Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005584.1 Corchorus capsularis cultivar CVL-1 contig05602, 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: 4989
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:2048 original size:31 final size:30
Alignment explanation
Indices: 2018--2186 Score: 153
Period size: 31 Copynumber: 5.8 Consensus size: 30
2008 GCCACGTGTC
2018 ACTTTTTGGTACACATGGCGTG-ACATGTGT
1 ACTTTTTGGTACACATGGCGTGCACATGT-T
* *
2048 CATTTTTTGGT--ACAT-GTG-GCAC--G--
1 -ACTTTTTGGTACACATGGCGTGCACATGTT
**
2071 ACTTTTTGGTACATGTGGCGTGCCACATGTT
1 ACTTTTTGGTACACATGGCGTG-CACATGTT
2102 ACTTTTTGGTACA-AGTGGCGTGCCACATGTT
1 ACTTTTTGGTACACA-TGGCGTG-CACATGTT
2133 ACTTTTTGGTACA-AGTGGCGTGCCACATGTT
1 ACTTTTTGGTACACA-TGGCGTG-CACATGTT
*
2164 ACTTTTTGGTACACGTGGCGTGC
1 ACTTTTTGGTACACATGGCGTGC
2187 CACGTCGAAC
Statistics
Matches: 118, Mismatches: 8, Indels: 25
0.78 0.05 0.17
Matches are distributed among these distances:
22 9 0.08
24 2 0.02
25 2 0.02
26 2 0.02
27 4 0.03
28 4 0.03
29 5 0.04
30 1 0.01
31 89 0.75
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.37
Consensus pattern (30 bp):
ACTTTTTGGTACACATGGCGTGCACATGTT
Found at i:2063 original size:62 final size:59
Alignment explanation
Indices: 1997--2191 Score: 192
Period size: 62 Copynumber: 3.3 Consensus size: 59
1987 ATTTTTTGAA
* *
1997 ACATGTGGCATGCCACGTGTCACTTTTTGGTACACATGGCGTG-ACATGTGTCATTTTTTGGT
1 ACATGTGGCGTGCCACGTGT-ACTTTTTGGTACA-ATGGCGTGCACATGT-T-ACTTTTTGGT
*
2059 ACATGT---G-G-CAC--G-ACTTTTTGGTACATGTGGCGTGCCACATGTTACTTTTTGGT
1 ACATGTGGCGTGCCACGTGTACTTTTTGGTACA-ATGGCGTG-CACATGTTACTTTTTGGT
* *
2112 ACAAGTGGCGTGCCACATGTTACTTTTTGGTACAAGTGGCGTGCCACATGTTACTTTTTGGT
1 ACATGTGGCGTGCCACGTG-TACTTTTTGGTACAA-TGGCGTG-CACATGTTACTTTTTGGT
*
2174 ACACGTGGCGTGCCACGT
1 ACATGTGGCGTGCCACGT
2192 CGAACACCGT
Statistics
Matches: 113, Mismatches: 8, Indels: 24
0.78 0.06 0.17
Matches are distributed among these distances:
53 34 0.30
54 1 0.01
55 7 0.06
56 1 0.01
57 4 0.04
58 4 0.04
60 1 0.01
62 61 0.54
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.35
Consensus pattern (59 bp):
ACATGTGGCGTGCCACGTGTACTTTTTGGTACAATGGCGTGCACATGTTACTTTTTGGT
Found at i:2077 original size:84 final size:83
Alignment explanation
Indices: 1989--2151 Score: 213
Period size: 84 Copynumber: 1.9 Consensus size: 83
1979 CACGTGCAAT
* *
1989 TTTTTGAAACATGTGGCATGCCACGTGTCACTTTTTGGTACACA-TGGCGTG-ACATGTGTCATT
1 TTTTTGAAACATGTGGCATGCCACATGTCACTTTTTGGTACA-AGTGGCGTGCACATGT-T-ACT
*
2052 TTTTGGTACATGTGGCACGAC
63 TTTTGGTACAAGTGGCACGAC
** * *
2073 TTTTTGGTACATGTGGCGTGCCACATGTTACTTTTTGGTACAAGTGGCGTGCCACATGTTACTTT
1 TTTTTGAAACATGTGGCATGCCACATGTCACTTTTTGGTACAAGTGGCGTG-CACATGTTACTTT
2138 TTGGTACAAGTGGC
65 TTGGTACAAGTGGC
2152 GTGCCACATG
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
83 1 0.01
84 61 0.88
85 1 0.01
86 6 0.09
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (83 bp):
TTTTTGAAACATGTGGCATGCCACATGTCACTTTTTGGTACAAGTGGCGTGCACATGTTACTTTT
TGGTACAAGTGGCACGAC
Found at i:2187 original size:31 final size:31
Alignment explanation
Indices: 2071--2189 Score: 220
Period size: 31 Copynumber: 3.8 Consensus size: 31
2061 ATGTGGCACG
*
2071 ACTTTTTGGTACATGTGGCGTGCCACATGTT
1 ACTTTTTGGTACAAGTGGCGTGCCACATGTT
2102 ACTTTTTGGTACAAGTGGCGTGCCACATGTT
1 ACTTTTTGGTACAAGTGGCGTGCCACATGTT
2133 ACTTTTTGGTACAAGTGGCGTGCCACATGTT
1 ACTTTTTGGTACAAGTGGCGTGCCACATGTT
*
2164 ACTTTTTGGTACACGTGGCGTGCCAC
1 ACTTTTTGGTACAAGTGGCGTGCCAC
2190 GTCGAACACC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 86 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (31 bp):
ACTTTTTGGTACAAGTGGCGTGCCACATGTT
Done.