Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002452.1 Corchorus olitorius cultivar O-4 contig02452, 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, 607
Length: 1012
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Found at i:112 original size:8 final size:8
Alignment explanation
Indices: 92--125 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
82 AAGTTTATTG
92 ATAATAT-
1 ATAATATA
99 ATAATATA
1 ATAATATA
107 ATAATATA
1 ATAATATA
115 ATAATATA
1 ATAATATA
123 ATA
1 ATA
126 TAACATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATATA
Found at i:115 original size:13 final size:13
Alignment explanation
Indices: 92--128 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
82 AAGTTTATTG
92 ATAAT-ATATAAT
1 ATAATAATATAAT
104 ATAATAATATAAT
1 ATAATAATATAAT
117 A-ATATAATATAA
1 ATA-ATAATATAA
129 CATTATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATAATATAAT
Found at i:279 original size:8 final size:8
Alignment explanation
Indices: 259--292 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
249 AAGTTTATTG
259 ATAATAT-
1 ATAATATA
266 ATAATATA
1 ATAATATA
274 ATAATATA
1 ATAATATA
282 ATAATATA
1 ATAATATA
290 ATA
1 ATA
293 TAACATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATATA
Found at i:282 original size:13 final size:13
Alignment explanation
Indices: 259--295 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
249 AAGTTTATTG
259 ATAAT-ATATAAT
1 ATAATAATATAAT
271 ATAATAATATAAT
1 ATAATAATATAAT
284 A-ATATAATATAA
1 ATA-ATAATATAA
296 CATTATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATAATATAAT
Found at i:306 original size:167 final size:167
Alignment explanation
Indices: 30--363 Score: 668
Period size: 167 Copynumber: 2.0 Consensus size: 167
20 AAGTGTAAGC
30 TCTTTTTAAAGATTTTTTTAAATAAAAATAATTGTTTTATCTTTTATATTATAAGTTTATTGATA
1 TCTTTTTAAAGATTTTTTTAAATAAAAATAATTGTTTTATCTTTTATATTATAAGTTTATTGATA
95 ATATATAATATAATAATATAATAATATAATATAACATTATTATCAATATATATAAAGATTGAATA
66 ATATATAATATAATAATATAATAATATAATATAACATTATTATCAATATATATAAAGATTGAATA
160 ATTGTTAAAAATTACTAACAAATTATTAATAGCGAAA
131 ATTGTTAAAAATTACTAACAAATTATTAATAGCGAAA
197 TCTTTTTAAAGATTTTTTTAAATAAAAATAATTGTTTTATCTTTTATATTATAAGTTTATTGATA
1 TCTTTTTAAAGATTTTTTTAAATAAAAATAATTGTTTTATCTTTTATATTATAAGTTTATTGATA
262 ATATATAATATAATAATATAATAATATAATATAACATTATTATCAATATATATAAAGATTGAATA
66 ATATATAATATAATAATATAATAATATAATATAACATTATTATCAATATATATAAAGATTGAATA
327 ATTGTTAAAAATTACTAACAAATTATTAATAGCGAAA
131 ATTGTTAAAAATTACTAACAAATTATTAATAGCGAAA
364 GAACAGTCTC
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 167 1.00
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (167 bp):
TCTTTTTAAAGATTTTTTTAAATAAAAATAATTGTTTTATCTTTTATATTATAAGTTTATTGATA
ATATATAATATAATAATATAATAATATAATATAACATTATTATCAATATATATAAAGATTGAATA
ATTGTTAAAAATTACTAACAAATTATTAATAGCGAAA
Done.