Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006357.1 Corchorus capsularis cultivar CVL-1 contig06378, 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: 4339
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2201 original size:32 final size:32
Alignment explanation
Indices: 2125--2272 Score: 171
Period size: 32 Copynumber: 4.7 Consensus size: 32
2115 TGCAGTTTTT
2125 TCGGGTCAT-CGGGT-TACGGGTCA-TCTGGGT-
1 TCGGGTCATACGGGTCT-CGGGTCATTC-GGGTC
* *
2155 TCGGGTTATTCGGGTCTCGGGTCATTCGGGTC
1 TCGGGTCATACGGGTCTCGGGTCATTCGGGTC
*
2187 TCGGGTCATACGGGTTTCGGGTCATTCGGGTC
1 TCGGGTCATACGGGTCTCGGGTCATTCGGGTC
* * *
2219 TTGGGTCATTCGGGTTTCGGGTCATTCGGGTC
1 TCGGGTCATACGGGTCTCGGGTCATTCGGGTC
*
2251 TCGGGTC-TACCGGGTCTTGGGT
1 TCGGGTCATA-CGGGTCTCGGGT
2273 TGGGCGGGTT
Statistics
Matches: 103, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
30 8 0.08
31 17 0.17
32 78 0.76
ACGTcount: A:0.07, C:0.21, G:0.39, T:0.33
Consensus pattern (32 bp):
TCGGGTCATACGGGTCTCGGGTCATTCGGGTC
Found at i:2225 original size:48 final size:46
Alignment explanation
Indices: 2127--2272 Score: 172
Period size: 48 Copynumber: 3.1 Consensus size: 46
2117 CAGTTTTTTC
* *
2127 GGGTCA-TCGGGTTACGGGTCATCTGGG-TTCGGGTTATTCGGGTCTC
1 GGGTCATTCGGGTT-CGGGTCATC-GGGTTTCGGGTCATTCGGGTCTT
2173 GGGTCATTCGGGTCTCGGGTCATACGGGTTTCGGGTCATTCGGGTCTT
1 GGGTCATTCGGGT-TCGGGTCAT-CGGGTTTCGGGTCATTCGGGTCTT
* *
2221 GGGTCATTCGGGTTTCGGGTCATTCGGGTCTCGGGTC-TACCGGGTCTT
1 GGGTCATTCGGG-TTCGGGTCA-TCGGGTTTCGGGTCAT-TCGGGTCTT
2269 GGGT
1 GGGT
2273 TGGGCGGGTT
Statistics
Matches: 89, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
46 6 0.07
47 18 0.20
48 63 0.71
49 2 0.02
ACGTcount: A:0.08, C:0.21, G:0.39, T:0.33
Consensus pattern (46 bp):
GGGTCATTCGGGTTCGGGTCATCGGGTTTCGGGTCATTCGGGTCTT
Found at i:2267 original size:16 final size:16
Alignment explanation
Indices: 2125--2257 Score: 175
Period size: 16 Copynumber: 8.4 Consensus size: 16
2115 TGCAGTTTTT
2125 TCGGGTCA-TCGGGT-
1 TCGGGTCATTCGGGTC
2139 TACGGGTCA-TCTGGGT-
1 T-CGGGTCATTC-GGGTC
*
2155 TCGGGTTATTCGGGTC
1 TCGGGTCATTCGGGTC
2171 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTC
* *
2187 TCGGGTCATACGGGTT
1 TCGGGTCATTCGGGTC
2203 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTC
* *
2219 TTGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTC
2235 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTC
2251 TCGGGTC
1 TCGGGTC
2258 TACCGGGTCT
Statistics
Matches: 105, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
14 1 0.01
15 19 0.18
16 85 0.81
ACGTcount: A:0.08, C:0.21, G:0.38, T:0.33
Consensus pattern (16 bp):
TCGGGTCATTCGGGTC
Found at i:2743 original size:21 final size:22
Alignment explanation
Indices: 2718--2766 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
2708 TAGCCTATTT
2718 ATAATAT-GTAAAATCATAACA
1 ATAATATGGTAAAATCATAACA
*
2739 ATAAT-TGGTAAAATTATAACA
1 ATAATATGGTAAAATCATAACA
2760 ATAATAT
1 ATAATAT
2767 AAATTGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (22 bp):
ATAATATGGTAAAATCATAACA
Found at i:2908 original size:32 final size:32
Alignment explanation
Indices: 2870--2983 Score: 135
Period size: 32 Copynumber: 3.6 Consensus size: 32
2860 TCGGGTTAAT
* *
2870 GTCTCGGGTTATTCGGGTTTCGGGTGATAC-GG
1 GTCTCGGGTCATTCGGGTTTCGGGTCAT-CTGG
2902 GTCTCGGGTCATTCGGGTTTCGGGTCATCTGG
1 GTCTCGGGTCATTCGGGTTTCGGGTCATCTGG
* *
2934 GT-TACGGGTCATTCGGGTCTCGGGTCAGCT-G
1 GTCT-CGGGTCATTCGGGTTTCGGGTCATCTGG
*
2965 GTTTGCGGGTCATTCGGGT
1 GTCT-CGGGTCATTCGGGT
2984 CACGGGTTAG
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
31 5 0.07
32 69 0.93
ACGTcount: A:0.08, C:0.19, G:0.39, T:0.33
Consensus pattern (32 bp):
GTCTCGGGTCATTCGGGTTTCGGGTCATCTGG
Found at i:2926 original size:48 final size:47
Alignment explanation
Indices: 2873--2990 Score: 139
Period size: 48 Copynumber: 2.5 Consensus size: 47
2863 GGTTAATGTC
* * * *
2873 TCGGGTTATTCGGGTTTCGGGTGATACGGGTCTCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTTACGGGTCATACGGGTCTCGGGTCA-GCGGGTT
* *
2921 TCGGGTCA-TCTGGGTTACGGGTCATTCGGGTCTCGGGTCAGCTGGTT
1 TCGGGTCATTC-GGGTTACGGGTCATACGGGTCTCGGGTCAGCGGGTT
*
2968 TGCGGGTCATTCGGGTCACGGGT
1 T-CGGGTCATTCGGGTTACGGGT
2991 TAGTTTGGTC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
47 8 0.13
48 50 0.83
49 2 0.03
ACGTcount: A:0.08, C:0.19, G:0.40, T:0.32
Consensus pattern (47 bp):
TCGGGTCATTCGGGTTACGGGTCATACGGGTCTCGGGTCAGCGGGTT
Found at i:2990 original size:16 final size:16
Alignment explanation
Indices: 2873--2983 Score: 118
Period size: 16 Copynumber: 6.9 Consensus size: 16
2863 GGTTAATGTC
*
2873 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* * *
2889 TCGGGTGATACGGGTC
1 TCGGGTCATTCGGGTT
2905 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
2921 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
2937 ACGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
* *
2953 TCGGGTCA-GCTGGTT
1 TCGGGTCATTCGGGTT
2968 TGCGGGTCATTCGGGT
1 T-CGGGTCATTCGGGT
2984 CACGGGTTAG
Statistics
Matches: 77, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
15 7 0.09
16 64 0.83
17 6 0.08
ACGTcount: A:0.08, C:0.19, G:0.40, T:0.33
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Done.