Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023385.1 Corchorus olitorius cultivar O-4 contig23418, 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: 2533
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30


Found at i:83 original size:21 final size:21

Alignment explanation


    Indices: 59--171  Score: 149
    Period size: 21  Copynumber: 5.4  Consensus size: 21

         49 CTTAGGCAAT

                         *        
         59 TCCAATGAGCTTGAAACCTT-C
          1 TCCAATGAGCTTGGAA-CTTGC

                      *           
         80 TCCAATGAGCGTGGAACCTT-C
          1 TCCAATGAGCTTGGAA-CTTGC

             **                  
        101 TTTAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                            *    
        122 TCCAATGAGCTTGGAATTTGC
          1 TCCAATGAGCTTGGAACTTGC

                                 
        143 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                    
        164 TCCAATGA
          1 TCCAATGA

        172 ACTCCTAGCA


Statistics
Matches: 82,  Mismatches: 9, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  20    3  0.04
  21   79  0.96

ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACTTGC

Found at i:966 original size:33 final size:34

Alignment explanation


    Indices: 894--967  Score: 82
    Period size: 33  Copynumber: 2.2  Consensus size: 34

        884 CTATGATCAA

                     *                 ** *   
        894 CCAAAAC-AGATTTGTTTTCATCACAATTAGCAT
          1 CCAAAACAAAATTTGTTTTCATCACAAACAACAT

                                              
        927 CCAAAACAAAATTTG-TTTCATCACAAACAACA-
          1 CCAAAACAAAATTTGTTTTCATCACAAACAACAT

                     
        959 CCTAAAACA
          1 CC-AAAACA

        968 GATTTAGTGT


Statistics
Matches: 35,  Mismatches: 4, Indels: 4
        0.81            0.09        0.09

Matches are distributed among these distances:
  32    2  0.06
  33   27  0.77
  34    6  0.17

ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26


Consensus pattern (34 bp):   
CCAAAACAAAATTTGTTTTCATCACAAACAACAT

Found at i:2440 original size:21 final size:21

Alignment explanation


    Indices: 2416--2528  Score: 133
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       2406 CTTAGGCAAT

                         *        
       2416 TCCAATGAGCTTGAAACCTT-C
          1 TCCAATGAGCTTGGAA-CTTGC

                      *           
       2437 TCCAATGAGCGTGGAACCTT-C
          1 TCCAATGAGCTTGGAA-CTTGC

             **                  
       2458 TTTAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                  *               
       2479 TCCAATAAGCTTGGAA-TTCGC
          1 TCCAATGAGCTTGGAACTT-GC

                                 
       2500 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                    
       2521 TCCAATGA
          1 TCCAATGA

       2529 ACTCC


Statistics
Matches: 80,  Mismatches: 9, Indels: 6
        0.84            0.09        0.06

Matches are distributed among these distances:
  20    5  0.06
  21   73  0.91
  22    2  0.03

ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACTTGC

Done.