Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010925.1 Corchorus olitorius cultivar O-4 contig10957, 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: 2292
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36


Found at i:1974 original size:16 final size:16

Alignment explanation


    Indices: 1941--1975  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       1931 TTGATGTTTT

                        *   
       1941 GAATAATAAAAATAAA
          1 GAATAATAAAAAGAAA

                         *  
       1957 GAATAATAAAAAGCAA
          1 GAATAATAAAAAGAAA

               
       1973 GAA
          1 GAA

       1976 AATTGAAAAC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.71, C:0.03, G:0.11, T:0.14


Consensus pattern (16 bp):   
GAATAATAAAAAGAAA

Found at i:2197 original size:22 final size:22

Alignment explanation


    Indices: 2169--2277  Score: 173
    Period size: 22  Copynumber: 4.9  Consensus size: 22

       2159 TGGAAACATT

                             *    
       2169 TTTGCAGAGCATTATTTACCAC
          1 TTTGCAGAGCATTATTTTCCAC

                               *  
       2191 TTTGCAGAGCATTATTTTCTAC
          1 TTTGCAGAGCATTATTTTCCAC

                                  
       2213 TTTGCAGAGCATTATTTTCCAC
          1 TTTGCAGAGCATTATTTTCCAC

                 *                
       2235 TTTGCGGAGCATTATTTTCCAC
          1 TTTGCAGAGCATTATTTTCCAC

                                 
       2257 TTTGCAGAGTGCATTATTTTC
          1 TTTGCAGA--GCATTATTTTC

       2278 TTCAACTTCA


Statistics
Matches: 80,  Mismatches: 5, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
  22   69  0.86
  24   11  0.14

ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42


Consensus pattern (22 bp):   
TTTGCAGAGCATTATTTTCCAC

Done.