Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019545.1 Corchorus olitorius cultivar O-4 contig19578, 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: 25360
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:346 original size:12 final size:13
Alignment explanation
Indices: 329--368 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
319 TTATGCACCC
329 AAAACATTTAT-T
1 AAAACATTTATAT
341 AAAACATTT-TAT
1 AAAACATTTATAT
*
353 AAAGCATTTATAT
1 AAAACATTTATAT
366 AAA
1 AAA
369 GCAGTTATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 1 0.04
12 18 0.72
13 6 0.24
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (13 bp):
AAAACATTTATAT
Found at i:364 original size:11 final size:11
Alignment explanation
Indices: 329--385 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 11
319 TTATGCACCC
329 AAAACATTTATT
1 AAAACATTTA-T
341 AAAACATTTTAT
1 AAAACA-TTTAT
*
353 AAAGCATTTAT
1 AAAACATTTAT
*
364 ATAAAGCAGTTAT
1 A-AAA-CATTTAT
*
377 GAAACATTT
1 AAAACATTT
386 CCTCAACGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 10 0.27
12 17 0.46
13 10 0.27
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (11 bp):
AAAACATTTAT
Found at i:366 original size:13 final size:13
Alignment explanation
Indices: 333--376 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
323 GCACCCAAAA
*
333 CATTTAT-TAAAA
1 CATTTATATAAAG
345 CATTT-TATAAAG
1 CATTTATATAAAG
357 CATTTATATAAAG
1 CATTTATATAAAG
*
370 CAGTTAT
1 CATTTAT
377 GAAACATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 1 0.04
12 14 0.50
13 13 0.46
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (13 bp):
CATTTATATAAAG
Found at i:4747 original size:19 final size:19
Alignment explanation
Indices: 4723--4763 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4713 GTTGAGTAGA
*
4723 TTTTAACTTT-TTGTTGGGC
1 TTTTAA-TTTCTTATTGGGC
4742 TTTTAATTTCTTATTGGGC
1 TTTTAATTTCTTATTGGGC
4761 TTT
1 TTT
4764 GCTAAGCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (19 bp):
TTTTAATTTCTTATTGGGC
Found at i:4785 original size:27 final size:26
Alignment explanation
Indices: 4755--4817 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 26
4745 TAATTTCTTA
**
4755 TTGGGCTTTGCTAAGCTATATATCTAT
1 TTGGGCTTTGCTAAGCTATAT-TAAAT
* * **
4782 TTGGGTTTTGTTTTGCTATATTAAAT
1 TTGGGCTTTGCTAAGCTATATTAAAT
4808 TTGGGCTTTG
1 TTGGGCTTTG
4818 ATTGTTATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.17, C:0.10, G:0.22, T:0.51
Consensus pattern (26 bp):
TTGGGCTTTGCTAAGCTATATTAAAT
Found at i:5091 original size:13 final size:13
Alignment explanation
Indices: 5073--5099 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5063 TTCATGTACA
5073 TCCATATTTAAAT
1 TCCATATTTAAAT
5086 TCCATATTTAAAT
1 TCCATATTTAAAT
5099 T
1 T
5100 TCTTTATGTT
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:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
TCCATATTTAAAT
Found at i:5675 original size:53 final size:53
Alignment explanation
Indices: 5595--5720 Score: 184
