Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014931.1 Corchorus capsularis cultivar CVL-1 contig14952, 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: 16394
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:5771 original size:15 final size:16
Alignment explanation
Indices: 5744--5773 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5734 TGGCAAAGTG
5744 AACCCGACCCGAAAAA
1 AACCCGACCCGAAAAA
5760 AACCCG-CCCGAAAA
1 AACCCGACCCGAAAA
5774 CCTGAACCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.40, G:0.13, T:0.00
Consensus pattern (16 bp):
AACCCGACCCGAAAAA
Found at i:5858 original size:17 final size:17
Alignment explanation
Indices: 5826--5890 Score: 64
Period size: 16 Copynumber: 4.0 Consensus size: 17
5816 AACCCACCTG
5826 AACCTGAACCCGAAAAA
1 AACCTGAACCCGAAAAA
5843 AACC-GAACCCG-AAAA
1 AACCTGAACCCGAAAAA
* * * *
5858 AGCTTAAACCTG-AAAA
1 AACCTGAACCCGAAAAA
*
5874 AACCCGAACCCGAAAAA
1 AACCTGAACCCGAAAAA
5891 GCTCAAACCC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
15 6 0.16
16 23 0.62
17 8 0.22
ACGTcount: A:0.52, C:0.29, G:0.12, T:0.06
Consensus pattern (17 bp):
AACCTGAACCCGAAAAA
Found at i:5899 original size:16 final size:16
Alignment explanation
Indices: 5848--5905 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
5838 AAAAAAACCG
*
5848 AACCCGAAAAAGCTTA
1 AACCCGAAAAAGCTCA
* * * *
5864 AACCTGAAAAAACCCG
1 AACCCGAAAAAGCTCA
5880 AACCCGAAAAAGCTCA
1 AACCCGAAAAAGCTCA
5896 AACCC-AAAAA
1 AACCCGAAAAA
5906 AACCCGAATT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
15 5 0.15
16 28 0.85
ACGTcount: A:0.53, C:0.29, G:0.10, T:0.07
Consensus pattern (16 bp):
AACCCGAAAAAGCTCA
Found at i:5921 original size:32 final size:32
Alignment explanation
Indices: 5832--5913 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
5822 CCTGAACCTG
*
5832 AACCCGAAAAAAA-CCGAACCCGAAAAAGCTTA
1 AACCC-AAAAAAACCCGAACCCGAAAAAGCTCA
**
5864 AACCTGAAAAAACCCGAACCCGAAAAAGCTCA
1 AACCCAAAAAAACCCGAACCCGAAAAAGCTCA
5896 AACCCAAAAAAACCCGAA
1 AACCCAAAAAAACCCGAA
5914 TTCGAAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 6 0.14
32 38 0.86
ACGTcount: A:0.54, C:0.30, G:0.11, T:0.05
Consensus pattern (32 bp):
AACCCAAAAAAACCCGAACCCGAAAAAGCTCA
Found at i:6105 original size:16 final size:15
Alignment explanation
Indices: 6082--6137 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 15
6072 CCCGAACTCG
6082 AATTAACCTGACCCA
1 AATTAACCTGACCCA
*
6097 AATTCAACCTGAACCCG
1 AATT-AACCTG-ACCCA
*
6114 AATTAACCGGACCCA
1 AATTAACCTGACCCA
6129 AATTCAACC
1 AATT-AACC
6138 CGAACCCGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 12 0.34
16 15 0.43
17 8 0.23
ACGTcount: A:0.39, C:0.34, G:0.09, T:0.18
Consensus pattern (15 bp):
AATTAACCTGACCCA
Found at i:6116 original size:32 final size:32
Alignment explanation
Indices: 6060--6146 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 32
6050 TCTGGCCAAA
* * * *
6060 ACCCAAACTGAACCCGAACTCGAATTAACCTG
1 ACCCAAATTCAACCCGAACCCGAATTAACCGG
*
6092 ACCCAAATTCAACCTGAACCCGAATTAACCGG
1 ACCCAAATTCAACCCGAACCCGAATTAACCGG
6124 ACCCAAATTCAACCCGAACCCGA
1 ACCCAAATTCAACCCGAACCCGA
6147 CTCAAGCACG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.38, C:0.37, G:0.11, T:0.14
Consensus pattern (32 bp):
ACCCAAATTCAACCCGAACCCGAATTAACCGG
Found at i:7610 original size:34 final size:35
Alignment explanation
Indices: 7546--7612 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
7536 GCTAAATATA
* *
7546 TTTTTTTTAGAAAAATCGGAAAAAGGAAAAACTTT
1 TTTTTTTTAGAAAAAACGGAAAAAGCAAAAACTTT
7581 TTTTTTTTAGAAAAAACGGAAAAA-CAAAAACT
1 TTTTTTTTAGAAAAAACGGAAAAAGCAAAAACT
7613 AATTCTTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 7 0.23
35 23 0.77
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.31
Consensus pattern (35 bp):
TTTTTTTTAGAAAAAACGGAAAAAGCAAAAACTTT
Found at i:10073 original size:11 final size:12
Alignment explanation
Indices: 10048--10079 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
10038 TGAAAAATTC
*
10048 AAAATTTTCGAA
1 AAAATTATCGAA
10060 AAAATTATCGAA
1 AAAATTATCGAA
10072 AAAATTAT
1 AAAATTAT
10080 GCCATTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (12 bp):
AAAATTATCGAA
Done.