Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020277.1 Corchorus olitorius cultivar O-4 contig20310, 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: 17944
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:13342 original size:1 final size:1
Alignment explanation
Indices: 13336--13361 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
13326 ACATTGGAGG
13336 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
13362 GGGTAGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13614 original size:43 final size:43
Alignment explanation
Indices: 13553--13638 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
13543 CAACTCTGTA
13553 CCAACTCTGCATAACTTGTATTTCAAACCTTTCAAATAGAGAT
1 CCAACTCTGCATAACTTGTATTTCAAACCTTTCAAATAGAGAT
13596 CCAACTCTGCATAACTTGTATTTCAAACCTTTCAAATAGAGAT
1 CCAACTCTGCATAACTTGTATTTCAAACCTTTCAAATAGAGAT
13639 TCAAAGTCGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (43 bp):
CCAACTCTGCATAACTTGTATTTCAAACCTTTCAAATAGAGAT
Found at i:17168 original size:24 final size:24
Alignment explanation
Indices: 17141--17253 Score: 115
Period size: 24 Copynumber: 4.8 Consensus size: 24
17131 GCGGTGGCGT
*
17141 CCAGCTTCCTCCTGGCGGCGCTGG
1 CCAGCTTCCCCCTGGCGGCGCTGG
*
17165 CCAGCTTCCCCCCGGCGGCG-T--
1 CCAGCTTCCCCCTGGCGGCGCTGG
* *
17186 CCAGCTTCCCCCTGGTGGTGCTGG
1 CCAGCTTCCCCCTGGCGGCGCTGG
* * * *
17210 TCAGCTTCCTCCTGGTGGTGCTGG
1 CCAGCTTCCCCCTGGCGGCGCTGG
* *
17234 TCAGCTTCCCCCTGGTGGCG
1 CCAGCTTCCCCCTGGCGGCG
17254 GCATGCTTCC
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
21 17 0.22
22 1 0.01
23 1 0.01
24 58 0.75
ACGTcount: A:0.04, C:0.40, G:0.32, T:0.24
Consensus pattern (24 bp):
CCAGCTTCCCCCTGGCGGCGCTGG
Found at i:17262 original size:69 final size:69
Alignment explanation
Indices: 17142--17274 Score: 178
Period size: 69 Copynumber: 1.9 Consensus size: 69
17132 CGGTGGCGTC
*
17142 CAGCTTCCTCCTGGCGGCGCTGGCCAGCTTCCCCCCGGCGGCGTCCAGCTTCCCCCTGGTGGTGC
1 CAGCTTCCTCCTGGCGGCGCTGGCCAGCTTCCCCCCGGCGGCGTCCAGCTTCCCCCTGGCGGTGC
17207 TGGT
66 TGGT
* * * * * * *
17211 CAGCTTCCTCCTGGTGGTGCTGGTCAGCTTCCCCCTGGTGGCG-GCATGCTTCCTCCTGGCGGTG
1 CAGCTTCCTCCTGGCGGCGCTGGCCAGCTTCCCCCCGGCGGCGTCCA-GCTTCCCCCTGGCGGTG
17275 GCATGCTGCT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
68 2 0.04
69 53 0.96
ACGTcount: A:0.05, C:0.38, G:0.32, T:0.25
Consensus pattern (69 bp):
CAGCTTCCTCCTGGCGGCGCTGGCCAGCTTCCCCCCGGCGGCGTCCAGCTTCCCCCTGGCGGTGC
TGGT
Found at i:17263 original size:21 final size:24
Alignment explanation
Indices: 17187--17251 Score: 121
Period size: 24 Copynumber: 2.7 Consensus size: 24
17177 CGGCGGCGTC
17187 CAGCTTCCCCCTGGTGGTGCTGGT
1 CAGCTTCCCCCTGGTGGTGCTGGT
*
17211 CAGCTTCCTCCTGGTGGTGCTGGT
1 CAGCTTCCCCCTGGTGGTGCTGGT
17235 CAGCTTCCCCCTGGTGG
1 CAGCTTCCCCCTGGTGG
17252 CGGCATGCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.05, C:0.34, G:0.32, T:0.29
Consensus pattern (24 bp):
CAGCTTCCCCCTGGTGGTGCTGGT
Found at i:17268 original size:21 final size:21
Alignment explanation
Indices: 17213--17281 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
17203 GTGCTGGTCA
17213 GCTTCCTCCTGGTGGTGCTGGTCA-
1 GCTTCCTCCTGGT-G-GC-GG-CAT
*
17237 GCTTCCCCCTGGTGGCGGCAT
1 GCTTCCTCCTGGTGGCGGCAT
* *
17258 GCTTCCTCCTGGCGGTGGCAT
1 GCTTCCTCCTGGTGGCGGCAT
17279 GCT
1 GCT
17282 GCTTCCCCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 2 0.05
21 23 0.57
22 2 0.05
23 1 0.03
24 12 0.30
ACGTcount: A:0.04, C:0.33, G:0.33, T:0.29
Consensus pattern (21 bp):
GCTTCCTCCTGGTGGCGGCAT
Found at i:17286 original size:69 final size:68
Alignment explanation
Indices: 17128--17287 Score: 171
Period size: 69 Copynumber: 2.3 Consensus size: 68
17118 ATCCCTGGAA
*
17128 CTGGCGGTGGCGTCCAGCTTCCTCCTGGCGGCGCTGGCCAGCTTCCCCCCGGCGGCGTCCAGCTT
1 CTGGCGGTGGC-TGCAGCTTCCTCCTGGCGGCGCTGGCCAGCTTCCCCCCGGCGGCGTCCAGCTT
17193 CCCC
65 CCCC
* * * * * * *
17197 CTGGTGGT-GCTGGTCAGCTTCCTCCTGGTGGTGCTGGTCAGCTTCCCCCTGGTGGCG-GCATGC
1 CTGGCGGTGGCT-G-CAGCTTCCTCCTGGCGGCGCTGGCCAGCTTCCCCCCGGCGGCGTCCA-GC
*
17260 TTCCTC
63 TTCCCC
*
17266 CTGGCGGTGGCATGCTGCTTCC
1 CTGGCGGTGGC-TGCAGCTTCC
17288 CCCTATATTT
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
67 1 0.01
68 4 0.05
69 66 0.88
70 3 0.04
71 1 0.01
ACGTcount: A:0.04, C:0.38, G:0.33, T:0.25
Consensus pattern (68 bp):
CTGGCGGTGGCTGCAGCTTCCTCCTGGCGGCGCTGGCCAGCTTCCCCCCGGCGGCGTCCAGCTTC
CCC
Done.