Period size: 53 Copynumber: 2.4 Consensus size: 53
5585 CACTCAAGTC
* * *
5595 TTCAAAA-TATTCAATTTAAGTTCTTTTTCAAGTCGGGAAAGCTCCCATCAGTT
1 TTCAAAAGTATTCAATTT-AGCTCTTTTTCAAATCGGGAAAGCTCCCATCAATT
* *
5648 TTCAAAAGTATTCAATCTAGCTCTTTTTCAAATCGGGAAAGTTCCCATCAATT
1 TTCAAAAGTATTCAATTTAGCTCTTTTTCAAATCGGGAAAGCTCCCATCAATT
5701 TTC-AAAGTATTCAATTTAGC
1 TTCAAAAGTATTCAATTTAGC
5721 CAGTCTTCAA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
52 16 0.24
53 41 0.62
54 9 0.14
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (53 bp):
TTCAAAAGTATTCAATTTAGCTCTTTTTCAAATCGGGAAAGCTCCCATCAATT
Found at i:5730 original size:52 final size:53
Alignment explanation
Indices: 5595--5748 Score: 161
Period size: 53 Copynumber: 2.9 Consensus size: 53
5585 CACTCAAGTC
* * * * * * *
5595 TTCAAAA-TATTCAATTTAAGTTCTTTTTCAAGTCGGGAAAGCTCCCATCAGTT
1 TTCAAAAGTATTCAATCT-AGCTCGTCTTCAAATCGGGAAAGTTCCCATCAATT
* *
5648 TTCAAAAGTATTCAATCTAGCTCTTTTTCAAATCGGGAAAGTTCCCATCAATT
1 TTCAAAAGTATTCAATCTAGCTCGTCTTCAAATCGGGAAAGTTCCCATCAATT
* * *
5701 TTC-AAAGTATTCAATTTAGC-CAGTCTTCAAATTGGGAAGGTTCCCATC
1 TTCAAAAGTATTCAATCTAGCTC-GTCTTCAAATCGGGAAAGTTCCCATC
5749 CAGTTTTTAA
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
51 1 0.01
52 38 0.43
53 41 0.46
54 9 0.10
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (53 bp):
TTCAAAAGTATTCAATCTAGCTCGTCTTCAAATCGGGAAAGTTCCCATCAATT
Found at i:5781 original size:37 final size:37
Alignment explanation
Indices: 5726--5932 Score: 196
Period size: 37 Copynumber: 5.6 Consensus size: 37
5716 TTAGCCAGTC
* *
5726 TTCAAATTGGGAAGGTTCCCATCCAGTTTTTAAAATT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTTAAAGTT
*
5763 GTCAAATTGGGAAAGTTCCCA-CCAAGTTTTT-AAGTT
1 TTCAAATTGGGAAAGTTCCCATCC-AGTTTTTAAAGTT
* * *
5799 TTCAAATTGGGAAAGTTCCCATCTAGTTTTCAGAGTT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTTAAAGTT
*
5836 TTCAAATTGGGAAAGTTCCCAT-CAGGTTTT--AGTT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTTAAAGTT
* * *
5870 TTCAATTTAGTGAAAGTTCCTGTCATTTTCAG-TTTT--AGTT
1 TTCAAATT-GGGAAAGTTCC---CA--TCCAGTTTTTAAAGTT
*
5910 TTCAAAGTGGGAAAGTTCCCATC
1 TTCAAATTGGGAAAGTTCCCATC
5933 AAAAGCATTT
Statistics
Matches: 144, Mismatches: 16, Indels: 23
0.79 0.09 0.13
Matches are distributed among these distances:
34 12 0.08
35 10 0.07
36 39 0.27
37 53 0.37
38 2 0.01
39 10 0.07
40 15 0.10
41 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (37 bp):
TTCAAATTGGGAAAGTTCCCATCCAGTTTTTAAAGTT
Found at i:5929 original size:74 final size:72
Alignment explanation
Indices: 5726--5933 Score: 224
Period size: 73 Copynumber: 2.8 Consensus size: 72
5716 TTAGCCAGTC
* * * * * * * *
5726 TTCAAATTGGGAAGGTTCCCATCCAGTTTTTAAAATTGTCAAATTGGGAAAGTTCCCACCAAGTT
1 TTCAAATTGGGAAAGTTCCCATCTAGTTTTCAGAGTTTTCAAATTGGGAAAGTTCCCATC-AGGT
5791 TTTAAGTT
65 TTTAAGTT
5799 TTCAAATTGGGAAAGTTCCCATCTAGTTTTCAGAGTTTTCAAATTGGGAAAGTTCCCATCAGGTT
1 TTCAAATTGGGAAAGTTCCCATCTAGTTTTCAGAGTTTTCAAATTGGGAAAGTTCCCATCAGGTT
5864 TT-AGTT
66 TTAAGTT
* * ** *
