Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006869.1 Corchorus capsularis cultivar CVL-1 contig06890, 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: 18774
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:3455 original size:36 final size:36
Alignment explanation
Indices: 3408--3483 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
3398 AAATAGCTCA
3408 CCAACCATAATTATCTTCATTTTCTTCCACTGATCT
1 CCAACCATAATTATCTTCATTTTCTTCCACTGATCT
*
3444 CCAACCATAATTCTCTTCATTTTCTTCCACTGATCT
1 CCAACCATAATTATCTTCATTTTCTTCCACTGATCT
3480 CCAA
1 CCAA
3484 GGGCACTACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.25, C:0.33, G:0.03, T:0.39
Consensus pattern (36 bp):
CCAACCATAATTATCTTCATTTTCTTCCACTGATCT
Found at i:6047 original size:15 final size:15
Alignment explanation
Indices: 6015--6048 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6005 TGGGTTGGAC
**
6015 GGGTTCGGGTCATCT
1 GGGTTCGGGTCAAAT
6030 GGGTTCGGGTCAAAT
1 GGGTTCGGGTCAAAT
6045 GGGT
1 GGGT
6049 CAGGCAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.15, G:0.44, T:0.29
Consensus pattern (15 bp):
GGGTTCGGGTCAAAT
Found at i:6085 original size:16 final size:16
Alignment explanation
Indices: 6061--6179 Score: 166
Period size: 16 Copynumber: 7.4 Consensus size: 16
6051 GGCAGTTTTC
6061 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
6077 TCGGTTCATTCGGATT
1 TCGGGTCATTCGGGTT
* *
6093 TCGGGTCATTCGAGTC
1 TCGGGTCATTCGGGTT
*
6109 TCGGGTCATACGGGTT
1 TCGGGTCATTCGGGTT
*
6125 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
*
6141 TCGGGTCATACGGGTT
1 TCGGGTCATTCGGGTT
*
6157 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
6173 TCGGGTC
1 TCGGGTC
6180 TACCGGGTCT
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 88 1.00
ACGTcount: A:0.09, C:0.22, G:0.35, T:0.34
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:6099 original size:32 final size:32
Alignment explanation
Indices: 6061--6187 Score: 193
Period size: 32 Copynumber: 4.0 Consensus size: 32
6051 GGCAGTTTTC
* * * *
6061 TCGGGTCATTCGGGTTTCGGTTCATTCGGATT
1 TCGGGTCATTCGGGTCTCGGGTCATACGGGTT
*
6093 TCGGGTCATTCGAGTCTCGGGTCATACGGGTT
1 TCGGGTCATTCGGGTCTCGGGTCATACGGGTT
6125 TCGGGTCATTCGGGTCTCGGGTCATACGGGTT
1 TCGGGTCATTCGGGTCTCGGGTCATACGGGTT
6157 TCGGGTCATTCGGGTCTCGGGTC-TACCGGGT
1 TCGGGTCATTCGGGTCTCGGGTCATA-CGGGT
6188 CTCGAGTTGG
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 2 0.02
32 86 0.98
ACGTcount: A:0.09, C:0.22, G:0.35, T:0.33
Consensus pattern (32 bp):
TCGGGTCATTCGGGTCTCGGGTCATACGGGTT
Found at i:6186 original size:16 final size:15
Alignment explanation
Indices: 6106--6191 Score: 91
Period size: 16 Copynumber: 5.4 Consensus size: 15
6096 GGTCATTCGA
6106 GTCTCGGGTCATACGG
1 GTCTCGGGTC-TACGG
* *
6122 GTTTCGGGTCATTCGG
1 GTCTCGGGTC-TACGG
6138 GTCTCGGGTCATACGG
1 GTCTCGGGTC-TACGG
* *
6154 GTTTCGGGTCATTCGG
1 GTCTCGGGTC-TACGG
6170 GTCTCGGGTCTACCGG
1 GTCTCGGGTCTA-CGG
6186 GTCTCG
1 GTCTCG
6192 AGTTGGGCGG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
15 1 0.02
16 60 0.98
ACGTcount: A:0.08, C:0.24, G:0.37, T:0.30
Consensus pattern (15 bp):
GTCTCGGGTCTACGG
Found at i:7107 original size:16 final size:16
Alignment explanation
Indices: 7085--7131 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
7075 GTCACTTGGA
7085 TTACGGGTCATTCGGG
1 TTACGGGTCATTCGGG
*
7101 TTTCGGGTCA-TCTGGG
1 TTACGGGTCATTC-GGG
*
7117 TTACGAGTCATTCGG
1 TTACGGGTCATTCGG
7132 ATCTCGGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.13, C:0.19, G:0.34, T:0.34
Consensus pattern (16 bp):
TTACGGGTCATTCGGG
Found at i:7156 original size:32 final size:32
Alignment explanation
Indices: 7085--7158 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
7075 GTCACTTGGA
* * * * *
7085 TTACGGGTCATTCGGGTTTCGGGTCATCTGGG
1 TTACGAGTCATTCGGATCTCGGATCATCTGAG
*
