Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006749.1 Corchorus capsularis cultivar CVL-1 contig06770, 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: 15226
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Found at i:2152 original size:27 final size:27
Alignment explanation
Indices: 2115--2187 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
2105 AGGGTCACAT
2115 AAGGG-ATTTTGGTCATTTTCACATTC
1 AAGGGCATTTTGGTCATTTTCACATTC
* * ** *
2141 AGGGGCATTTTGGTCTTTTTTGCATTT
1 AAGGGCATTTTGGTCATTTTCACATTC
*
2168 AAGGGTATTTTGGTCATTTT
1 AAGGGCATTTTGGTCATTTT
2188 AAGTTCACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 4 0.11
27 34 0.89
ACGTcount: A:0.18, C:0.11, G:0.23, T:0.48
Consensus pattern (27 bp):
AAGGGCATTTTGGTCATTTTCACATTC
Found at i:7283 original size:28 final size:28
Alignment explanation
Indices: 7230--7285 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
7220 AGGGGCATGG
*
7230 TTCTTCTTTAACTTTCCTTTATTTACTA
1 TTCTTCTTTAACTTTCCTTTAGTTACTA
* *
7258 TTCTTGTTTAA-TTTCCTTGTGGTTACTA
1 TTCTTCTTTAACTTTCCTT-TAGTTACTA
7286 ACTTCTCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.16, C:0.18, G:0.07, T:0.59
Consensus pattern (28 bp):
TTCTTCTTTAACTTTCCTTTAGTTACTA
Found at i:10806 original size:3 final size:3
Alignment explanation
Indices: 10800--10875 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
10790 AAAATTATCG
10800 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10848 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10876 AGGAATAAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11570 original size:20 final size:22
Alignment explanation
Indices: 11527--11572 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
11517 CCCAGTAAAA
11527 AAAGAAGAAGACGAGAAAAGGAG
1 AAAGAAGAAGAC-AGAAAAGGAG
*
11550 AAAGAAGAAGA-ATAAAA-GAG
1 AAAGAAGAAGACAGAAAAGGAG
11570 AAA
1 AAA
11573 AAAAAAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 5 0.23
23 11 0.50
ACGTcount: A:0.67, C:0.02, G:0.28, T:0.02
Consensus pattern (22 bp):
AAAGAAGAAGACAGAAAAGGAG
Found at i:11632 original size:12 final size:12
Alignment explanation
Indices: 11615--11657 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
11605 AAAGAGTCAT
11615 GGTTTTCAAAAA
1 GGTTTTCAAAAA
*
11627 GGTTTTAATAAAA
1 GGTTTTCA-AAAA
11640 TGGTTTTC-AAAA
1 -GGTTTTCAAAAA
11652 GGTTTT
1 GGTTTT
11658 GATAAAACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 6 0.22
12 11 0.41
13 4 0.15
14 6 0.22
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.42
Consensus pattern (12 bp):
GGTTTTCAAAAA
Found at i:11657 original size:25 final size:25
Alignment explanation
Indices: 11613--11679 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 25
11603 TAAAAGAGTC
11613 ATGGTTTTCAAAAAGGTTTTAATAAA
1 ATGGTTTTC-AAAAGGTTTTAATAAA
*
11639 ATGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTCAAAAGGTTTTAATAAA
* *
11664 ACAGTTTTTCAAAAGG
1 A-TGGTTTTCAAAAGG
11680 AGTCATGGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 16 0.43
26 21 0.57
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ATGGTTTTCAAAAGGTTTTAATAAA
Found at i:12292 original size:17 final size:17
Alignment explanation
Indices: 12272--12341 Score: 53
Period size: 17 Copynumber: 4.4 Consensus size: 17
12262 ACTGGGCCTA
12272 AAAAAGAAAGAGGTCGC
1 AAAAAGAAAGAGGTCGC
*
12289 AAAAAGAAA-AAG--G-
