Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016299.1 Corchorus olitorius cultivar O-4 contig16332, 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: 15195
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:287 original size:31 final size:31
Alignment explanation
Indices: 158--294 Score: 136
Period size: 31 Copynumber: 4.5 Consensus size: 31
148 TCTTAACTGA
*
158 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTGAAATAGAAAACG
*
189 TCATATCCTTAATTGCTTGAAATCA-AAAACG
1 TTATATCCTTAATTGCTTGAAAT-AGAAAACG
* ** * * *
220 TTATATCATTAATTGCTTG-TTTTG-TAACA
1 TTATATCCTTAATTGCTTGAAATAGAAAACG
** *
249 TTATATCCTTAATTGCTTGTGATAGCAAACG
1 TTATATCCTTAATTGCTTGAAATAGAAAACG
*
280 TTATATCCTAAATTG
1 TTATATCCTTAATTG
295 ATTATTCAAC
Statistics
Matches: 86, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
29 21 0.24
30 3 0.03
31 62 0.72
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAATAGAAAACG
Found at i:1212 original size:187 final size:187
Alignment explanation
Indices: 897--1269 Score: 737
Period size: 187 Copynumber: 2.0 Consensus size: 187
887 GTCCTCATTG
897 AGCGCCACATGGCATTTGGTTTCTTTGACAAGTGTCAACAGTTAATTTTCTAATATTTTGTTTAT
1 AGCGCCACATGGCATTTGGTTTCTTTGACAAGTGTCAACAGTTAATTTTCTAATATTTTGTTTAT
962 TATATTTTTATTCATTTAATTGGGAAAAATTAAAAGACATTCATCCCCTTTCCTATATAAAATAA
66 TATATTTTTATTCATTTAATTGGGAAAAATTAAAAGACATTCATCCCCTTTCCTATATAAAATAA
1027 ATTATCAAATAATTATAAATTTGTTATGAATATACATGTATGTTGTGGATGTCTATA
131 ATTATCAAATAATTATAAATTTGTTATGAATATACATGTATGTTGTGGATGTCTATA
*
1084 AGCGCCACATGGCATTTGGTTTCTTTGACAAGTGTCAATAGTTAATTTTCTAATATTTTGTTTAT
1 AGCGCCACATGGCATTTGGTTTCTTTGACAAGTGTCAACAGTTAATTTTCTAATATTTTGTTTAT
1149 TATATTTTTATTCATTTAATTGGGAAAAATTAAAAGACATTCATCCCCTTTCCTATATAAAATAA
66 TATATTTTTATTCATTTAATTGGGAAAAATTAAAAGACATTCATCCCCTTTCCTATATAAAATAA
1214 ATTATCAAATAATTATAAATTTGTTATGAATATACATGTATGTTGTGGATGTCTAT
131 ATTATCAAATAATTATAAATTTGTTATGAATATACATGTATGTTGTGGATGTCTAT
1270 GAATCTAATT
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
187 185 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (187 bp):
AGCGCCACATGGCATTTGGTTTCTTTGACAAGTGTCAACAGTTAATTTTCTAATATTTTGTTTAT
TATATTTTTATTCATTTAATTGGGAAAAATTAAAAGACATTCATCCCCTTTCCTATATAAAATAA
ATTATCAAATAATTATAAATTTGTTATGAATATACATGTATGTTGTGGATGTCTATA
Found at i:1616 original size:28 final size:30
Alignment explanation
Indices: 1545--1605 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
1535 TTGTGTTGAT
* *
1545 TCAATAGTTATTTTTTTGTGTATTATTAGTA
1 TCAATA-TTAATTTTTTGTGTATTATTAATA
1576 TGCAATATTAATTTTTTGTGTATTA-TAATA
1 T-CAATATTAATTTTTTGTGTATTATTAATA
1606 ATAAATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 4 0.15
31 18 0.67
32 5 0.19
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (30 bp):
TCAATATTAATTTTTTGTGTATTATTAATA
Found at i:2589 original size:29 final size:31
Alignment explanation
Indices: 2526--2592 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2516 TCTTACGGAC
*
2526 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAACTGCTCGCTTTTCGTAACGT
*
2557 TATATCCTTAACTGCTTG-TTTT-GTAACGT
1 TATATCCTTAACTGCTCGCTTTTCGTAACGT
2586 TATATCC
1 TATATCC
2593 CAAATTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (31 bp):
TATATCCTTAACTGCTCGCTTTTCGTAACGT
Found at i:3320 original size:8 final size:8
Alignment explanation
Indices: 3304--3335 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
3294 TTTTCATTAG
*
3304 TTGAGCAC
1 TTGATCAC
3312 TTGATCAC
1 TTGATCAC
3320 TTGATCAC
1 TTGATCAC
3328 TTGATCAC
1 TTGATCAC
3336 ACATATATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (8 bp):
TTGATCAC
Found at i:12441 original size:12 final size:12
Alignment explanation
Indices: 12424--12448 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12414 AGTTGTAATA
12424 TTTATTATTATT
1 TTTATTATTATT
12436 TTTATTATTATT
1 TTTATTATTATT
12448 T
1 T
12449 ATTAATGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTATTATT
Done.