Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018838.1 Corchorus olitorius cultivar O-4 contig18871, 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: 12235
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Found at i:169 original size:96 final size:96
Alignment explanation
Indices: 8--321 Score: 342
Period size: 96 Copynumber: 3.3 Consensus size: 96
1 AGGCGAA
* * * * * * * *
8 GGAGATGGTGGTGGTGGTGATTTGTAAATATAAGGAGGAGGTGGTGAAGGAGAAGGAGGAGGAGG
1 GGAGATGGTGGAGGAGGTGACTTGTAAATGTATGGTGGAGGAGGTGAAGGAGATGGAGGAGGAGG
* * * *
73 GGACTTATAAGCATAGGGTGGTGGTGGTGAT
66 GGACTTATAAGCATAAGGAGGAGGTGGTGAC
* * * * *
104 GGAGATGGTGGAGGAGGAGACTTATAAATGTATGGTGGAGGGGGTGATGGGGATGGAGGAGGAGG
1 GGAGATGGTGGAGGAGGTGACTTGTAAATGTATGGTGGAGGAGGTGAAGGAGATGGAGGAGGAGG
* * *
169 GGACTTATAAACATAAGGAGGAGGAGGTGAG
66 GGACTTATAAGCATAAGGAGGAGGTGGTGAC
* * * * * *
200 GGAGATGGTGGAGGAGGGGATTTGTAAATGTATGGTGGTGGAGGCGAAGGAGATGGTGGGGGAGG
1 GGAGATGGTGGAGGAGGTGACTTGTAAATGTATGGTGGAGGAGGTGAAGGAGATGGAGGAGGAGG
* * *
265 AGACTTGT-AGACATAAGGAGGAGGTGGCGAC
66 GGACTTATAAG-CATAAGGAGGAGGTGGTGAC
*
296 GGAGATGGTGGGGGAGGTGACTTGTA
1 GGAGATGGTGGAGGAGGTGACTTGTA
322 GTAGTATGGA
Statistics
Matches: 180, Mismatches: 37, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
95 1 0.01
96 179 0.99
ACGTcount: A:0.27, C:0.04, G:0.49, T:0.20
Consensus pattern (96 bp):
GGAGATGGTGGAGGAGGTGACTTGTAAATGTATGGTGGAGGAGGTGAAGGAGATGGAGGAGGAGG
GGACTTATAAGCATAAGGAGGAGGTGGTGAC
Found at i:303 original size:144 final size:144
Alignment explanation
Indices: 32--318 Score: 322
Period size: 144 Copynumber: 2.0 Consensus size: 144
22 TGGTGATTTG
* * *
32 TAAATATAAGGAGGAGGTGGTGAAGGAGAAGGAGGAGGAGGGGACTTATAAGCATAGGGTGGTGG
1 TAAACATAAGGAGGAGGAGGTGAAGGAGAAGGAGGAGGAGGGGACTTATAAACATAGGGTGGTGG
* * * ** * * * * *
97 TGGTGATGGAGATGGTGGAGGAGGAGACTTATAAATGTATGGTGGAGGGGGTGATGGGGATGGAG
66 AGGCGAAGGAGATGGTGGAGGAGGAGACTTATAAACATAAGGAGGAGGGGGCGACGGAGATGGAG
162 GAGGAGGGGACTTA
131 GAGGAGGGGACTTA
* * * * * ** *
176 TAAACATAAGGAGGAGGAGGTGAGGGAGATGGTGGAGGAGGGGATTTGTAAATGTATGGTGGTGG
1 TAAACATAAGGAGGAGGAGGTGAAGGAGAAGGAGGAGGAGGGGACTTATAAACATAGGGTGGTGG
* * * * *
241 AGGCGAAGGAGATGGTGGGGGAGGAGACTTGTAGACATAAGGAGGAGGTGGCGACGGAGATGGTG
66 AGGCGAAGGAGATGGTGGAGGAGGAGACTTATAAACATAAGGAGGAGGGGGCGACGGAGATGGAG
* *
306 GGGGAGGTGACTT
131 GAGGAGGGGACTT
319 GTAGTAGTAT
Statistics
Matches: 115, Mismatches: 28, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
144 115 1.00
ACGTcount: A:0.28, C:0.04, G:0.49, T:0.19
Consensus pattern (144 bp):
TAAACATAAGGAGGAGGAGGTGAAGGAGAAGGAGGAGGAGGGGACTTATAAACATAGGGTGGTGG
AGGCGAAGGAGATGGTGGAGGAGGAGACTTATAAACATAAGGAGGAGGGGGCGACGGAGATGGAG
GAGGAGGGGACTTA
Found at i:322 original size:48 final size:48
Alignment explanation
Indices: 5--321 Score: 265
