Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011983.1 Corchorus capsularis cultivar CVL-1 contig12004, 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: 17786
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36 TCTCTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:749 original size:107 final size:106
Alignment explanation
Indices: 512--774 Score: 367
Period size: 107 Copynumber: 2.5 Consensus size: 106
502 AATTTTTCTA
* **
512 ACCCTTAAAATAAAATTTTAATTTTAATTT-GG-CTAAACTTAGTG-AATTAATTATATTATTTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAATTATATTATTTT
*
574 ATTTCTAAAACTCTATAACAATATTATTAATTATGGAATTT
66 ATTTCTAAAACTCTATAACAATATTATTAATTATGAAATTT
* *
615 ACCCTTAAAATGAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTT-T-TGTATTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAATTATAT-TATTT
*
678 TATTTCTAAAAC-CATATAACAATAAATTATTAATTTTGAAATTT
65 TATTTCTAAAACTC-TATAACAAT--ATTATTAATTATGAAATTT
* *
722 ACCCTTAAAATAAAAATAAAACTTTAATTTGGGACTAAACTTAGTGAATTTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAA
775 GGTTAAACTT
Statistics
Matches: 142, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
103 26 0.18
104 4 0.03
105 39 0.27
106 7 0.05
107 66 0.46
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAATTATATTATTTT
ATTTCTAAAACTCTATAACAATATTATTAATTATGAAATTT
Found at i:5352 original size:231 final size:236
Alignment explanation
Indices: 4777--5502 Score: 1059
Period size: 246 Copynumber: 3.0 Consensus size: 236
4767 TCCCTAAACA
*
4777 ACAGGGTCCTAATCTAGTTGCCATACTTCTTGAAATCCCACTTCCTATCACCTGCAAAAGCAACA
1 ACAGGGTCCTAATCTAGTTGCCATACTTCTTGAAATCCCACTTCCTATCACCTGCAGAAGCAACA
*
4842 AAATAAAACAAAGAAGACATTAATACCATGCAGATAGTAAAATGAGGCAGGAGACTATCCAATCC
66 AAATGAAACAAAGAAGACATTAATACCATGCAGATAGTAAAATGAGGCAGGAGACTATCCAATCC
*
4907 AAGCAAGAGAAGTAGTAACATACGCAGTGGATAATAAGGCAATGGACAAAAATGACTATGCTTGA
131 AAGCAAGAGAAGCAGTAACATAC-C---GG---A-AAGG--ATGGACAAAAATGACTATGCTTGA
* * *
4972 GCCACTTGTCGATGCAGTGGACGTGAAATACATGATCACATACACCTACAT
186 GCCACTTGTCGATGCAGTGGACGTGAAATACGTGATCACAGACACCTGCAT
* * *
5023 ACA-GGTACCTAATCTAGTAGCCATACTTCTTAAAATCCCACTTCCTATCACCTGCAGAAGCAAT
1 ACAGGGT-CCTAATCTAGTTGCCATACTTCTTGAAATCCCACTTCCTATCACCTGCAGAAGCAAC
*
5087 AAAATGAAACAAAGAAGACATTAATATCATGCAGATAGTAAAATGAGGCAGGAGACTATCCAATC
65 AAAATGAAACAAAGAAGACATTAATACCATGCAGATAGTAAAATGAGGCAGGAGACTATCCAATC
* * *
5152 CAACCAAGTGAAGCAGTAACATA-C-G-AA-G-TGGACAAAAATGACTATGTTTGAGCCACTTGT
130 CAAGCAAGAGAAGCAGTAACATACCGGAAAGGATGGACAAAAATGACTATGCTTGAGCCACTTGT
*
5212 CGATGCAGTGGACGTGAAATACGTGATCACAGACACCTGCGT
195 CGATGCAGTGGACGTGAAATACGTGATCACAGACACCTGCAT
* *
5254 ACAGGGTCCTAATCTAGTTGCCATACATCTTGAAATCCCACTTCCTATCACCTGCAGAAGCAACC
1 ACAGGGTCCTAATCTAGTTGCCATACTTCTTGAAATCCCACTTCCTATCACCTGCAGAAGCAACA
**
5319 AAATGAAACAAAGAAGACATTAATACCATGCAGATAGTAAAATGAGGCATTAGACTATCCAATCC
66 AAATGAAACAAAGAAGACATTAATACCATGCAGATAGTAAAATGAGGCAGGAGACTATCCAATCC
5384 AAGCAAGAGAAGCAGTAACATACGCAGTGGACAATAAGGCAATGGACAAAAATGACTATGCTTGA
131 AAGCAAGAGAAGCAGTAACATAC-C---GG---A-AAGG--ATGGACAAAAATGACTATGCTTGA
