Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021072.1 Corchorus olitorius cultivar O-4 contig21105, 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: 4266
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33


Found at i:2202 original size:21 final size:22

Alignment explanation


    Indices: 2158--2200  Score: 59
    Period size: 23  Copynumber: 1.9  Consensus size: 22

       2148 AGTTTTGGAA

                     *    *        
       2158 ATATGTATCCACTATTATAAAAT
          1 ATATGTATCAACTAGTAT-AAAT

                                
       2181 ATATGTATCAACTAGTATAA
          1 ATATGTATCAACTAGTATAA

       2201 TATTTGTTTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  22    2  0.11
  23   16  0.89

ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37


Consensus pattern (22 bp):   
ATATGTATCAACTAGTATAAAT

Found at i:2358 original size:22 final size:22

Alignment explanation


    Indices: 2330--2374  Score: 81
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2320 CGGCCAAGAT

                                  
       2330 TTTCTAATTTCACATCCCTTTC
          1 TTTCTAATTTCACATCCCTTTC

                       *          
       2352 TTTCTAATTTCTCATCCCTTTC
          1 TTTCTAATTTCACATCCCTTTC

             
       2374 T
          1 T

       2375 ATGGTTCTAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.16, C:0.31, G:0.00, T:0.53


Consensus pattern (22 bp):   
TTTCTAATTTCACATCCCTTTC

Found at i:2740 original size:20 final size:20

Alignment explanation


    Indices: 2715--2753  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2705 CATATAAAAT

                          *     
       2715 AATAATAAATAATTTTTAAA
          1 AATAATAAATAATTATTAAA

                    *          
       2735 AATAATAACTAATTATTAA
          1 AATAATAAATAATTATTAA

       2754 TTTTTTTTAA


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

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38


Consensus pattern (20 bp):   
AATAATAAATAATTATTAAA
Done.