1 AAAAAGAAAGAGGTCGC
* **
12302 AAAAA-AACTG-GGTCTA
1 AAAAAGAA-AGAGGTCGC
12318 AAAAAGAAAGAGGTCGC
1 AAAAAGAAAGAGGTCGC
12335 AAAAAGA
1 AAAAAGA
12342 GAAATAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 14
0.65 0.12 0.23
Matches are distributed among these distances:
12 2 0.05
13 6 0.15
14 1 0.03
16 8 0.21
17 22 0.56
ACGTcount: A:0.60, C:0.09, G:0.24, T:0.07
Consensus pattern (17 bp):
AAAAAGAAAGAGGTCGC
Found at i:12313 original size:46 final size:47
Alignment explanation
Indices: 12245--12341 Score: 160
Period size: 46 Copynumber: 2.1 Consensus size: 47
12235 CGAAGAAAAG
*
12245 AAGAAAAGAAGAAAAAGACTGGGCCTAAAAAAGAAAGAGGTCGCAAA
1 AAGAAAAGAAGAAAAAAACTGGGCCTAAAAAAGAAAGAGGTCGCAAA
* *
12292 AAGAAAA-AGGAAAAAAACTGGGTCTAAAAAAGAAAGAGGTCGCAAA
1 AAGAAAAGAAGAAAAAAACTGGGCCTAAAAAAGAAAGAGGTCGCAAA
12338 AAGA
1 AAGA
12342 GAAATAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 40 0.85
47 7 0.15
ACGTcount: A:0.59, C:0.09, G:0.25, T:0.07
Consensus pattern (47 bp):
AAGAAAAGAAGAAAAAAACTGGGCCTAAAAAAGAAAGAGGTCGCAAA
Found at i:12914 original size:5 final size:6
Alignment explanation
Indices: 12887--12935 Score: 53
Period size: 6 Copynumber: 7.5 Consensus size: 6
12877 GTAAAAAATG
*
12887 AAAGAA AACGAGAA AAAGAA AAAGAA AAAGAAA AAAGAA TGAAGAA AAA
1 AAAGAA AA--AGAA AAAGAA AAAGAA AAAG-AA AAAGAA -AAAGAA AAA
12936 AGGCTCTAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 20 0.54
7 11 0.30
8 6 0.16
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:12931 original size:14 final size:13
Alignment explanation
Indices: 12887--12937 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
12877 GTAAAAAATG
*
12887 AAAGAAAACGAGAA
1 AAAGAAAA-AAGAA
12901 AAAG-AAAAAGAA
1 AAAGAAAAAAGAA
12913 AAAGAAAAAAGAA
1 AAAGAAAAAAGAA
*
12926 TGAAGAAAAAAG
1 -AAAGAAAAAAG
12938 GCTCTAGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 8 0.24
13 11 0.33
14 14 0.42
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:12931 original size:20 final size:21
Alignment explanation
Indices: 12879--12935 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
12869 AAGTGCATGT
*
12879 AAAA-AATGAAAGAAAACGAGA
1 AAAAGAATG-AAGAAAAAGAGA
*
12900 AAAAGAA-AAAGAAAAAGA-A
1 AAAAGAATGAAGAAAAAGAGA
12919 AAAAGAATGAAGAAAAA
1 AAAAGAATGAAGAAAAA
12936 AGGCTCTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 8 0.26
20 17 0.55
21 4 0.13
22 2 0.06
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (21 bp):
AAAAGAATGAAGAAAAAGAGA
Found at i:13915 original size:69 final size:69
Alignment explanation
Indices: 13833--14187 Score: 389
Period size: 69 Copynumber: 5.1 Consensus size: 69
13823 GAATGCTTCA
* *
13833 GCTTTTCCACAAGCCAAACTCGTTTCCACATGAGTCAGTTTAGCCTTGGTTCCATCCAAGCATTC
1 GCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGTTTAGCTTTGGTTCCATCCAAGCATTC
13898 AGGG
66 AGGG
** * *
13902 GCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAGGCA-A
1 GCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAG-TTTAGCTTTGGTTCCATCCAAGCATT
*
13966 GAGAGG
65 CAG-GG
* * * * *
13972 G-TTTTCCATAAGCCAAACTCGCTTCCACGCGAGAT-AGTTTCAGATTTGGTTTCATCCAAGCAT
1 GCTTTTCCACAAGCCAAACTCGTTTCCACACGAG-TCAGTTT-AGCTTTGGTTCCATCCAAGCAT
14035 TCAGGG
64 TCAGGG
* * * *
14041 GTTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCTAGCTTTGGTTCCATCC-AGGA-A
1 GCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAG-TTTAGCTTTGGTTCCATCCAAGCATT