5870 TTCAATTTAGTGAAAGTTCCTGTC-A-TTTTCAGTTTTAGTTTTCAAAGTGGGAAAGTTCCCATC
1 TTCAAATT-GGGAAAGTTCCCATCTAGTTTTCAG----AGTTTTCAAATTGGGAAAGTTCCCATC
5933 A
61 A
5934 AAAGCATTTT
Statistics
Matches: 117, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
70 7 0.06
71 12 0.10
72 18 0.15
73 53 0.45
74 27 0.23
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (72 bp):
TTCAAATTGGGAAAGTTCCCATCTAGTTTTCAGAGTTTTCAAATTGGGAAAGTTCCCATCAGGTT
TTAAGTT
Found at i:6762 original size:37 final size:37
Alignment explanation
Indices: 6720--6804 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
6710 AATAATTTAT
*
6720 TAAAACATTTTATAAAGCATTTAAATAAAATCAGTAA
1 TAAAACATTTTATAAAGCATTTAAATAAAAACAGTAA
6757 TAAAACATTTTATAAAGCATTTAAATAAAAACAGTAA
1 TAAAACATTTTATAAAGCATTTAAATAAAAACAGTAA
*
6794 TAGAACATTTT
1 TAAAACATTTT
6805 CCTCAACGGG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (37 bp):
TAAAACATTTTATAAAGCATTTAAATAAAAACAGTAA
Found at i:7356 original size:27 final size:26
Alignment explanation
Indices: 7303--7375 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
7293 ACAAGGTTAA
*
7303 AAGGGTAAAACTGTAAATTTAACATTCT
1 AAGGGTAAAACGGT-AA-TTAACATTCT
*
7331 AAGGGTAAAACGGTAATTACTCATTCT
1 AAGGGTAAAACGGTAATTA-ACATTCT
* *
7358 TAGGGTAAAATGGTAATT
1 AAGGGTAAAACGGTAATT
7376 TTGCCTTTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.08
27 24 0.60
28 13 0.32
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (26 bp):
AAGGGTAAAACGGTAATTAACATTCT
Found at i:9721 original size:176 final size:178
Alignment explanation
Indices: 9425--9766 Score: 580
Period size: 176 Copynumber: 1.9 Consensus size: 178
9415 GGCAAAAAAA
* * * *
9425 ATTAAAAACTTGGATATATTCAAAAATTTCAATATACAGTTTTATTCTACTAAAAACCTCTATTT
1 ATTAAAAACTTGAATACATTCAAAAATTTCAATATACAATTTTATTCTACTAAAAACCTATATTT
* * *
9490 TCATTTAATTAAATTCAATATTTTTATAATTGTTTTATTTTTACCATTTTAATTAGTTTAATTTA
66 TCATTTAATTAAATTAAATATTTTTATAATTATTTTATTTTTACCATTTTAATTAGTTTAATGTA
* *
9555 TTTTGATTAAAATTTATTATTTTCCTGATGTGCAATTTACTATTTTTC
131 TATTAATTAAAATTTATTATTTTCCTGATGTGCAATTTACTATTTTTC
*
9603 ATTAAAAACTTGAATACATTCAAAAATTTTAATATACAATTTTATTCTACT-AAAA-CTATATTT
1 ATTAAAAACTTGAATACATTCAAAAATTTCAATATACAATTTTATTCTACTAAAAACCTATATTT
9666 TCATTTAATTAAATTAAATATTTTTATAATTATTTTATTTTTACCATTTTAATTAGTTTAATGTA
66 TCATTTAATTAAATTAAATATTTTTATAATTATTTTATTTTTACCATTTTAATTAGTTTAATGTA
9731 TATTAATTAAAATTTATTATTTTCCTGATGTGCAAT
131 TATTAATTAAAATTTATTATTTTCCTGATGTGCAAT
9767 CATTTTATTT
Statistics
Matches: 154, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
176 103 0.67
177 4 0.03
178 47 0.31
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.50
Consensus pattern (178 bp):
ATTAAAAACTTGAATACATTCAAAAATTTCAATATACAATTTTATTCTACTAAAAACCTATATTT
TCATTTAATTAAATTAAATATTTTTATAATTATTTTATTTTTACCATTTTAATTAGTTTAATGTA
TATTAATTAAAATTTATTATTTTCCTGATGTGCAATTTACTATTTTTC
Found at i:12322 original size:233 final size:232
Alignment explanation
Indices: 11909--12328 Score: 655
Period size: 233 Copynumber: 1.8 Consensus size: 232
