Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006947.1 Corchorus olitorius cultivar O-4 contig06972, 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, 652

Length: 1088
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31


Found at i:120 original size:21 final size:22

Alignment explanation


    Indices: 94--164  Score: 112
    Period size: 21  Copynumber: 3.4  Consensus size: 22

         84 TGCTAGGAGT

                                  
         94 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAGCAAGGTTCCAAGC

                                  
        115 TCATTGGAG-AAGGTTCCAAGC
          1 TCATTGGAGCAAGGTTCCAAGC

                                  
        136 TCATTGGAGCAAGGTT-CAAGC
          1 TCATTGGAGCAAGGTTCCAAGC

               *    
        157 TCAATGGA
          1 TCATTGGA

        165 ATCGCCTAAG


Statistics
Matches: 47,  Mismatches: 1, Indels: 4
        0.90            0.02        0.08

Matches are distributed among these distances:
  20    2  0.04
  21   39  0.83
  22    6  0.13

ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24


Consensus pattern (22 bp):   
TCATTGGAGCAAGGTTCCAAGC

Found at i:447 original size:65 final size:66

Alignment explanation


    Indices: 360--489  Score: 183
    Period size: 65  Copynumber: 2.0  Consensus size: 66

        350 CTTGCTATTG

                *        *                                               *   
        360 ATTCCAACTTTCTGCACTAGCCCAGAC-ATGGGTAGGCCAAGGGTACCCCATG-CATGGGTTGGA
          1 ATTCAAACTTTCTACACTAGCCCAGACGA-GGGTAGGCCAAGGGTACCCCATGTCATGGGTAGGA

              
        423 CA
         65 CA

                                     *             **                        
        425 ATTCAAACTTTCTACACTAGCCCAGGCGAGGGTAGGCCATTGGTACCCCATGTCATGGGTAGGAC
          1 ATTCAAACTTTCTACACTAGCCCAGACGAGGGTAGGCCAAGGGTACCCCATGTCATGGGTAGGAC

        490 CAGTTTTTCC


Statistics
Matches: 57,  Mismatches: 6, Indels: 3
        0.86            0.09        0.05

Matches are distributed among these distances:
  65   45  0.79
  66   12  0.21

ACGTcount: A:0.25, C:0.27, G:0.26, T:0.22


Consensus pattern (66 bp):   
ATTCAAACTTTCTACACTAGCCCAGACGAGGGTAGGCCAAGGGTACCCCATGTCATGGGTAGGAC
A

Found at i:598 original size:11 final size:11

Alignment explanation


    Indices: 566--604  Score: 60
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        556 AAAAAGGATC

                      *
        566 TTTCCTAGCTC
          1 TTTCCTAGCTT

            *          
        577 CTTCCTAGCTT
          1 TTTCCTAGCTT

                       
        588 TTTCCTAGCTT
          1 TTTCCTAGCTT

                  
        599 TTTCCT
          1 TTTCCT

        605 TTACTCTTAG


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  11   25  1.00

ACGTcount: A:0.08, C:0.33, G:0.08, T:0.51


Consensus pattern (11 bp):   
TTTCCTAGCTT
Done.