7117 TTACGAGTCATTCGGATCTCGGATCATTTGAG
1 TTACGAGTCATTCGGATCTCGGATCATCTGAG
*
7149 TTGCGAGTCA
1 TTACGAGTCA
7159 CTCAGATCGG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.16, C:0.19, G:0.31, T:0.34
Consensus pattern (32 bp):
TTACGAGTCATTCGGATCTCGGATCATCTGAG
Found at i:10832 original size:5 final size:5
Alignment explanation
Indices: 10822--10854 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
10812 TCGCTGCTCT
10822 TTTTC TTTTC TTTTC TTTTC TTTT- TCTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC TTT
10855 CTTCCTCCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 24 0.92
6 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:12090 original size:32 final size:33
Alignment explanation
Indices: 12033--12097 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
12023 GGGTCTGAGT
*
12033 TGATTTTGCTGGTATTTTTTTTGTTAAATTTTGC
1 TGATTTTCCTGGTA-TTTTTTTGTTAAATTTTGC
*
12067 TGATTTTCCTGGTA-TTTTTTGTTACATTTTG
1 TGATTTTCCTGGTATTTTTTTGTTAAATTTTG
12098 TTGAGGAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 16 0.55
34 13 0.45
ACGTcount: A:0.14, C:0.08, G:0.17, T:0.62
Consensus pattern (33 bp):
TGATTTTCCTGGTATTTTTTTGTTAAATTTTGC
Found at i:15883 original size:16 final size:16
Alignment explanation
Indices: 15864--15917 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
15854 GTTTAAGTCA
15864 GGTCAGGTTGAATTTG
1 GGTCAGGTTGAATTTG
*
15880 GGTCAGGTT-AATTCG
1 GGTCAGGTTGAATTTG
*
15895 GGTCCGGGTTGAATTTG
1 GGT-CAGGTTGAATTTG
15912 GGTCAG
1 GGTCAG
15918 TTTAATTCGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 8 0.25
16 16 0.50
17 8 0.25
ACGTcount: A:0.17, C:0.11, G:0.39, T:0.33
Consensus pattern (16 bp):
GGTCAGGTTGAATTTG
Found at i:15897 original size:15 final size:16
Alignment explanation
Indices: 15864--15927 Score: 69
Period size: 15 Copynumber: 4.1 Consensus size: 16
15854 GTTTAAGTCA
*
15864 GGTCAGGTTGAATTTG
1 GGTCAGGTTGAATTCG
15880 GGTCAGGTT-AATTCG
1 GGTCAGGTTGAATTCG
* *
15895 GGTCCGGGTTGAATTTG
1 GGT-CAGGTTGAATTCG
*
15912 GGTCA-GTTTAATTCG
1 GGTCAGGTTGAATTCG
15927 G
1 G
15928 ATTCGAGTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
15 17 0.43
16 15 0.38
17 8 0.20
ACGTcount: A:0.17, C:0.11, G:0.36, T:0.36
Consensus pattern (16 bp):
GGTCAGGTTGAATTCG
Found at i:15944 original size:32 final size:32
Alignment explanation
Indices: 15874--15946 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
15864 GGTCAGGTTG
* * *
15874 AATTTGGGTCAGGTTAATTCGGGTCCGGGTTG
1 AATTTGGGTCAGGTTAATTCGGATCCGAGTTC
* *
15906 AATTTGGGTCAGTTTAATTCGGATTCGAGTTC
1 AATTTGGGTCAGGTTAATTCGGATCCGAGTTC
*
15938 AGTTTGGGT
1 AATTTGGGT
15947 TTTGGCCAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.18, C:0.11, G:0.33, T:0.38
Consensus pattern (32 bp):
AATTTGGGTCAGGTTAATTCGGATCCGAGTTC
Found at i:16113 original size:16 final size:16
Alignment explanation
Indices: 16092--16166 Score: 78
Period size: 16 Copynumber: 4.7 Consensus size: 16
16082 CATTTTCGGA
16092 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
* *
16108 TTCGGGTTCTGATTTT
1 TTCGGGTTCGGGTTTT
* * * *
16124 TTCGGATTTGAGCTTT
1 TTCGGGTTCGGGTTTT
*
16140 TTCGGATTCGGGTTTT
1 TTCGGGTTCGGGTTTT
*
16156 TCCGGGTTCGG
1 TTCGGGTTCGG
16167 ATTCGGGTAT
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.05, C:0.15, G:0.32, T:0.48
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:18440 original size:38 final size:38
Alignment explanation
Indices: 18388--18460 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
18378 ATAATAATAC
*
18388 CCTCTCTCAGAAATATATTCCATAGTACCGAATCCTAA
1 CCTCTCTCAGAAATATATTCCAAAGTACCGAATCCTAA
*
18426 CCTCTCTCATAAATATATTCCAAAGTACCGAATCC
1 CCTCTCTCAGAAATATATTCCAAAGTACCGAATCC
18461 CAAAACACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.29
Consensus pattern (38 bp):
CCTCTCTCAGAAATATATTCCAAAGTACCGAATCCTAA
Done.