Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014333.1 Corchorus capsularis cultivar CVL-1 contig14354, 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: 57702
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:524 original size:21 final size:21
Alignment explanation
Indices: 500--550 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
490 GCAAGTCTGG
500 GCACCCAGCTGGAAAGCCCCA
1 GCACCCAGCTGGAAAGCCCCA
*
521 GCACCCAACTGGAAAGCCCCA
1 GCACCCAGCTGGAAAGCCCCA
542 GCACCCAGC
1 GCACCCAGC
551 CGCAAGGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.45, G:0.22, T:0.04
Consensus pattern (21 bp):
GCACCCAGCTGGAAAGCCCCA
Found at i:666 original size:13 final size:13
Alignment explanation
Indices: 648--675 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
638 GCCGCTGACA
648 GCACCCATGCCAT
1 GCACCCATGCCAT
661 GCACCCATGCCAT
1 GCACCCATGCCAT
674 GC
1 GC
676 CGATGTCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.46, G:0.18, T:0.14
Consensus pattern (13 bp):
GCACCCATGCCAT
Found at i:15939 original size:65 final size:66
Alignment explanation
Indices: 15834--15974 Score: 223
Period size: 65 Copynumber: 2.1 Consensus size: 66
15824 AACTGCACAC
*
15834 AAAAAAAAAGCTCACTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTT-AAA-GCGAA
1 AAAAAAAAAGCTCACTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTAAAACCCGAA
15897 A
66 A
* *
15898 AAAAAAAAGAGCTCGCTAAGTTGAAAATCCTGTAAATGACGGCTTAGGCAAAAGTTAGAAACCCG
1 AAAAAAAA-AGCTCACTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTA-AAACCCG
15963 AAA
64 AAA
15966 AAAAAAAAA
1 AAAAAAAAA
15975 AAAAAAAAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
64 8 0.11
65 45 0.64
67 4 0.06
68 13 0.19
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.16
Consensus pattern (66 bp):
AAAAAAAAAGCTCACTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTAAAACCCGAA
A
Found at i:16028 original size:1 final size:1
Alignment explanation
Indices: 15963--16010 Score: 87
Period size: 1 Copynumber: 48.0 Consensus size: 1
15953 TAGAAACCCG
*
15963 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16011 CTCGCTAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.98, C:0.00, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:17250 original size:50 final size:51
Alignment explanation
Indices: 17157--17252 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 51
17147 AGTCAAATTA
*
17157 TCATCAATTCGAGATCAAGTCATCAAGACCCTCGAATCAAATCAAACTCAC
1 TCATCAATTCAAGATCAAGTCATCAAGACCCTCGAATCAAATCAAACTCAC
* ** *
17208 TCATCAATTCAAGATTAAGTCAT-TTGACCCTTGAATCAAATCAAA
1 TCATCAATTCAAGATCAAGTCATCAAGACCCTCGAATCAAATCAAA
17253 TCAAACTCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 19 0.47
51 21 0.52
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (51 bp):
TCATCAATTCAAGATCAAGTCATCAAGACCCTCGAATCAAATCAAACTCAC
Found at i:19826 original size:37 final size:37
Alignment explanation
Indices: 19785--19888 Score: 199
Period size: 37 Copynumber: 2.8 Consensus size: 37
19775 ATCCTCACGG
19785 AGGGAAAATTAATAATCAATGAGAAGAAATATTTAAC
1 AGGGAAAATTAATAATCAATGAGAAGAAATATTTAAC
*
