Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012293.1 Corchorus capsularis cultivar CVL-1 contig12314, 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: 17613
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1785 original size:27 final size:28
Alignment explanation
Indices: 1711--1790 Score: 144
Period size: 28 Copynumber: 2.9 Consensus size: 28
1701 TGATTTATAA
1711 AAATTTTAAAAGGTATAATTATAAATAC
1 AAATTTTAAAAGGTATAATTATAAATAC
1739 AAATTTTAAAAGGTATAATTATAAATAC
1 AAATTTTAAAAGGTATAATTATAAATAC
*
1767 AAATTTT-AAAGGTATAATTCTAAA
1 AAATTTTAAAAGGTATAATTATAAA
1791 AGTAAAGTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 16 0.31
28 35 0.69
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (28 bp):
AAATTTTAAAAGGTATAATTATAAATAC
Found at i:3171 original size:7 final size:7
Alignment explanation
Indices: 3159--3196 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
3149 AATTTAATGC
3159 ATATAAT
1 ATATAAT
3166 ATATAAT
1 ATATAAT
3173 ATATAAT
1 ATATAAT
*
3180 ATCT-AT
1 ATATAAT
3186 ATAT-AT
1 ATATAAT
3192 ATATA
1 ATATA
3197 TGCATATACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 11 0.39
7 17 0.61
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (7 bp):
ATATAAT
Found at i:10861 original size:19 final size:18
Alignment explanation
Indices: 10828--10863 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10818 TTGAAATAAT
10828 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
10846 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
10864 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:16280 original size:10 final size:10
Alignment explanation
Indices: 16265--16289 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16255 TAACTCCAAT
16265 TATGGACTTA
1 TATGGACTTA
16275 TATGGACTTA
1 TATGGACTTA
16285 TATGG
1 TATGG
16290 GCTGAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (10 bp):
TATGGACTTA
Found at i:16442 original size:19 final size:18
Alignment explanation
Indices: 16409--16445 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
16399 TTGAAATAAT
16409 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
16427 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
16446 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:16945 original size:61 final size:61
Alignment explanation
Indices: 16850--16974 Score: 250
Period size: 61 Copynumber: 2.0 Consensus size: 61
16840 CCAAAGATCA
16850 ATCAATAATAAGTATCATCATTCTTAAGTAGCCATAATCAAAGTAGCTCTAATCACTTACC
1 ATCAATAATAAGTATCATCATTCTTAAGTAGCCATAATCAAAGTAGCTCTAATCACTTACC
16911 ATCAATAATAAGTATCATCATTCTTAAGTAGCCATAATCAAAGTAGCTCTAATCACTTACC
1 ATCAATAATAAGTATCATCATTCTTAAGTAGCCATAATCAAAGTAGCTCTAATCACTTACC
16972 ATC
1 ATC
16975 CTTTACTCTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (61 bp):
ATCAATAATAAGTATCATCATTCTTAAGTAGCCATAATCAAAGTAGCTCTAATCACTTACC
Done.