Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013023.1 Corchorus olitorius cultivar O-4 contig13056, 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: 5510
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Found at i:1242 original size:21 final size:20
Alignment explanation
Indices: 1197--1244 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
1187 CATATAAGTT
*
1197 TTTGGGTATAATGAGATATAT
1 TTTGGGTATAA-GAGATATAC
1218 TTTGGGTATAA-AGTATATTAC
1 TTTGGGTATAAGAG-ATA-TAC
1239 TTTGGG
1 TTTGGG
1245 GATACTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 19 0.79
ACGTcount: A:0.29, C:0.02, G:0.25, T:0.44
Consensus pattern (20 bp):
TTTGGGTATAAGAGATATAC
Found at i:1324 original size:224 final size:221
Alignment explanation
Indices: 885--1455 Score: 930
Period size: 224 Copynumber: 2.6 Consensus size: 221
875 TTCAATTAAT
* * *
885 ATATGAATTAAAACACCTTTTAAAGTCAATTTTGGGTATATGAGAAAAAATGTCAATCACTATTG
1 ATATGGATTAAAGCA-CTTTTAAA-TCAATTTTGGATATATGAGAAAAAATGTCAATCACTATTG
*
950 AATTTGGGGATGG-GCATATAAGTTTTTGGGTATAATGAAATATATTTTGGGTATAAAGTATATT
64 AATTTGGGGATGGTGCATATAAGTTTTTGGGTATAATGAGATATATTTTGGGTATAAAGTATATT
* *
1014 ACTTTGGGGATACTGAATTTTGCATTATGTTTAATTATTAGATGGCACTGAAATTCATATAGACG
129 ACTTTGGGGATACTGAATTTTGCATTATGTTTAATTATTAAATGGCACTGAAATCCATATAGACG
*
1079 GGTTTTATTCAATAAATTAGAATGAAAA
194 GGGTTTATTCAATAAATTAGAATGAAAA
*
1107 ATATGGATTAAAGCACTATTTCAAATCAATTTTGGATATATGAGAAAAAATGCCAATCACTATTG
1 ATATGGATTAAAGCACT-TTT-AAATCAATTTTGGATATATGAGAAAAAATGTCAATCACTATTG
*
1172 AATTTAGGGATGGTGCATATAAGTTTTTGGGTATAATGAGATATATTTTGGGTATAAAGTATATT
64 AATTTGGGGATGGTGCATATAAGTTTTTGGGTATAATGAGATATATTTTGGGTATAAAGTATATT
* *
1237 ACTTTGGGGATACT-ATTTGTTTGCATTTTGTTTAATTATTAAATGGCACTGAAATCCATATAGA
129 ACTTTGGGGATACTGA-AT-TTTGCATTATGTTTAATTATTAAATGGCACTGAAATCCATATAGA
*
1301 CGGGGTTTATTCAATTAATTAGAATGAAAA
192 CGGGGTTTATTCAATAAATTAGAATGAAAA
*
1331 ATATGGATTGAAGCACTTTTTAAATCCAATTTTGGATATATGAGAAAAAATGTCAATCACTATTG
1 ATATGGATTAAAGCAC-TTTTAAAT-CAATTTTGGATATATGAGAAAAAATGTCAATCACTATTG
*
1396 AATTTGGGGATGGTGCATATAAGTTTTTGGGTATAATGAGATATATTTTGGGTATGAAGT
64 AATTTGGGGATGGTGCATATAAGTTTTTGGGTATAATGAGATATATTTTGGGTATAAAGT
1456 TACCACGTCG
Statistics
Matches: 326, Mismatches: 16, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
221 2 0.01
222 67 0.21
223 72 0.22
224 184 0.56
225 1 0.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (221 bp):
ATATGGATTAAAGCACTTTTAAATCAATTTTGGATATATGAGAAAAAATGTCAATCACTATTGAA
TTTGGGGATGGTGCATATAAGTTTTTGGGTATAATGAGATATATTTTGGGTATAAAGTATATTAC
TTTGGGGATACTGAATTTTGCATTATGTTTAATTATTAAATGGCACTGAAATCCATATAGACGGG
GTTTATTCAATAAATTAGAATGAAAA
Found at i:3626 original size:24 final size:24
Alignment explanation
Indices: 3594--3642 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3584 AAAACGAAGC
* *
3594 AGAAAACGGGGAAGAAGAGAATAA
1 AGAAAACGGAGAAGAAAAGAATAA
3618 AGAAAACGGAGAAGAAAAGAATAA
1 AGAAAACGGAGAAGAAAAGAATAA
3642 A
1 A
3643 AAATAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.63, C:0.04, G:0.29, T:0.04
Consensus pattern (24 bp):
AGAAAACGGAGAAGAAAAGAATAA
Found at i:5143 original size:27 final size:27
Alignment explanation
Indices: 5113--5178 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
5103 TGAATTGAAT
5113 TCAAAATTCCATTAGAAAAGACAGAAC
1 TCAAAATTCCATTAGAAAAGACAGAAC
5140 TCAAAATTCCATTAGAAAAGACAGAAC
1 TCAAAATTCCATTAGAAAAGACAGAAC
5167 TCAAAATTCCAT
1 TCAAAATTCCAT
5179 CAAACCTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.21
Consensus pattern (27 bp):
TCAAAATTCCATTAGAAAAGACAGAAC
Done.