Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008936.1 Corchorus capsularis cultivar CVL-1 contig08957, 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: 5066
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Found at i:340 original size:8 final size:8
Alignment explanation
Indices: 327--386 Score: 86
Period size: 8 Copynumber: 7.5 Consensus size: 8
317 GCCGTGAAAA
*
327 AAAAAAAG
1 AAAAAATG
335 AAAAAATG
1 AAAAAATG
343 AAAAAATG
1 AAAAAATG
*
351 ATGAAAATG
1 A-AAAAATG
360 AAAAAATG
1 AAAAAATG
368 AAAAAATG
1 AAAAAATG
376 AAAAAA-G
1 AAAAAATG
383 AAAA
1 AAAA
387 GAAAAGAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
7 5 0.10
8 36 0.75
9 7 0.15
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:357 original size:25 final size:23
Alignment explanation
Indices: 328--386 Score: 91
Period size: 25 Copynumber: 2.5 Consensus size: 23
318 CCGTGAAAAA
328 AAAAAAGAAAAAATGAAAAAATG
1 AAAAAAGAAAAAATGAAAAAATG
*
351 ATGAAAATGAAAAAATGAAAAAATG
1 A--AAAAAGAAAAAATGAAAAAATG
376 AAAAAAGAAAA
1 AAAAAAGAAAA
387 GAAAAGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 10 0.31
25 22 0.69
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (23 bp):
AAAAAAGAAAAAATGAAAAAATG
Found at i:1744 original size:14 final size:14
Alignment explanation
Indices: 1725--1755 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1715 GTCAATTCAG
1725 AGTTTGCATTGGTA
1 AGTTTGCATTGGTA
1739 AGTTTGCATTGGTA
1 AGTTTGCATTGGTA
1753 AGT
1 AGT
1756 CCTCCGGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.29, T:0.42
Consensus pattern (14 bp):
AGTTTGCATTGGTA
Found at i:1963 original size:22 final size:22
Alignment explanation
Indices: 1938--2011 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
1928 TCTGGGCACA
*
1938 AATTCAGAAACCTCCGGGTGTT
1 AATTCAGAAACCTCCGGGTATT
* * **
1960 AATTCTGATAAGTCCTCCGGGCACA
1 AATTCAGA-AA--CCTCCGGGTATT
1985 AATTCAGAAACCTCCGGGTATT
1 AATTCAGAAACCTCCGGGTATT
2007 AATTC
1 AATTC
2012 TGATAAGTCC
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
22 21 0.52
23 2 0.05
24 2 0.05
25 15 0.38
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (22 bp):
AATTCAGAAACCTCCGGGTATT
Found at i:1977 original size:25 final size:25
Alignment explanation
Indices: 1948--2027 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
1938 AATTCAGAAA
*
1948 CCTCCGGGTGTTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
* ** *
1973 CCTCCGGGCACAAATTCAGA-AA--
1 CCTCCGGGTATTAATTCTGATAAGT
1995 CCTCCGGGTATTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
2020 CCTCCGGG
1 CCTCCGGG
2028 CAATTGGTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
22 16 0.37
23 2 0.05
24 2 0.05
25 23 0.53
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (25 bp):
CCTCCGGGTATTAATTCTGATAAGT
Found at i:1990 original size:47 final size:47
Alignment explanation
Indices: 1921--2029 Score: 200
Period size: 47 Copynumber: 2.3 Consensus size: 47
1911 TTTGCATTGG
* *
1921 TAAGTCCTCTGGGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
1968 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
2015 TAAGTCCTCCGGGCA
1 TAAGTCCTCCGGGCA
2030 ATTGGTAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (47 bp):
TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
Found at i:2032 original size:22 final size:23
Alignment explanation
Indices: 1960--2032 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 23
1950 TCCGGGTGTT
1960 AATTCTGATAAGTCCTCCGGGCAC
1 AATTCTGATAAGTCCTCCGGG-AC
* *
1984 AAATTCAGA-AA--CCTCCGGGTATT
1 -AATTCTGATAAGTCCTCCGGG-A-C
2007 AATTCTGATAAGTCCTCCGGG-C
1 AATTCTGATAAGTCCTCCGGGAC
2029 AATT
1 AATT
2033 GGTAAAACCT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
24 2 0.05
25 15 0.38
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (23 bp):
AATTCTGATAAGTCCTCCGGGAC
Done.