Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001027.1 Corchorus olitorius cultivar O-4 contig01027, 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, 777
Length: 1295
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Found at i:82 original size:28 final size:28
Alignment explanation
Indices: 45--117 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
35 TGTATTGACT
45 AAAAAGAAATATTGTTTTGTTGGCCAAA
1 AAAAAGAAATATTGTTTTGTTGGCCAAA
73 AAAAAGAAATATTGTTTTGTTGGCCAAA
1 AAAAAGAAATATTGTTTTGTTGGCCAAA
101 AAAAAGAAATATTGTTT
1 AAAAAGAAATATTGTTT
118 CCTTAATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.33
Consensus pattern (28 bp):
AAAAAGAAATATTGTTTTGTTGGCCAAA
Found at i:510 original size:202 final size:203
Alignment explanation
Indices: 126--535 Score: 709
Period size: 202 Copynumber: 2.0 Consensus size: 203
116 TTCCTTAATA
* *
126 ATAAATAAATTGGATCTTAATATCTTTTATATTTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
*
191 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAGTA
66 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAATA
*
256 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTT-AAAAATT-ATAACATT
131 ATGTATTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTTAAAAAATTAATAACATT
319 CACCATTG
196 CACCATTG
*
327 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAATTTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
392 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTGGGTATAGTTTTATATATATAATAA
65 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTT-GGTATAGTTCTATATATATAATAA
*
457 TAATGTATTGTATCTTATTCACTACAACTTTGTTAGTAATTTTAGAC-TTAAAAAATTAATAACA
129 TAATGTATTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTTAAAAAATTAATAACA
521 TTCACCATTG
194 TTCACCATTG
531 ATAAA
1 ATAAA
536 GTTATTAAGC
Statistics
Matches: 197, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
201 15 0.08
202 87 0.44
203 74 0.38
204 21 0.11
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.45
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAATA
ATGTATTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTTAAAAAATTAATAACATT
CACCATTG
Found at i:1089 original size:36 final size:36
Alignment explanation
Indices: 1042--1111 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1032 GAGATTTTGG
* *
1042 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
1078 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
1112 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.