11899 TAAGGCTAAA
* * * * * *
11909 TATACAATACACTGTTAGTAGAGTTTAGTAGACTATATATGCTGGTCCTGAAGGGTGACATGTGT
1 TATACAATACACCGTTAGTAGAGTTTAGCAGACTACACAAGCTGGTCCTGAAGGGTGACATATGT
** *
11974 CCCTTAGGGACTAAATTGAAATATTTAAAACTTAATTAATTAAAAAAATGGTCATGTGTCAACTC
66 CCCTTAGGGACTAAATTGAAATATTTAAAACAAAATTAATTAAAAAAATGGACATGTGTCAACTC
** *
12039 CACAACCCGCTTGTGGAGTCCAAAATTTACATTGCCGGTGTATTAAATAATTACCCTAAAAATAA
131 CACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAATAA-TACCCTAAAAATAA
12104 TTGTTTTGAATTACAAATTGTAATGAACATTGGCAAAT
195 TTGTTTTGAATTACAAATTGTAATGAACATTGGCAAAT
* *
12142 TATACAATACACCGTTAGTGGAGTTTAGCAGACTACACAAGC-GCGTCCTGGAGGGTGACATATG
1 TATACAATACACCGTTAGTAGAGTTTAGCAGACTACACAAGCTG-GTCCTGAAGGGTGACATATG
* *
12206 T-CCTCTAGGGACTAGATTGAAATATTTAAAACAAAATTAATTCAAAAAATGGACATGTGTCAAC
65 TCCCT-TAGGGACTAAATTGAAATATTTAAAACAAAATTAATTAAAAAAATGGACATGTGTCAAC
12270 TCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAATAATACCCTA
129 TCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAATAATACCCTA
12329 TATATATATA
Statistics
Matches: 169, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
232 11 0.07
233 158 0.93
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (232 bp):
TATACAATACACCGTTAGTAGAGTTTAGCAGACTACACAAGCTGGTCCTGAAGGGTGACATATGT
CCCTTAGGGACTAAATTGAAATATTTAAAACAAAATTAATTAAAAAAATGGACATGTGTCAACTC
CACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAATAATACCCTAAAAATAAT
TGTTTTGAATTACAAATTGTAATGAACATTGGCAAAT
Found at i:12516 original size:34 final size:35
Alignment explanation
Indices: 12452--12522 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
12442 TAATCTATCC
12452 AACCAAATTTTATTTCCATATTTAAAAAAGTCTAA
1 AACCAAATTTTATTTCCATATTTAAAAAAGTCTAA
12487 AACCAAATTTTATTTCCATA-TTAAAAAAGTCTAA
1 AACCAAATTTTATTTCCATATTTAAAAAAGTCTAA
12521 AA
1 AA
12523 TAATAACAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 16 0.44
35 20 0.56
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (35 bp):
AACCAAATTTTATTTCCATATTTAAAAAAGTCTAA
Found at i:15841 original size:23 final size:23
Alignment explanation
Indices: 15811--15858 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
15801 ATTTGTAATT
* *
15811 ACCTTTATTATTGGCGAAATGAA
1 ACCTTTATTATTGACGAAAGGAA
15834 ACCTTTATTATTGACGAAAGGAA
1 ACCTTTATTATTGACGAAAGGAA
15857 AC
1 AC
15859 TAAAATATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (23 bp):
ACCTTTATTATTGACGAAAGGAA
Found at i:17773 original size:2 final size:2
Alignment explanation
Indices: 17766--17795 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17756 TATTTACTAG
17766 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17796 GGGTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18828 original size:2 final size:2
Alignment explanation
Indices: 18821--18848 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18811 TATAATAATC
18821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18849 GTTTGCCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.