Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008748.1 Corchorus capsularis cultivar CVL-1 contig08769, 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: 9778
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Found at i:1067 original size:22 final size:24
Alignment explanation
Indices: 1034--1077 Score: 58
Period size: 22 Copynumber: 1.9 Consensus size: 24
1024 CCTTATACCT
1034 TTTTAACTCTTT-GA-AATTGAGA
1 TTTTAACTCTTTGGATAATTGAGA
1056 TTTT-ACTGCTTTGGATAATTGA
1 TTTTAACT-CTTTGGATAATTGA
1078 ATGCCAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.16
22 8 0.42
23 2 0.11
24 6 0.32
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.48
Consensus pattern (24 bp):
TTTTAACTCTTTGGATAATTGAGA
Found at i:2347 original size:27 final size:27
Alignment explanation
Indices: 2317--2387 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
2307 GAACTTAGAT
2317 TGACCAAAATGCCCCTGAATGTGAAAA
1 TGACCAAAATGCCCCTGAATGTGAAAA
*
2344 TGACCAAAATGCCCCTGAATGTGAGAA
1 TGACCAAAATGCCCCTGAATGTGAAAA
2371 TGACCAAAATGCCCCTG
1 TGACCAAAATGCCCCTG
2388 TATGACCCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (27 bp):
TGACCAAAATGCCCCTGAATGTGAAAA
Found at i:2765 original size:48 final size:48
Alignment explanation
Indices: 2707--2798 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
2697 AAAACCCGTT
* *
2707 GACCAACTTTGGTCACTAAATTGCAGACTCGCATGGAAGCGAGAAAAA
1 GACCAACTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAAAAA
* **
2755 GACCATCTTTGGTCACTAGTTTGAAAACTCGCATGGAAGCGAGA
1 GACCAACTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGA
2799 GAAGATTGCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (48 bp):
GACCAACTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAAAAA
Found at i:3044 original size:69 final size:69
Alignment explanation
Indices: 2936--3276 Score: 354
Period size: 69 Copynumber: 4.9 Consensus size: 69
2926 AAGCCCTTGA
* * * * * *
2936 ATGCTTGGATGGAACCAAATCTTAAACT-ATCTCGCGTGGAAGCGAGTTTGGCTTATGGAAAAGC
1 ATGCCTGGATGGAACCAAAGCTGAAACTGA-CTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGC
3000 CTCCCT
65 C-CCCT
* * * *
3006 -TGCCTGGATGGAACCGAAGCTGGATCTGACTCGTGTGGAAATGAGTTTGGCTTGTGGAAAAG-C
1 ATGCCTGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCC
3069 CCCT
66 CCCT
* * * * *
3073 GAATGCTTGGATGGAACCAAATCTGAAACT-ATCTCGCGTGGAAGCGAGTTTGGCTTATGGAAAA
1 --ATGCCTGGATGGAACCAAAGCTGAAACTGA-CTCGTGTGGAAACGAGTTTGGCTTGTGGAAAA
*
3137 GCCTCTCT
63 GCC-CCCT
* * * *
3145 -TGCCTGGATGGAACCAAAGTTGGATCTGACTCGTGTGGAAACAAGTTTGGCTTGTGGAAAAG-C
1 ATGCCTGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCC
3208 CCCT
66 CCCT
* * *
3212 GAATGCTTGGATGGAACCAAGGCT-AAACTGACTCGTGTGGAAACGAGTTTAGCTTGTGGAAAAG
1 --ATGCCTGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAG
3276 C
64 C
3277 TGGAGCATTC
Statistics
Matches: 222, Mismatches: 37, Indels: 24
0.78 0.13 0.08
Matches are distributed among these distances:
67 7 0.03
68 2 0.01
69 138 0.62
70 71 0.32
71 1 0.00
72 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.26
Consensus pattern (69 bp):
