Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006370.1 Corchorus capsularis cultivar CVL-1 contig06391, 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: 31947
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:1755 original size:17 final size:16
Alignment explanation
Indices: 1733--1766 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1723 ACTTAATTAG
1733 ACAAGGCCCAAACCTAA
1 ACAAGGCCCAAA-CTAA
*
1750 ACAAGGTCCAAACTAA
1 ACAAGGCCCAAACTAA
1766 A
1 A
1767 TAATTAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.29, G:0.12, T:0.09
Consensus pattern (16 bp):
ACAAGGCCCAAACTAA
Found at i:1928 original size:21 final size:20
Alignment explanation
Indices: 1889--1930 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1879 TCCTTTGCTT
*
1889 ATTGTCTTCAATGCTCTTCA
1 ATTGTCTTCAATGCACTTCA
*
1909 ATTGATCTTCAATGGACTTCA
1 ATTG-TCTTCAATGCACTTCA
1930 A
1 A
1931 ACCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (20 bp):
ATTGTCTTCAATGCACTTCA
Found at i:4261 original size:18 final size:20
Alignment explanation
Indices: 4238--4283 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
4228 GACTCATCAA
4238 GGTGAA-ATCAAGT-CATGT
1 GGTGAACATCAAGTACATGT
4256 GGTGAACCATCAAGTACATGT
1 GGTGAA-CATCAAGTACATGT
*
4277 GGGGAAC
1 GGTGAAC
4284 CATATATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
20 8 0.33
21 10 0.42
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (20 bp):
GGTGAACATCAAGTACATGT
Found at i:4269 original size:20 final size:21
Alignment explanation
Indices: 4244--4286 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4234 TCAAGGTGAA
*
4244 ATCAAGT-CATGTGGTGAACC
1 ATCAAGTACATGTGGGGAACC
4264 ATCAAGTACATGTGGGGAACC
1 ATCAAGTACATGTGGGGAACC
4285 AT
1 AT
4287 ATATGATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATCAAGTACATGTGGGGAACC
Found at i:5967 original size:28 final size:30
Alignment explanation
Indices: 5925--5993 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
5915 TACAAGTGCA
5925 GGTTGTGCACTTGGG-TTG-ATTCAAGTGTG
1 GGTT-TGCACTTGGGATTGTATTCAAGTGTG
**
5954 GGTTTGCACTTGGGATTGTATTTGAGTGTG
1 GGTTTGCACTTGGGATTGTATTCAAGTGTG
5984 GGTTTGCACT
1 GGTTTGCACT
5994 CGGTGTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 10 0.28
29 7 0.19
30 19 0.53
ACGTcount: A:0.13, C:0.10, G:0.36, T:0.41
Consensus pattern (30 bp):
GGTTTGCACTTGGGATTGTATTCAAGTGTG
Found at i:19720 original size:6 final size:6
Alignment explanation
Indices: 19709--19735 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19699 CAACAGGAGA
19709 AAAAGG AAAAGG AAAAGG AAAAGG AAA
1 AAAAGG AAAAGG AAAAGG AAAAGG AAA
19736 TTAAGGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:31045 original size:19 final size:18
Alignment explanation
Indices: 31021--31056 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
31011 TGAAGATTTC
31021 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
31040 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
31057 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.