Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012257.1 Corchorus olitorius cultivar O-4 contig12290, 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: 11018
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:9154 original size:33 final size:33

Alignment explanation


    Indices: 9112--9197  Score: 100
    Period size: 33  Copynumber: 2.6  Consensus size: 33

       9102 AAATGGTCGG

                                           * 
       9112 TGCCGCCCTCGGAGGGCGGCATGGCCATGGGGA
          1 TGCCGCCCTCGGAGGGCGGCATGGCCATGGGCA

                      * *       *         *  
       9145 TGCCGCCCTCAGTGGGCGGCGTGGCCATGGTCA
          1 TGCCGCCCTCGGAGGGCGGCATGGCCATGGGCA

              *     **          
       9178 TGTCGCCCAAGGAGGGCGGC
          1 TGCCGCCCTCGGAGGGCGGC

       9198 CTAACCATTT


Statistics
Matches: 43,  Mismatches: 10, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  33   43  1.00

ACGTcount: A:0.12, C:0.31, G:0.43, T:0.14


Consensus pattern (33 bp):   
TGCCGCCCTCGGAGGGCGGCATGGCCATGGGCA

Found at i:9280 original size:66 final size:65

Alignment explanation


    Indices: 9157--9284  Score: 150
    Period size: 66  Copynumber: 1.9  Consensus size: 65

       9147 CCGCCCTCAG

                    **             *        *      *                         
       9157 TGGGCGGCGTGGCCATGGTCATGTCGCCCAAGGAGGGCGGCCTAACCATTTGGATGCCGCCCAAC
          1 TGGGCGGCACGGCCATGGTCATGCCGCCCAAGCAGGGCGACCTAACCA-TTGGATGCCGCCCAAC

             
       9222 T
         65 T

                                      *  *           *                     
       9223 TGGGCGGCACGGCCATGGTCATGCCGTCCTAGCAGGGCGACGTAACCA-TGGCCATGCCGCCC
          1 TGGGCGGCACGGCCATGGTCATGCCGCCCAAGCAGGGCGACCTAACCATTGG--ATGCCGCCC

       9285 TTAGAGGGCG


Statistics
Matches: 52,  Mismatches: 8, Indels: 4
        0.81            0.12        0.06

Matches are distributed among these distances:
  64    3  0.06
  66   49  0.94

ACGTcount: A:0.16, C:0.33, G:0.34, T:0.16


Consensus pattern (65 bp):   
TGGGCGGCACGGCCATGGTCATGCCGCCCAAGCAGGGCGACCTAACCATTGGATGCCGCCCAACT
Done.