ATGCCTGGATGGAACCAAAGCTGAAACTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCC
CCCT
Found at i:3169 original size:139 final size:138
Alignment explanation
Indices: 2915--3276 Score: 573
Period size: 139 Copynumber: 2.6 Consensus size: 138
2905 CATTGAACTC
* *
2915 GGCTTATGGAAAAGCCCTTGAATGCTTGGATGGAACCAAATCTTAAACTATCTCGCGTGGAAGCG
1 GGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATC-TAAACTATCTCGCGTGGAAGCG
*
2980 AGTTTGGCTTATGGAAAAGCCTCCCTTGCCTGGATGGAACCGAAGCTGGATCTGACTCGTGTGGA
65 AGTTTGGCTTATGGAAAAGCCTCCCTTGCCTGGATGGAACCAAAGCTGGATCTGACTCGTGTGGA
**
3045 AATGAGTTT
130 AACAAGTTT
3054 GGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTGAAACTATCTCGCGTGGAAGCG
1 GGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCT-AAACTATCTCGCGTGGAAGCG
* *
3119 AGTTTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCAAAGTTGGATCTGACTCGTGTGGA
65 AGTTTGGCTTATGGAAAAGCCTCCCTTGCCTGGATGGAACCAAAGCTGGATCTGACTCGTGTGGA
3184 AACAAGTTT
130 AACAAGTTT
** * *
3193 GGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAGGCTAAACTGA-CTCGTGTGGAAACG
1 GGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTAAACT-ATCTCGCGTGGAAGCG
* *
3257 AGTTTAGCTTGTGGAAAAGC
65 AGTTTGGCTTATGGAAAAGC
3277 TGGAGCATTC
Statistics
Matches: 208, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
138 36 0.17
139 172 0.83
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (138 bp):
GGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAATCTAAACTATCTCGCGTGGAAGCGA
GTTTGGCTTATGGAAAAGCCTCCCTTGCCTGGATGGAACCAAAGCTGGATCTGACTCGTGTGGAA
ACAAGTTT
Found at i:3903 original size:50 final size:50
Alignment explanation
Indices: 3800--3907 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
3790 CTAAAATGCC
* ** * *
3800 TTTTGAAAAGTGAATTTTGATCTTGGACTCACAAGTGGAATGCAAGCTTA
1 TTTTGAAAAGTGAATCTTGATAATGGACTCACAAATGGAATGCAAGCTCA
* *
3850 TTTTGAAAA-TCGAATCTTGATAATGGACTCACAAATGGAATGCCATCTCA
1 TTTTGAAAAGT-GAATCTTGATAATGGACTCACAAATGGAATGCAAGCTCA
3900 TTTT-AAAA
1 TTTTGAAAA
3908 CTTCTTGTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
49 5 0.10
50 45 0.90
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (50 bp):
TTTTGAAAAGTGAATCTTGATAATGGACTCACAAATGGAATGCAAGCTCA
Found at i:5394 original size:45 final size:45
Alignment explanation
Indices: 5343--5443 Score: 125
Period size: 45 Copynumber: 2.2 Consensus size: 45
5333 GAAAAACGAG
* *
5343 TTTGAAAACACAACTTT-GGAAAACCTTTTTGAAAACCATGACTC-T
1 TTTGAAAAC-CAACTTTAGCAAAACC-ATTTGAAAACCATGACTCTT
* * *
5388 TTTGAAAACCCATTTTATCAAAACCATTTGAAAACCATGACTCTT
1 TTTGAAAACCAACTTTAGCAAAACCATTTGAAAACCATGACTCTT
5433 TTTGAAAACCA
1 TTTGAAAACCA
5444 TCGTTGCTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 22 0.46
45 26 0.54
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.32
Consensus pattern (45 bp):
TTTGAAAACCAACTTTAGCAAAACCATTTGAAAACCATGACTCTT
Found at i:9238 original size:6 final size:6
Alignment explanation
Indices: 9227--9259 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
9217 AAAGCAAAGC
9227 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
9260 GCAAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Done.