Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020255.1 Corchorus olitorius cultivar O-4 contig20288, 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: 7231
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Found at i:101 original size:15 final size:15
Alignment explanation
Indices: 81--112 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
71 GTTCAACTAA
81 TTTTTTTTGGTATAG
1 TTTTTTTTGGTATAG
*
96 TTTTTTTTGGTGTAG
1 TTTTTTTTGGTATAG
111 TT
1 TT
113 CTATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.00, G:0.22, T:0.69
Consensus pattern (15 bp):
TTTTTTTTGGTATAG
Found at i:463 original size:203 final size:201
Alignment explanation
Indices: 96--609 Score: 904
Period size: 203 Copynumber: 2.5 Consensus size: 201
86 TTTGGTATAG
* *
96 TTTTTTTTGGTGTAGTTCTATATATATAATAGTAATGTGTTATATCTTATTCACTACAACTTTGT
1 TTTTTTTTGGTATAG-T-TATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
161 TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATAT
64 TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATAT
226 CTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATG
129 CTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAAT-AATCAACCACTAATG
*
291 TTCTAACTAC
193 TAC-AACTAC
*
301 TTTTTTTTGGTATAGTTATATATATAATAGTATTGTGTTGTATCTTATTCACTACAACTTTGTTA
1 TTTTTTTTGGTATAGTTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTA
*
366 GTAATCTTAAACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATATCT
66 GTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATATCT
431 TTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAATCAACCACTAATGTAC
131 TTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAATCAACCACTAATGTAC
496 AACTAC
196 AACTAC
* * * *
502 -TTTTTTTGGTATTGTTTTATATATAATAATAATGTGTTGTATCTTATTTACTACAACTTTGTTA
1 TTTTTTTTGGTATAGTTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTA
566 GTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAA
66 GTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAA
610 GTTATTAAGC
Statistics
Matches: 298, Mismatches: 11, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
200 102 0.34
201 6 0.02
202 17 0.06
203 158 0.53
204 1 0.00
205 14 0.05
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (201 bp):
TTTTTTTTGGTATAGTTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTA
GTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATATCT
TTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAATCAACCACTAATGTAC
AACTAC
Found at i:1168 original size:36 final size:36
Alignment explanation
Indices: 1121--1190 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1111 GAGATTTTGG
* *
1121 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
1157 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
1191 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.