Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019756.1 Corchorus olitorius cultivar O-4 contig19789, 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: 18774
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2166 original size:28 final size:28
Alignment explanation
Indices: 2126--2183 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
2116 GTTTAAGGGT
*
2126 TGACATGTGGAGTTTAGCAGACTACACA
1 TGACATGTGGAGTTTAGCAAACTACACA
2154 TGACATGTGGAGTTTAGCAAACTACACA
1 TGACATGTGGAGTTTAGCAAACTACACA
2182 TG
1 TG
2184 CGGGGTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (28 bp):
TGACATGTGGAGTTTAGCAAACTACACA
Found at i:2191 original size:23 final size:23
Alignment explanation
Indices: 2093--2192 Score: 60
Period size: 23 Copynumber: 4.2 Consensus size: 23
2083 TATCAGTGGA
*
2093 GTTTAGCAAACAACACATGCGGG
1 GTTTAGCAAACTACACATGCGGG
*** ** * *
2116 GTTTA--AGGGTTGACATGTGGA
1 GTTTAGCAAACTACACATGCGGG
*
2137 GTTTAGCAGACTACACATGACATGTGG
1 GTTTAGCAAACTACACATG-C--G-GG
2164 AGTTTAGCAAACTACACATGCGGG
1 -GTTTAGCAAACTACACATGCGGG
2188 GTTTA
1 GTTTA
2193 AGGGTTGACA
Statistics
Matches: 55, Mismatches: 15, Indels: 14
0.65 0.18 0.17
Matches are distributed among these distances:
21 13 0.24
23 18 0.33
24 2 0.04
25 1 0.02
26 1 0.02
27 2 0.04
28 18 0.33
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (23 bp):
GTTTAGCAAACTACACATGCGGG
Found at i:2724 original size:47 final size:49
Alignment explanation
Indices: 2634--2726 Score: 127
Period size: 47 Copynumber: 1.9 Consensus size: 49
2624 AATGTAGTTT
* *
2634 GTACTCTCTAATTTTATTATGTTTATTTTAAACTCTGTCTTTATGGGAAA
1 GTACTCTCTAA-TTTATTATGTTTATTCTAAACTCTATCTTTATGGGAAA
* *
2684 GTACTCTCTAA-TT-TTATGTTTATTCTAAACTTTATGTTTATGG
1 GTACTCTCTAATTTATTATGTTTATTCTAAACTCTATCTTTATGG
2727 TGGGGATGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
47 26 0.67
48 2 0.05
50 11 0.28
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.52
Consensus pattern (49 bp):
GTACTCTCTAATTTATTATGTTTATTCTAAACTCTATCTTTATGGGAAA
Found at i:4847 original size:20 final size:20
Alignment explanation
Indices: 4822--4860 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4812 CTAACTCTAT
* *
4822 TCCCAACTTCATTTCAAACA
1 TCCCAACCTCACTTCAAACA
4842 TCCCAACCTCACTTCAAAC
1 TCCCAACCTCACTTCAAAC
4861 CTCCTCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26
Consensus pattern (20 bp):
TCCCAACCTCACTTCAAACA
Found at i:4904 original size:20 final size:20
Alignment explanation
Indices: 4879--4921 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
4869 AACGGCCTAT
*
4879 TCCCAACTTCACTTCAAACC
1 TCCCAACCTCACTTCAAACC
4899 TCCCAACCTCACTTCAAACC
1 TCCCAACCTCACTTCAAACC
4919 TCC
1 TCC
4922 TCTGAACGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.49, G:0.00, T:0.23
Consensus pattern (20 bp):
TCCCAACCTCACTTCAAACC
Found at i:4906 original size:57 final size:57
Alignment explanation
Indices: 4818--4931 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
4808 AACCCTAACT
*
4818 CTATTCCCAACTTCATTTCAAACATCCCAACCTCACTTCAAACCTCCTCTAAACGGC
1 CTATTCCCAACTTCACTTCAAACATCCCAACCTCACTTCAAACCTCCTCTAAACGGC
* *
4875 CTATTCCCAACTTCACTTCAAACCTCCCAACCTCACTTCAAACCTCCTCTGAACGGC
1 CTATTCCCAACTTCACTTCAAACATCCCAACCTCACTTCAAACCTCCTCTAAACGGC
4932 AAAATTGTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.28, C:0.42, G:0.04, T:0.25
Consensus pattern (57 bp):
CTATTCCCAACTTCACTTCAAACATCCCAACCTCACTTCAAACCTCCTCTAAACGGC
Found at i:6308 original size:42 final size:44
Alignment explanation
Indices: 6256--6343 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
6246 TGCATTACCT
*
6256 AAATTCTACT-C-CATCTCTA-AGTAATTCATCAAAATAAAGCTA
1 AAATTCTACTCCTCATCTCTAGA-TAATTCATCAAAATAAAACTA
*
6298 AAATTTTACTCCTTCATCTCTAGATAATTCATCAAAATAAAACTA
1 AAATTCTACTCC-TCATCTCTAGATAATTCATCAAAATAAAACTA
6343 A
1 A
6344 TATCAATTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
42 9 0.22
43 1 0.03
45 29 0.73
46 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.33
Consensus pattern (44 bp):
AAATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAACTA
Found at i:11615 original size:15 final size:15
Alignment explanation
Indices: 11595--11627 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11585 ATCCGCATCA
11595 TTCGATTGCCAAGTC
1 TTCGATTGCCAAGTC
*
11610 TTCGATTGCTAAGTC
1 TTCGATTGCCAAGTC
11625 TTC
1 TTC
11628 AGCTCCTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (15 bp):
TTCGATTGCCAAGTC
Found at i:17057 original size:2 final size:2
Alignment explanation
Indices: 17050--17085 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17040 ATTGAAACTC
17050 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17086 GCATGATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.