5449 GCCACTTGTCGATGCAGTGGACGTGAAATACGTGATCACAGACACCTGCAT
186 GCCACTTGTCGATGCAGTGGACGTGAAATACGTGATCACAGACACCTGCAT
5500 ACA
1 ACA
5503 CAAAAGGAAA
Statistics
Matches: 437, Mismatches: 26, Indels: 34
0.88 0.05 0.07
Matches are distributed among these distances:
231 207 0.47
232 3 0.01
233 1 0.00
234 1 0.00
235 2 0.00
237 1 0.00
240 1 0.00
242 2 0.00
243 1 0.00
244 1 0.00
245 3 0.01
246 214 0.49
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (236 bp):
ACAGGGTCCTAATCTAGTTGCCATACTTCTTGAAATCCCACTTCCTATCACCTGCAGAAGCAACA
AAATGAAACAAAGAAGACATTAATACCATGCAGATAGTAAAATGAGGCAGGAGACTATCCAATCC
AAGCAAGAGAAGCAGTAACATACCGGAAAGGATGGACAAAAATGACTATGCTTGAGCCACTTGTC
GATGCAGTGGACGTGAAATACGTGATCACAGACACCTGCAT
Found at i:8998 original size:43 final size:43
Alignment explanation
Indices: 8937--9023 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
8927 TGTGGCATTT
* * *
8937 TTTTTAGGCATGAGGGGATTGTCTCAAAGGGGAAAAGGTTTGA
1 TTTTGAGGCATGAAGGGATTGTCTCAAAGGGAAAAAGGTTTGA
*
8980 TTTTGAGGCATGAAGGGATTGTCTTAAAGGGAAAAAGGTTTGA
1 TTTTGAGGCATGAAGGGATTGTCTCAAAGGGAAAAAGGTTTGA
9023 T
1 T
9024 AATGCATACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.30, C:0.06, G:0.33, T:0.31
Consensus pattern (43 bp):
TTTTGAGGCATGAAGGGATTGTCTCAAAGGGAAAAAGGTTTGA
Found at i:10180 original size:53 final size:53
Alignment explanation
Indices: 10095--10197 Score: 147
Period size: 53 Copynumber: 1.9 Consensus size: 53
10085 GACGTGGCAC
* * *
10095 GCCACGTGTACCAAAAAGTGACATGTAGCACGCCA-GATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACATATAGCACGCAACG-TGTACCAAAAAGTCGT
10148 GCCACATGTACCAAAAAGTGACATAT-GTCACGCAACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACATATAG-CACGCAACGTGTACCAAAAAGT
10198 GACACATGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
52 1 0.02
53 43 0.96
54 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACATATAGCACGCAACGTGTACCAAAAAGTCGT
Found at i:10192 original size:31 final size:31
Alignment explanation
Indices: 10154--10233 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
10144 TCGTGCCACA
*
10154 TGTACCAAAAAGTGACATATGTCACGCAACG
1 TGTACCAAAAAGTGACACATGTCACGCAACG
*
10185 TGTACCAAAAAGTGACACATGTCACGCCACG
1 TGTACCAAAAAGTGACACATGTCACGCAACG
10216 TGTACCAAAAAGTGACAC
1 TGTACCAAAAAGTGACAC
10234 GTGGCATGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (31 bp):
TGTACCAAAAAGTGACACATGTCACGCAACG
Found at i:10245 original size:31 final size:31
Alignment explanation
Indices: 10147--10279 Score: 140
Period size: 31 Copynumber: 4.3 Consensus size: 31
10137 CAAAAAGTCG
* *
10147 TGCCACATGTACCAAAAAGTGACATATGTCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
* * * *
10178 CGCAACGTGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
* * *
10209 CGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
** * * *
10240 TGCCACATGTTTCAAAAAATGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
10271 TGCCACATG
1 TGCCACATG
10280 CACAAAAGGA
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 89 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACATGGCA
