Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020910.1 Corchorus olitorius cultivar O-4 contig20943, 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: 2434
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Found at i:94 original size:36 final size:36
Alignment explanation
Indices: 1--246 Score: 334
Period size: 36 Copynumber: 6.9 Consensus size: 36
*
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATTCA
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCA
* *
37 GGGCGGTC-TTTCTTCAGTTTATTTCAGTTGATCCA
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCA
* *
72 GGGCAATCTTTTCTTCAATTTATTTCAATTGATCCA
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCA
*
108 GGGCGATCTTTTCTTCAGTTTATTTCACTTGATCCA
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCA
*
144 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCTA
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCA
* * * * * *
180 GGACGATC-TTTCCTCAATTTACTTCAGTAGATCCA
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCA
* * *
215 GGGCGATCTTCTCTGCAGTTTATTTCGATTGA
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGA
247 CTGCAAAATG
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
35 59 0.33
36 121 0.67
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (36 bp):
GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCA
Found at i:197 original size:107 final size:107
Alignment explanation
Indices: 1--246 Score: 350
Period size: 107 Copynumber: 2.3 Consensus size: 107
* * *
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATTCAGGGCGGTCTTTCTTCAGTTTATTTCAGTT
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAATT
* * * *
66 GATCCAGGGCAATCTTTTCTTCAATTTATTTCAATTGATCCA
66 GATCCAGGACAATCTTTTCCTCAATTTACTTCAATAGATCCA
*
108 GGGCGATCTTTTCTTCAGTTTATTTCACTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAAT
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATC-TTTCTTCAGTTTATTTCAAT
* * *
173 TGATCTAGGACGATC-TTTCCTCAATTTACTTCAGTAGATCCA
65 TGATCCAGGACAATCTTTTCCTCAATTTACTTCAATAGATCCA
* * *
215 GGGCGATCTTCTCTGCAGTTTATTTCGATTGA
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGA
247 CTGCAAAATG
Statistics
Matches: 123, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
107 92 0.75
108 31 0.25
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (107 bp):
GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAATT
GATCCAGGACAATCTTTTCCTCAATTTACTTCAATAGATCCA
Found at i:237 original size:71 final size:71
Alignment explanation
Indices: 1--246 Score: 350
Period size: 71 Copynumber: 3.5 Consensus size: 71
*
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGAT-TCAGGGCGGTCTTTCTTCAGTTTATTTCAGT
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCT-AGGGCGATCTTTCTTCAGTTTATTTCAGT
65 TGATCCA
65 TGATCCA
* * * *
72 GGGCAATCTTTTCTTCAATTTATTTCAATTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCACT
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCTAGGGCGATC-TTTCTTCAGTTTATTTCAGT
137 TGATCCA
65 TGATCCA
* * * * *
144 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCTAGGACGATCTTTCCTCAATTTACTTCAGTA
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCTAGGGCGATCTTTCTTCAGTTTATTTCAGTT
209 GATCCA
66 GATCCA
* * *
215 GGGCGATCTTCTCTGCAGTTTATTTCGATTGA
1 GGGCGATCTTTTCTTCAGTTTATTTCAATTGA
247 CTGCAAAATG
Statistics
Matches: 156, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
71 90 0.58
72 66 0.42
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (71 bp):
GGGCGATCTTTTCTTCAGTTTATTTCAATTGATCTAGGGCGATCTTTCTTCAGTTTATTTCAGTT
GATCCA
Found at i:550 original size:30 final size:30
Alignment explanation
Indices: 510--1384 Score: 1074
Period size: 30 Copynumber: 29.1 Consensus size: 30
500 CTTTATCAGT
*
510 TTTATTTTAATCCTGTTTGAGGATCATTAC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * *
540 CTTATGTTAATCCTGCTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * *
570 TTTATTTTAATCATGTTTGAGGAGCACTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
600 TTTGTGTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * *
630 TTTATGTTAATCCTGGTTGAGGATCAATGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
660 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
690 TTCATTTTTAATCTTGTTTGAGGATCATTGC
1 TTTA-TTTTAATCCTGTTTGAGGATCATTGC
* * * *
721 TTCATTTAAATCCTGGTTGAGGATCAATGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
751 TTTATTTTAATCCTGTTTGAGGATCAATGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
781 TTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * *
811 TTGATTTTAATCCTGGTTGAGGATAATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * *
841 TTCATTTTTAATCCTGTTTGAGGAACAATGC
1 TTTA-TTTTAATCCTGTTTGAGGATCATTGC
*
872 TTTATTTTAATCATGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
902 TTTATTTTAATCCTGTTTGAGGATCGTTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
932 TTTATTTTAATCCTGTTTGAAGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
962 TTTATGTTAATCTTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * * *
992 TTTATGTTAATCCTGTTTGAAGATCCTTAC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
1022 TTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
1052 TTTATTATAATCCCGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
1082 TTTATGTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* **
1112 TTTATTCTAATCCTAG-TTGAGGATCATCAC
1 TTTATTTTAATCCT-GTTTGAGGATCATTGC
* *
1142 TTCATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * *
1172 TTTGTTTTAATCCTGGTTAAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
1202 TTCATTTTAATCCTGATTGAGGAT-ATTCGC
1 TTTATTTTAATCCTGTTTGAGGATCATT-GC
** *
1232 TCCATTTTAATCCTGGTTGAGGAT-ATTTGC
1 TTTATTTTAATCCTGTTTGAGGATCA-TTGC
* * * **
1262 ATCATTTTAATCCTGGTTGAGGATTGTTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * * *
1292 TTTATTTTAATCATGGTTGAAGACCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
1322 TTTATTTTAATCCTGGTTGAGGATCATCGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * * *
1352 TATATTTTTATCCTGATTT-AGGATTATTAC
1 TTTATTTTAATCCTG-TTTGAGGATCATTGC
1382 TTT
1 TTT
1385 GGTTTATTTG
Statistics
Matches: 736, Mismatches: 101, Indels: 16
0.86 0.12 0.02
Matches are distributed among these distances:
29 4 0.01
30 674 0.92
31 58 0.08
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (30 bp):
TTTATTTTAATCCTGTTTGAGGATCATTGC
Found at i:1882 original size:27 final size:26
Alignment explanation
Indices: 1844--1900 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 26
1834 TTTCCAAAAA
*
1844 TTCAGGGGCATTTTGGCCATTTGTACG
1 TTCAGGGGCATTTAGGCCATTT-TACG
* *
1871 TTCAGGGGCATTTAGGTCATTTTAGG
1 TTCAGGGGCATTTAGGCCATTTTACG
1897 TTCA
1 TTCA
1901 CTTTTAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.18, C:0.16, G:0.28, T:0.39
Consensus pattern (26 bp):
TTCAGGGGCATTTAGGCCATTTTACG
Done.