Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005161.1 Corchorus capsularis cultivar CVL-1 contig05179, 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: 2961
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:536 original size:39 final size:39
Alignment explanation
Indices: 493--584 Score: 148
Period size: 39 Copynumber: 2.3 Consensus size: 39
483 TCATAAGTAG
* *
493 CATGATTCAATTCAACTGGCAACTCTTCCCATATCGCCT
1 CATGATTCAATTCAACTGGCAACTCTTCCAATATCACCT
532 CATGATTCAATTCAACTGGCAACTCTTCCAATATCACCT
1 CATGATTCAATTCAACTGGCAACTCTTCCAATATCACCT
*
571 CATTATTCATATTC
1 CATGATTCA-ATTC
585 TTGTTTTGAC
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 45 0.92
40 4 0.08
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (39 bp):
CATGATTCAATTCAACTGGCAACTCTTCCAATATCACCT
Found at i:1225 original size:7 final size:7
Alignment explanation
Indices: 1213--1247 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
1203 CAGGGGAAGT
1213 CAAGAAA
1 CAAGAAA
1220 CAAGAAA
1 CAAGAAA
1227 CAAGAAAA
1 CAAG-AAA
1235 TCAAGAAA
1 -CAAGAAA
1243 CAAGA
1 CAAGA
1248 GAAGGTATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 16 0.62
8 6 0.23
9 4 0.15
ACGTcount: A:0.69, C:0.14, G:0.14, T:0.03
Consensus pattern (7 bp):
CAAGAAA
Found at i:1777 original size:34 final size:34
Alignment explanation
Indices: 1734--1802 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1724 TTAGAATGCA
1734 ATTGAAGCTGCTATTAAGTAGAGAACAATTCCCT
1 ATTGAAGCTGCTATTAAGTAGAGAACAATTCCCT
*
1768 ATTGAAGCTGCTATTAAGTAGAGAAGAATTCCCT
1 ATTGAAGCTGCTATTAAGTAGAGAACAATTCCCT
1802 A
1 A
1803 ACTCTATCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (34 bp):
ATTGAAGCTGCTATTAAGTAGAGAACAATTCCCT
Found at i:2163 original size:19 final size:18
Alignment explanation
Indices: 2139--2182 Score: 72
Period size: 17 Copynumber: 2.4 Consensus size: 18
2129 TTGAGTATGC
2139 ATAAAAATCTAATTATTAT
1 ATAAAAAT-TAATTATTAT
2158 ATAAAAA-TAATTATTAT
1 ATAAAAATTAATTATTAT
2175 ATAAAAAT
1 ATAAAAAT
2183 AAAATATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 17 0.71
19 7 0.29
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAAAATTAATTATTAT
Found at i:2170 original size:17 final size:17
Alignment explanation
Indices: 2148--2184 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
2138 CATAAAAATC
2148 TAATTATTATATAAAAA
1 TAATTATTATATAAAAA
2165 TAATTATTATATAAAAA
1 TAATTATTATATAAAAA
2182 TAA
1 TAA
2185 AATATGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTATTATATAAAAA
Found at i:2434 original size:21 final size:21
Alignment explanation
Indices: 2409--2455 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2399 CTAATTATAT
2409 TTTCATCTATACAGTATCTAA
1 TTTCATCTATACAGTATCTAA
* * * *
2430 TTTCATCTGTATAGTGTTTAA
1 TTTCATCTATACAGTATCTAA
2451 TTTCA
1 TTTCA
2456 CCATTTCAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.49
Consensus pattern (21 bp):
TTTCATCTATACAGTATCTAA
Done.