Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002458.1 Corchorus olitorius cultivar O-4 contig02458, 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, 610
Length: 1017
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Found at i:163 original size:8 final size:8
Alignment explanation
Indices: 150--237 Score: 54
Period size: 8 Copynumber: 9.8 Consensus size: 8
140 TCAAAATGAC
150 ATATAAAA
1 ATATAAAA
158 ATATAAAA
1 ATATAAAA
166 ATATAATGAA
1 ATATAA--AA
176 ATCA-AAATGA
1 AT-ATAAA--A
186 CATATAAAA
1 -ATATAAAA
195 ATATAATGAA
1 ATATAA--AA
205 ATCA-AAATGA
1 AT-ATAAA--A
215 CATATAAAA
1 -ATATAAAA
224 ATATAAAA
1 ATATAAAA
232 ATATAA
1 ATATAA
238 TGAAATCAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
8 36 0.55
9 2 0.03
10 16 0.24
11 12 0.18
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (8 bp):
ATATAAAA
Found at i:190 original size:37 final size:37
Alignment explanation
Indices: 140--266 Score: 198
Period size: 37 Copynumber: 3.6 Consensus size: 37
130 CAGAGTCAAT
140 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
177 TCAAAATGAC--------ATATAAAAATATAATGAAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
206 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
243 TCAAAATGACATATAAAAATATAA
1 TCAAAATGACATATAAAAATATAA
267 TGAAATCAAA
Statistics
Matches: 82, Mismatches: 0, Indels: 16
0.84 0.00 0.16
Matches are distributed among these distances:
29 29 0.35
37 53 0.65
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (37 bp):
TCAAAATGACATATAAAAATATAAAAATATAATGAAA
Found at i:191 original size:29 final size:29
Alignment explanation
Indices: 158--291 Score: 196
Period size: 29 Copynumber: 4.3 Consensus size: 29
148 ACATATAAAA
158 ATATAAAAATATAATGAAATCAAAATGAC
1 ATATAAAAATATAATGAAATCAAAATGAC
187 ATATAAAAATATAATGAAATCAAAATGAC
1 ATATAAAAATATAATGAAATCAAAATGAC
216 ATATAAAAATATAAAAATATAATGAAATCAAAATGAC
1 --------ATATAAAAATATAATGAAATCAAAATGAC
253 ATATAAAAATATAATGAAATCAAAATGAC
1 ATATAAAAATATAATGAAATCAAAATGAC
282 ATATAAAAAT
1 ATATAAAAAT
292 GACATATAAT
Statistics
Matches: 97, Mismatches: 0, Indels: 16
0.86 0.00 0.14
Matches are distributed among these distances:
29 68 0.70
37 29 0.30
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (29 bp):
ATATAAAAATATAATGAAATCAAAATGAC
Found at i:246 original size:66 final size:66
Alignment explanation
Indices: 140--291 Score: 304
Period size: 66 Copynumber: 2.3 Consensus size: 66
130 CAGAGTCAAT
140 TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
205 A
66 A
206 TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
271 A
66 A
272 TCAAAATGACATATAAAAAT
1 TCAAAATGACATATAAAAAT
292 GACATATAAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 86 1.00
ACGTcount: A:0.63, C:0.07, G:0.06, T:0.24
Consensus pattern (66 bp):
TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
A
Found at i:292 original size:13 final size:13
Alignment explanation
Indices: 274--300 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
264 TAATGAAATC
274 AAAATGACATATA
1 AAAATGACATATA
287 AAAATGACATATA
1 AAAATGACATATA
300 A
1 A
301 TTAAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (13 bp):
AAAATGACATATA
Done.