Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022217.1 Corchorus olitorius cultivar O-4 contig22250, 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: 2779
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:969 original size:12 final size:12
Alignment explanation
Indices: 952--977 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
942 CAGAAACTTA
952 TAGGGCCAAAGT
1 TAGGGCCAAAGT
964 TAGGGCCAAAGT
1 TAGGGCCAAAGT
976 TA
1 TA
978 TAGGTAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (12 bp):
TAGGGCCAAAGT
Found at i:1063 original size:100 final size:100
Alignment explanation
Indices: 951--1249 Score: 589
Period size: 100 Copynumber: 3.0 Consensus size: 100
941 TCAGAAACTT
951 ATAGGGCCAAAGTTAGGGCCAAAGTTATAGGTAAAGGGATTTTAAACTTTGGCCGTATAATGGAA
1 ATAGGGCCAAAGTTAGGGCCAAAGTTATAGGTAAAGGGATTTTAAACTTTGGCCGTATAATGGAA
1016 ATTTTCAGAAACAAATTTAATTCTTCCATTATAGC
66 ATTTTCAGAAACAAATTTAATTCTTCCATTATAGC
1051 ATAGGGCCAAAGTTAGGGCCAAAGTTATAGGTAAAGGGATTTTAAACTTTGGCCGTATAATGGAA
1 ATAGGGCCAAAGTTAGGGCCAAAGTTATAGGTAAAGGGATTTTAAACTTTGGCCGTATAATGGAA
1116 ATTTTCAGAAACAAATTTAATTCTTCCATTATAGC
66 ATTTTCAGAAACAAATTTAATTCTTCCATTATAGC
*
1151 ATAGGGCCAAAGTTAGGGCCAAAGTTATAGGTAAAGGGATTTTAAACTTTGGCCGTATAGTGGAA
1 ATAGGGCCAAAGTTAGGGCCAAAGTTATAGGTAAAGGGATTTTAAACTTTGGCCGTATAATGGAA
1216 ATTTTCAGAAACAAATTTAATTCTTCCATTATAG
66 ATTTTCAGAAACAAATTTAATTCTTCCATTATAG
1250 GGCCAAAGTT
Statistics
Matches: 198, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 198 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (100 bp):
ATAGGGCCAAAGTTAGGGCCAAAGTTATAGGTAAAGGGATTTTAAACTTTGGCCGTATAATGGAA
ATTTTCAGAAACAAATTTAATTCTTCCATTATAGC
Found at i:1069 original size:12 final size:12
Alignment explanation
Indices: 1052--1077 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1042 CATTATAGCA
1052 TAGGGCCAAAGT
1 TAGGGCCAAAGT
1064 TAGGGCCAAAGT
1 TAGGGCCAAAGT
1076 TA
1 TA
1078 TAGGTAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (12 bp):
TAGGGCCAAAGT
Found at i:1169 original size:12 final size:12
Alignment explanation
Indices: 1152--1177 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1142 CATTATAGCA
1152 TAGGGCCAAAGT
1 TAGGGCCAAAGT
1164 TAGGGCCAAAGT
1 TAGGGCCAAAGT
1176 TA
1 TA
1178 TAGGTAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (12 bp):
TAGGGCCAAAGT
Found at i:2661 original size:45 final size:45
Alignment explanation
Indices: 2612--2741 Score: 242
Period size: 45 Copynumber: 2.9 Consensus size: 45
2602 CTAAATTCTA
2612 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
*
2657 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTC
1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
*
2702 CTCCATCTCTAGGTAATTCATCATAATAAAGCTAATATTA
1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
2742 ATTGTTGCTT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (45 bp):
CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
Done.