19822 AGGGAAAATTTATAATCAATGAGAAGAAATATTTAAC
1 AGGGAAAATTAATAATCAATGAGAAGAAATATTTAAC
19859 AGGGAAAATTAATAATCAATGAGAAGAAAT
1 AGGGAAAATTAATAATCAATGAGAAGAAAT
19889 TAACAAAGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.54, C:0.05, G:0.17, T:0.24
Consensus pattern (37 bp):
AGGGAAAATTAATAATCAATGAGAAGAAATATTTAAC
Found at i:19888 original size:21 final size:21
Alignment explanation
Indices: 19790--19891 Score: 57
Period size: 21 Copynumber: 5.3 Consensus size: 21
19780 CACGGAGGGA
19790 AAATTAATAATCAATGAGAAG
1 AAATTAATAATCAATGAGAAG
* *
19811 AAA-TATTTAA-C-A-G-GGA-
1 AAATTA-ATAATCAATGAGAAG
*
19827 AAATTTATAATCAATGAGAAG
1 AAATTAATAATCAATGAGAAG
* *
19848 AAA-TATTTAA-C-A-G-GGA-
1 AAATTA-ATAATCAATGAGAAG
19864 AAATTAATAATCAATGAGAAG
1 AAATTAATAATCAATGAGAAG
19885 AAATTAA
1 AAATTAA
19892 CAAAGAATAT
Statistics
Matches: 57, Mismatches: 10, Indels: 28
0.60 0.11 0.29
Matches are distributed among these distances:
16 12 0.21
17 9 0.16
18 4 0.07
19 4 0.07
20 9 0.16
21 19 0.33
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (21 bp):
AAATTAATAATCAATGAGAAG
Found at i:39339 original size:21 final size:22
Alignment explanation
Indices: 39283--39343 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
39273 ACATATGTAT
*
39283 ATTAAAGCCCAACCTTGCAAAAA
1 ATTAAAGCCCAAAC-TGCAAAAA
* *
39306 ATTACAAGTCCCAAAC-GGAAAAC
1 ATTA-AAG-CCCAAACTGCAAAAA
39329 ATTAAAGCCCAAACT
1 ATTAAAGCCCAAACT
39344 AAACTAATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 7 0.22
22 3 0.09
23 13 0.41
24 3 0.09
25 6 0.19
ACGTcount: A:0.48, C:0.26, G:0.10, T:0.16
Consensus pattern (22 bp):
ATTAAAGCCCAAACTGCAAAAA
Found at i:44159 original size:28 final size:28
Alignment explanation
Indices: 44119--44200 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
44109 CCCAAGTGCA
* *
44119 CAACCCAAGTGCAAACTCACACTTGAAT
1 CAACCCAAGTGCAAACCCACACTTGAAG
44147 CAACCCAAGTGCAAACCCACACTTGAAG
1 CAACCCAAGTGCAAACCCACACTTGAAG
*
44175 CAACCCAAGTGCATAACCCGCACTTG
1 CAACCCAAGTGCA-AACCCACACTTG
44201 TAAAAAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
28 39 0.78
29 11 0.22
ACGTcount: A:0.37, C:0.35, G:0.13, T:0.15
Consensus pattern (28 bp):
CAACCCAAGTGCAAACCCACACTTGAAG
Found at i:44568 original size:28 final size:28
Alignment explanation
Indices: 44536--44589 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
44526 CGCGCCAGCT
*
44536 GTTGATAGCTTTAGCGCGTCCGTACTTC
1 GTTGATAGCTTCAGCGCGTCCGTACTTC
* *
44564 GTTGATCGCTTCAGCGTGTCCGTACT
1 GTTGATAGCTTCAGCGCGTCCGTACT
44590 GTTTGTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.26, T:0.35
Consensus pattern (28 bp):
GTTGATAGCTTCAGCGCGTCCGTACTTC
Found at i:47119 original size:21 final size:21
Alignment explanation
Indices: 47095--47162 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
47085 ATGTTTTGAG
47095 CAAGAATATTCCAATCGATTC
1 CAAGAATATTCCAATCGATTC
** * *
47116 CAAGCTTCTTACAATCGATTC
1 CAAGAATATTCCAATCGATTC
* * *
47137 TAGGAATATTCCAACCGATTC
1 CAAGAATATTCCAATCGATTC
47158 CAAGA
1 CAAGA
47163 TTTGCACATT
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (21 bp):
CAAGAATATTCCAATCGATTC