Period size: 48 Copynumber: 6.6 Consensus size: 48
1 AGGC
* * * * *
5 GAAGGAGATGGTGGTGGTGGTGATTTGTAAATATAAGGAGGAGGTGGT
1 GAAGGAGATGGTGGAGGAGGGGACTTGTAAACATAAGGAGGAGGTGGT
* * * * * * *
53 GAAGGAGAAGGAGGAGGAGGGGACTTATAAGCATAGGGTGGTGGTGGT
1 GAAGGAGATGGTGGAGGAGGGGACTTGTAAACATAAGGAGGAGGTGGT
* * * ** * * *
101 GATGGAGATGGTGGAGGAGGAGACTTATAAATGTATGGTGGAGGGGGT
1 GAAGGAGATGGTGGAGGAGGGGACTTGTAAACATAAGGAGGAGGTGGT
* * * * *
149 GATGGGGATGGAGGAGGAGGGGACTTATAAACATAAGGAGGAGGAGGT
1 GAAGGAGATGGTGGAGGAGGGGACTTGTAAACATAAGGAGGAGGTGGT
* * ** * * * * *
197 GAGGGAGATGGTGGAGGAGGGGATTTGTAAATGTATGGTGGTGGAGGC
1 GAAGGAGATGGTGGAGGAGGGGACTTGTAAACATAAGGAGGAGGTGGT
* * * *
245 GAAGGAGATGGTGGGGGAGGAGACTTGTAGACATAAGGAGGAGGTGGC
1 GAAGGAGATGGTGGAGGAGGGGACTTGTAAACATAAGGAGGAGGTGGT
* * *
293 GACGGAGATGGTGGGGGAGGTGACTTGTA
1 GAAGGAGATGGTGGAGGAGGGGACTTGTA
322 GTAGTATGGA
Statistics
Matches: 215, Mismatches: 54, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 215 1.00
ACGTcount: A:0.27, C:0.03, G:0.49, T:0.20
Consensus pattern (48 bp):
GAAGGAGATGGTGGAGGAGGGGACTTGTAAACATAAGGAGGAGGTGGT
Found at i:333 original size:144 final size:142
Alignment explanation
Indices: 2--336 Score: 310
Period size: 144 Copynumber: 2.3 Consensus size: 142
1 A
* * * *
2 GGCGAAGGAGATGGTGGTGGTGGTGATTTGTAAATATAAGGAGGAGGTGGTGAAGGAGAAGGAGG
1 GGCGAAGGAGATGGTGGAGGAGGTGACTTGT--ATATAAGGAGGAGGAGGTGAAGGAGAAGGAGG
* * * *
67 AGGAGGGGACTTATAAGCATAGGGTGGTGGTGGTGATGGAGATGGTGGAGGAGGAGACTTATAAA
64 AGGAGGGGACTTATAAACATAGGGTGGTGGAGGCGAAGGAGATGGTGGAGGAGGAGACTTATAAA
** * *
132 TGTATGGTGGAGGG
129 CATAAGGAGGAGGG
* * * * * * * * * *
146 GGTGATGGGGATGGAGGAGGAGGGGACTTATAAACATAAGGAGGAGGAGGTGAGGGAGATGGTGG
1 GGCGAAGGAGATGGTGGAGGAGGTGACTTGT--ATATAAGGAGGAGGAGGTGAAGGAGAAGGAGG
* * ** * * * *
211 AGGAGGGGATTTGTAAATGTATGGTGGTGGAGGCGAAGGAGATGGTGGGGGAGGAGACTTGTAGA
64 AGGAGGGGACTTATAAACATAGGGTGGTGGAGGCGAAGGAGATGGTGGAGGAGGAGACTTATAAA
*
276 CATAAGGAGGAGGT
129 CATAAGGAGGAGGG
* * *
290 GGCGACGGAGATGGTGGGGGAGGTGACTTGTAGTAGTATGGAGGAGG
1 GGCGAAGGAGATGGTGGAGGAGGTGACTTGTA-TA-TAAGGAGGAGG
337 TGATCCATAG
Statistics
Matches: 149, Mismatches: 40, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
142 1 0.01
143 1 0.01
144 147 0.99
ACGTcount: A:0.27, C:0.04, G:0.50, T:0.20
Consensus pattern (142 bp):
GGCGAAGGAGATGGTGGAGGAGGTGACTTGTATATAAGGAGGAGGAGGTGAAGGAGAAGGAGGAG
GAGGGGACTTATAAACATAGGGTGGTGGAGGCGAAGGAGATGGTGGAGGAGGAGACTTATAAACA
TAAGGAGGAGGG
Found at i:5904 original size:21 final size:22
Alignment explanation
Indices: 5878--5920 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5868 ACAGGGACTT
*
5878 AGATA-TATGCTTTCCAGAATG
1 AGATATTATGCTGTCCAGAATG
5899 AGATATTATGCTGTCCAGAATG
1 AGATATTATGCTGTCCAGAATG
5921 CATGAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (22 bp):
AGATATTATGCTGTCCAGAATG
Done.