACAACTATTGGTATCAAGTT
259 ATGGCAACCTTACCCTCAAGGTTGAAGATAGGATAGGTGGAGAGCACAACTATTGGTATCAAGTT
* * *
21603 CTTTGGTTCCCCTGGCCGAAATCCAGTGAAAACATCCAAAGGAAGTTGCATTGTAGCCGGTCGTA
324 CTTTGGTTCCCCTAGCCGAAACCCAATGAAAACATCCAAAGGAAGTTGCATTGTAGCCGGTCGTA
21668 TCTCTTCCACCA
389 TCTCTTCCACCA
21680 TAGAATCCAT
Statistics
Matches: 380, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
406 48 0.13
408 332 0.87
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (407 bp):
GAAACAGAGAGAATAATTTGGGAGAGAAGTTAATTCTTTTCTTGTTACATTGCCAAGCCACAACG
TGGTATTTAAACAGATATGTTCACAAGTTGCTTCCTAAAATCAAGCCACTACTAAGAGACAAGTT
AAAACCAACTACAAAGAGAAATAACTGAATTAAACAACTAAATGGAAATTAACTAGTTATAAGAG
ATACTCTAAATCGAAATTAACTTCTTGTCACGGCAGTTGAGTTTGTATCATTACTCCTCTTCTAT
GGCAACCTTACCCTCAAGGTTGAAGATAGGATAGGTGGAGAGCACAACTATTGGTATCAAGTTCT
TTGGTTCCCCTAGCCGAAACCCAATGAAAACATCCAAAGGAAGTTGCATTGTAGCCGGTCGTATC
TCTTCCACCACATATTC
Found at i:40897 original size:74 final size:74
Alignment explanation
Indices: 40805--40953 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
40795 CAATATTTCA
40805 ACCCATCTTTATTTTTCCAAACTCAATCTTATCTCTCACTAATCAAATCTCCTTTATTCACTCAT
1 ACCCATCTTTATTTTTCCAAACTCAATCTTATCTCTCACTAATCAAATCTCCTTTATTCACTCAT
40870 TAATTAATT
66 TAATTAATT
40879 ACCCATCTTTATTTTTCCAAACTCAATCTTATCTCTCACTAATCAAATCTCCTTTATTCACTCAT
1 ACCCATCTTTATTTTTCCAAACTCAATCTTATCTCTCACTAATCAAATCTCCTTTATTCACTCAT
40944 TAATTAATT
66 TAATTAATT
40953 A
1 A
40954 ATAATAATAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (74 bp):
ACCCATCTTTATTTTTCCAAACTCAATCTTATCTCTCACTAATCAAATCTCCTTTATTCACTCAT
TAATTAATT
Done.