Found at i:53191 original size:253 final size:255
Alignment explanation
Indices: 52874--53379 Score: 962
Period size: 253 Copynumber: 2.0 Consensus size: 255
52864 AAGAAAATCA
*
52874 TTTTTTGAAAAAAGGTTTGAATGTCGAGAATTTTGAAGTATATAATCGAACGATTGTCGATTAAT
1 TTTTTTGAAAAAAGGTTTGAATGTCGAGAATTTTGAAGCATATAATCGAACGATTGTCGATTAAT
52939 TCAACTTTCAATCCTCTTTCACTATTTGTTCTCTTGTTGACCC-TTTTCTCTTCAAAAAGAGAGT
66 TCAACTTTCAATCCTCTTTCACTATTTGTTCTCTTGTTGACCCTTTTTCTCTTCAAAAAGAGAGT
53003 TTGAAAATGTTGTGTCAAAATCTTTTTACCATTTTTTATTT-TTAAAACTTGATCAATTTTATTA
131 TTGAAAATGTTGTGTCAAAATCTTTTTACCATTTTTTATTTATTAAAACTTGATCAATTTTATTA
* *
53067 ATTTCTAAAAGTCTTCTCTTGGATTTTTAAAAAAACATTTACTTTCTAAAAAGTCTTCTT
196 ATTTCTAAAAGTCTTCTCTTGGATTTCTAAAAAAACATTTACTTTCCAAAAAGTCTTCTT
53127 TTTTTTGAAAAAAGGTTTGAATGTCGAGAATTTTGAAGCATATAATCGAACGATTGTCGATTAAT
1 TTTTTTGAAAAAAGGTTTGAATGTCGAGAATTTTGAAGCATATAATCGAACGATTGTCGATTAAT
53192 TCAACTTTCAATCCTCTTTCACTATTTGTTCTCTTGTTGACCCTTTTTCTCTTCAAAAAGAGAGT
66 TCAACTTTCAATCCTCTTTCACTATTTGTTCTCTTGTTGACCCTTTTTCTCTTCAAAAAGAGAGT
53257 TTGAAAATGTTGTGTCAAAATCTTTTTACCATTTTTTATTTATTAAAACTTGATCAATTTTATTA
131 TTGAAAATGTTGTGTCAAAATCTTTTTACCATTTTTTATTTATTAAAACTTGATCAATTTTATTA
*
53322 ATTTCTAAAAGTCTTCTCTTGGATTTCTAAAGAAACATTTACTTTCCAAAAAGTCTTC
196 ATTTCTAAAAGTCTTCTCTTGGATTTCTAAAAAAACATTTACTTTCCAAAAAGTCTTC
53380 GCTTGGAATT
Statistics
Matches: 247, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
253 107 0.43
254 62 0.25
255 78 0.32
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.44
Consensus pattern (255 bp):
TTTTTTGAAAAAAGGTTTGAATGTCGAGAATTTTGAAGCATATAATCGAACGATTGTCGATTAAT
TCAACTTTCAATCCTCTTTCACTATTTGTTCTCTTGTTGACCCTTTTTCTCTTCAAAAAGAGAGT
TTGAAAATGTTGTGTCAAAATCTTTTTACCATTTTTTATTTATTAAAACTTGATCAATTTTATTA
ATTTCTAAAAGTCTTCTCTTGGATTTCTAAAAAAACATTTACTTTCCAAAAAGTCTTCTT
Found at i:53427 original size:41 final size:41
Alignment explanation
Indices: 53323--53470 Score: 210
Period size: 40 Copynumber: 3.6 Consensus size: 41
53313 ATTTTATTAA
* * *
53323 TTTCTAAAAGTCTTCTCTTGG-ATTTCTAAAGAAACATTTAC
1 TTTCCAAAAGTCTTCTCTTGGAATTACTAAA-AAACATTTAT
*
53364 TTTCCAAAAAGTCTTCGCTTGGAATTACTAAAAAACATTTAT
1 TTTCC-AAAAGTCTTCTCTTGGAATTACTAAAAAACATTTAT
53406 TTTCCAAAAGTCTTCTCTTGGAATTACT-AAAAACATTTAT
1 TTTCCAAAAGTCTTCTCTTGGAATTACTAAAAAACATTTAT
* *
53446 TTTTCAAAAGTCTTCTCTTGAAATT
1 TTTCCAAAAGTCTTCTCTTGGAATT
53471 GCTTAAACAG
Statistics
Matches: 98, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
40 35 0.36
41 26 0.27
42 29 0.30
43 8 0.08
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.41
Consensus pattern (41 bp):
TTTCCAAAAGTCTTCTCTTGGAATTACTAAAAAACATTTAT
Found at i:57275 original size:21 final size:22
Alignment explanation
Indices: 57251--57295 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
57241 TTAATGGGGG
57251 TTGCTAAAT-ACCGCCCCA-TTT
1 TTGCT-AATCACCGCCCCACTTT
*
57272 TTGCTATTCACCGCCCCACTTT
1 TTGCTAATCACCGCCCCACTTT
57294 TT
1 TT
57296 ACACTTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 14 0.67
22 5 0.24
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.38
Consensus pattern (22 bp):
TTGCTAATCACCGCCCCACTTT
Done.