Found at i:11848 original size:22 final size:23
Alignment explanation
Indices: 11813--11859 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
11803 GTAGTTAATC
*
11813 ATAAATTAACTAATTAAA-ACTA
1 ATAAACTAACTAATTAAATACTA
*
11835 ATAAACTAAGTAATTAAATACTA
1 ATAAACTAACTAATTAAATACTA
11858 AT
1 AT
11860 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAACTAACTAATTAAATACTA
Found at i:11871 original size:22 final size:22
Alignment explanation
Indices: 11824--11873 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
11814 TAAATTAACT
*
11824 AATTAAAACTAATAAACTAAGT
1 AATTAAAACTAATAAACTAAGA
* *
11846 AATTAAATACTAATTAATTAA-A
1 AATTAAA-ACTAATAAACTAAGA
11868 AATTAA
1 AATTAA
11874 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (22 bp):
AATTAAAACTAATAAACTAAGA
Found at i:11874 original size:15 final size:15
Alignment explanation
Indices: 11837--11875 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
11827 TAAAACTAAT
*
11837 AAACTAAGTAATTAA
1 AAACTAATTAATTAA
*
11852 ATACTAATTAATTAA
1 AAACTAATTAATTAA
*
11867 AAATTAATT
1 AAACTAATT
11876 TTTTTAAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (15 bp):
AAACTAATTAATTAA
Found at i:13065 original size:12 final size:12
Alignment explanation
Indices: 13048--13077 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
13038 AAGTGCAGAA
13048 GCAGAAATCGCC
1 GCAGAAATCGCC
13060 GCAGAAATCGCC
1 GCAGAAATCGCC
13072 GCAGAA
1 GCAGAA
13078 TTGTAACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.30, G:0.27, T:0.07
Consensus pattern (12 bp):
GCAGAAATCGCC
Found at i:14934 original size:29 final size:30
Alignment explanation
Indices: 14893--14966 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
14883 TGACATGTGG
*
14893 CACATATC-CTTTTGTG-CATATGGCATGC
1 CACATGTCACTTTTGTGACATATGGCATGC
*
14921 CACATGTCACTTTT-TGAAACATGTGGCATGC
1 CACATGTCACTTTTGTG--ACATATGGCATGC
*
14952 CACGTGTCACTTTTG
1 CACATGTCACTTTTG
14967 GAAACATGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 9 0.24
29 5 0.13
31 24 0.63
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (30 bp):
CACATGTCACTTTTGTGACATATGGCATGC
Found at i:14948 original size:31 final size:31
Alignment explanation
Indices: 14913--15011 Score: 137
Period size: 31 Copynumber: 3.2 Consensus size: 31
14903 TTTGTGCATA
*
14913 TGGCATGCCACATGTCACTTTTTGAAACATG
1 TGGCATGCCACGTGTCACTTTTTGAAACATG
*
14944 TGGCATGCCACGTGTCACTTTTGGAAACATG
1 TGGCATGCCACGTGTCACTTTTTGAAACATG
* * * *
14975 TGACATACCACGTGTCACTTTTTG-TACACG
1 TGGCATGCCACGTGTCACTTTTTGAAACATG
15005 TGGCATG
1 TGGCATG
15012 ATATGTGTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
30 9 0.15
31 50 0.85
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.31
Consensus pattern (31 bp):
TGGCATGCCACGTGTCACTTTTTGAAACATG
Found at i:17760 original size:2 final size:2
Alignment explanation
Indices: 17748--17786 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
17738 AGTACTAAAT
17748 TA TA CTA TA 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 TA TA TA TA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.