Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017080.1 Corchorus olitorius cultivar O-4 contig17113, 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: 17247
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:10148 original size:19 final size:18
Alignment explanation
Indices: 10115--10150 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10105 TGGAAATAAT
10115 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
10133 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
10151 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:11241 original size:5 final size:5
Alignment explanation
Indices: 11231--11255 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11221 AGTTGACAAC
11231 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
11256 TGTCTTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:16976 original size:24 final size:23
Alignment explanation
Indices: 16944--17074 Score: 91
Period size: 24 Copynumber: 5.5 Consensus size: 23
16934 TTTCGGTGGA
* *
16944 GGCGCTGGTGGTGGAGGTGGTCTT
1 GGCGGTGGTGGAGGAGGTGGT-TT
* * * *
16968 GGGGGTGGTGGGGGTGGAGGATTT
1 GGCGGTGGTGGAGGAGGTGG-TTT
*
16992 GGCGGAGGTGGAGGAGGTGGTTT
1 GGCGGTGGTGGAGGAGGTGGTTT
* *
17015 AGGTGGTGGTGCAGGAGGTGGTTT
1 -GGCGGTGGTGGAGGAGGTGGTTT
* * * *
17039 AGGTGGTGGAGCAGGAGGTGGATTA
1 -GGCGGTGGTGGAGGAGGTGG-TTT
*
17064 GGTGGTGGTGG
1 GGCGGTGGTGG
17075 CGGCCTTGGT
Statistics
Matches: 87, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
23 3 0.03
24 81 0.93
25 3 0.03
ACGTcount: A:0.11, C:0.05, G:0.59, T:0.25
Consensus pattern (23 bp):
GGCGGTGGTGGAGGAGGTGGTTT
Found at i:17024 original size:12 final size:12
Alignment explanation
Indices: 17007--17072 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 12
16997 AGGTGGAGGA
17007 GGTGGTTTAGGT
1 GGTGGTTTAGGT
** *
17019 GGTGGTGCAGGA
1 GGTGGTTTAGGT
17031 GGTGGTTTAGGT
1 GGTGGTTTAGGT
*** *
17043 GGTGGAGCAGGA
1 GGTGGTTTAGGT
*
17055 GGTGGATTAGGT
1 GGTGGTTTAGGT
17067 GGTGGT
1 GGTGGT
17073 GGCGGCCTTG
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.14, C:0.03, G:0.55, T:0.29
Consensus pattern (12 bp):
GGTGGTTTAGGT
Found at i:17100 original size:18 final size:18
Alignment explanation
Indices: 17064--17102 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17054 AGGTGGATTA
* * *
17064 GGTGGTGGTGGCGGCCTT
1 GGTGGTGGAGGAGGACTT
17082 GGTGGTGGAGGAGGACTT
1 GGTGGTGGAGGAGGACTT
17100 GGT
1 GGT
17103 CATGGCCATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.10, G:0.56, T:0.26
Consensus pattern (18 bp):
GGTGGTGGAGGAGGACTT
Found at i:17128 original size:36 final size:36
Alignment explanation
Indices: 17088--17173 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
17078 CCTTGGTGGT
*
17088 GGAGGAGGACTT-GGTCATGGCCATGGACTTGGCAAA
1 GGAGGAGGA-TTAGGGCATGGCCATGGACTTGGCAAA
* ** *
17124 GGAGGTGGATTAGGGGGTGGTCATGGACTTGGCAAA
1 GGAGGAGGATTAGGGCATGGCCATGGACTTGGCAAA
*
17160 GGAGGTGGATTAGG
1 GGAGGAGGATTAGG
17174 TGGTGGTGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 2 0.05
36 42 0.95
ACGTcount: A:0.23, C:0.10, G:0.45, T:0.21
Consensus pattern (36 bp):
GGAGGAGGATTAGGGCATGGCCATGGACTTGGCAAA
Found at i:17179 original size:36 final size:36
Alignment explanation
Indices: 17109--17180 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
17099 TGGTCATGGC
17109 CATGGACTTGGCAAAGGAGGTGGATTAGGGGGTGGT
1 CATGGACTTGGCAAAGGAGGTGGATTAGGGGGTGGT
*
17145 CATGGACTTGGCAAAGGAGGTGGATTAGGTGGTGGT
1 CATGGACTTGGCAAAGGAGGTGGATTAGGGGGTGGT
17181 GGGGGACTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.22, C:0.08, G:0.46, T:0.24
Consensus pattern (36 bp):
CATGGACTTGGCAAAGGAGGTGGATTAGGGGGTGGT
Found at i:17188 original size:36 final size:36
Alignment explanation
Indices: 17112--17191 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
17102 TCATGGCCAT
*
17112 GGACTTGGCAAAGGAGGTGGATTAGGGGGTGGTCAT
1 GGACTTGGCAAAGGAGGTGGATTAGGGGGTGGTCAG
* **
17148 GGACTTGGCAAAGGAGGTGGATTAGGTGGTGGTGGG
1 GGACTTGGCAAAGGAGGTGGATTAGGGGGTGGTCAG
17184 GGACTTGG
1 GGACTTGG
17192 TGGTGGTCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.20, C:0.07, G:0.50, T:0.23
Consensus pattern (36 bp):
GGACTTGGCAAAGGAGGTGGATTAGGGGGTGGTCAG
Found at i:17197 original size:54 final size:54
Alignment explanation
Indices: 17139--17245 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 54
17129 TGGATTAGGG
*
17139 GGTGGTCATGGACTTGGCAAAGGAGGTGGATTAGGTGGTGGTGGGGGACTTGGT
1 GGTGGTCATGGACTTGGCAAAGGAGGTGGATTAGGTGGTGGTGGAGGACTTGGT
*
17193 GGTGGTCATGGACTTGGCAAAGGAGGTGGATTGGGTGGTGGTGGAGGACTTGG
1 GGTGGTCATGGACTTGGCAAAGGAGGTGGATTAGGTGGTGGTGGAGGACTTGG
17246 AG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.17, C:0.07, G:0.50, T:0.25
Consensus pattern (54 bp):
GGTGGTCATGGACTTGGCAAAGGAGGTGGATTAGGTGGTGGTGGAGGACTTGGT
Done.