* *
14104 GAGAG
65 CAGGG
* * * * * *
14109 GCTTTTCCATAAGCCAAACTCGCTTCCACGCAAGAT-AGTTTCAGATTTGGTTCCATCCGAGCAT
1 GCTTTTCCACAAGCCAAACTCGTTTCCACACGAG-TCAGTTT-AGCTTTGGTTCCATCCAAGCAT
14173 TCAGGG
64 TCAGGG
14179 GCTTTTCCA
1 GCTTTTCCA
14188 TATGCCAAGT
Statistics
Matches: 236, Mismatches: 38, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
67 2 0.01
68 50 0.21
69 99 0.42
70 83 0.35
71 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (69 bp):
GCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGTTTAGCTTTGGTTCCATCCAAGCATTC
AGGG
Found at i:14087 original size:139 final size:138
Alignment explanation
Indices: 13833--14187 Score: 570
Period size: 138 Copynumber: 2.6 Consensus size: 138
13823 GAATGCTTCA
* * ** **
13833 GCTTTTCCACAAGCCAAACTCGTTTCCACATGAG-TCAGTTT-AGCCTTGGTTCCATCCAAGCAT
1 GCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGAT-AGTTTCAGATTTGGTTCCATCCAAGCAT
13896 TCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCA
65 TCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCA
13961 GGCAAGAGAG
130 GG-AAGAGAG
* *
13971 GGTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTCAGATTTGGTTTCATCCAAGCATT
1 GCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTCAGATTTGGTTCCATCCAAGCATT
* *
14036 CAGGGGTTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCTAGCTTTGGTTCCATCCAG
66 CAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAG
14101 GAAGAGAG
131 GAAGAGAG
* *
14109 GCTTTTCCATAAGCCAAACTCGCTTCCACGCAAGATAGTTTCAGATTTGGTTCCATCCGAGCATT
1 GCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTCAGATTTGGTTCCATCCAAGCATT
14174 CAGGGGCTTTTCCA
66 CAGGGGCTTTTCCA
14188 TATGCCAAGT
Statistics
Matches: 200, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
138 115 0.57
139 85 0.43
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (138 bp):
GCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTCAGATTTGGTTCCATCCAAGCATT
CAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAG
GAAGAGAG
Found at i:14377 original size:48 final size:48
Alignment explanation
Indices: 14307--14443 Score: 202
Period size: 48 Copynumber: 2.9 Consensus size: 48
14297 CCAGGCAATC
* *
14307 TTCTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATTATCT
1 TTCTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGATAT
* * *
14355 TTCTCTCGCTTCCACGCAAGTTTTCAATTTAGTGACCAAAGATGGTAT
1 TTCTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGATAT
* * *
14403 TTCTCTCGCTTCCATGCGAGTCTGCAATTTACTGACCAAAG
1 TTCTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAG
14444 TTAGTCAATT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 79 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (48 bp):
TTCTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGATAT
Found at i:14799 original size:27 final size:27
Alignment explanation
Indices: 14762--14834 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
14752 AGGGTCACAT
14762 AAGGG-ATTTTGGTCATTTTCACATTC
1 AAGGGCATTTTGGTCATTTTCACATTC
* * ** *
14788 AGGGGCATTTTGGTCTTTTTTGCATTT
1 AAGGGCATTTTGGTCATTTTCACATTC
*
14815 AAGGGTATTTTGGTCATTTT
1 AAGGGCATTTTGGTCATTTT
14835 AAGTTCACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 4 0.11
27 34 0.89
ACGTcount: A:0.18, C:0.11, G:0.23, T:0.48
Consensus pattern (27 bp):
AAGGGCATTTTGGTCATTTTCACATTC
Done.