Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016032.1 Corchorus capsularis cultivar CVL-1 contig16053, 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: 10568
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36


Found at i:950 original size:30 final size:28

Alignment explanation


    Indices: 888--952  Score: 78
    Period size: 29  Copynumber: 2.2  Consensus size: 28

        878 CAAAACGGCT

                                    *    
        888 AAATAAGCCCCTGAATTCTAATTACAGCC
          1 AAATAAGCCCCTGAATTCTAA-TAAAGCC

                                           
        917 AAATAAGCCCCTGAATTCTTGAA-AAATGCC
          1 AAATAAGCCCCTGAATTC-T-AATAAA-GCC

                  
        947 AAATAA
          1 AAATAA

        953 ACCCTTTTTT


Statistics
Matches: 32,  Mismatches: 1, Indels: 5
        0.84            0.03        0.13

Matches are distributed among these distances:
  29   20  0.62
  30   10  0.31
  31    2  0.06

ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23


Consensus pattern (28 bp):   
AAATAAGCCCCTGAATTCTAATAAAGCC

Found at i:10194 original size:22 final size:23

Alignment explanation


    Indices: 10142--10195  Score: 74
    Period size: 22  Copynumber: 2.4  Consensus size: 23

      10132 ATAATAATTT

                  *                
      10142 TTAATTAATTAGTATTTAATTAC
          1 TTAATTTATTAGTATTTAATTAC

               *                  *
      10165 TTAGTTTATTAGT-TTTAATTAG
          1 TTAATTTATTAGTATTTAATTAC

                     
      10187 TTAATTTAT
          1 TTAATTTAT

      10196 GATTAACTAC


Statistics
Matches: 27,  Mismatches: 4, Indels: 1
        0.84            0.12        0.03

Matches are distributed among these distances:
  22   16  0.59
  23   11  0.41

ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57


Consensus pattern (23 bp):   
TTAATTTATTAGTATTTAATTAC
Done.