Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023512.1 Corchorus olitorius cultivar O-4 contig23545, 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: 11072
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:8125 original size:31 final size:31
Alignment explanation
Indices: 8050--8183 Score: 129
Period size: 31 Copynumber: 4.5 Consensus size: 31
8040 GCATGCCATA
* **
8050 TGTCACTTTTTGGCACACATGGCGTGACACG
1 TGTCACTTTTTGGTACATGTGGCGTGACACG
*
8081 TGTCACTTTTTGGTACATGTGGCGTGCCACG
1 TGTCACTTTTTGGTACATGTGGCGTGACACG
*
8112 TGTCACTGTTTGGTACATGT-G-GT-----G
1 TGTCACTTTTTGGTACATGTGGCGTGACACG
* * * *
8136 TGTCGCTTTTTGGTACACGTGGCGTGTCACA
1 TGTCACTTTTTGGTACATGTGGCGTGACACG
*
8167 TGTCGCTTTTTGGTACA
1 TGTCACTTTTTGGTACA
8184 CATGGCATGT
Statistics
Matches: 87, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
24 18 0.21
25 1 0.01
26 2 0.02
29 2 0.02
30 1 0.01
31 63 0.72
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.37
Consensus pattern (31 bp):
TGTCACTTTTTGGTACATGTGGCGTGACACG
Found at i:8147 original size:24 final size:24
Alignment explanation
Indices: 8110--8165 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
8100 TGGCGTGCCA
*
8110 CGTGTCACTGTTTGGTACATGTGG
1 CGTGTCACTGTTTGGTACACGTGG
* * *
8134 TGTGTCGCTTTTTGGTACACGTGG
1 CGTGTCACTGTTTGGTACACGTGG
8158 CGTGTCAC
1 CGTGTCAC
8166 ATGTCGCTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.11, C:0.20, G:0.32, T:0.38
Consensus pattern (24 bp):
CGTGTCACTGTTTGGTACACGTGG
Found at i:8158 original size:55 final size:55
Alignment explanation
Indices: 8080--8183 Score: 154
Period size: 55 Copynumber: 1.9 Consensus size: 55
8070 GGCGTGACAC
* *
8080 GTGTCACTTTTTGGTACATGTGGCGTGCCACGTGTCACTGTTTGGTACATGTGGT
1 GTGTCACTTTTTGGTACACGTGGCGTGCCACATGTCACTGTTTGGTACATGTGGT
* * * *
8135 GTGTCGCTTTTTGGTACACGTGGCGTGTCACATGTCGCTTTTTGGTACA
1 GTGTCACTTTTTGGTACACGTGGCGTGCCACATGTCACTGTTTGGTACA
8184 CATGGCATGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.12, C:0.19, G:0.30, T:0.38
Consensus pattern (55 bp):
GTGTCACTTTTTGGTACACGTGGCGTGCCACATGTCACTGTTTGGTACATGTGGT
Found at i:8184 original size:31 final size:31
Alignment explanation
Indices: 8136--8198 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
8126 ACATGTGGTG
* *
8136 TGTCGCTTTTTGGTACACGTGGCGTGTCACA
1 TGTCGCTTTTTGGTACACATGGCATGTCACA
8167 TGTCGCTTTTTGGTACACATGGCATGTCACA
1 TGTCGCTTTTTGGTACACATGGCATGTCACA
8198 T
1 T
8199 CGAACACCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (31 bp):
TGTCGCTTTTTGGTACACATGGCATGTCACA
Found at i:8603 original size:17 final size:17
Alignment explanation
Indices: 8581--8614 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
8571 ATGATACCAG
8581 ATTGGATCAAGTGGTAA
1 ATTGGATCAAGTGGTAA
8598 ATTGGATCAAGTGGTAA
1 ATTGGATCAAGTGGTAA
8615 GTAGTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (17 bp):
ATTGGATCAAGTGGTAA
Found at i:8769 original size:49 final size:49
Alignment explanation
Indices: 8697--8792 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
8687 AAACTTACCT
8697 ATCAAAATCAAGTTCACGACACAGGTTAGAAAAATCAAGTATGTAACCC
1 ATCAAAATCAAGTTCACGACACAGGTTAGAAAAATCAAGTATGTAACCC
8746 ATCAAAATCAAGTTCACGACACAGGTTAGAAAAATCAAGTATGTAAC
1 ATCAAAATCAAGTTCACGACACAGGTTAGAAAAATCAAGTATGTAAC
8793 GTCTCTCATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.21
Consensus pattern (49 bp):
ATCAAAATCAAGTTCACGACACAGGTTAGAAAAATCAAGTATGTAACCC
Done.