Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024383.1 Corchorus olitorius cultivar O-4 contig24416, 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: 23238
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31


Found at i:3164 original size:21 final size:21

Alignment explanation


    Indices: 3140--3210  Score: 117
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       3130 CTTAGGCAAT

                         *       
       3140 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       3161 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       3182 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       3203 TCCAATGA
          1 TCCAATGA

       3211 TCTCCTAGCA


Statistics
Matches: 48,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  20    3  0.06
  21   45  0.94

ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:17016 original size:21 final size:21

Alignment explanation


    Indices: 16990--17081  Score: 132
    Period size: 21  Copynumber: 4.4  Consensus size: 21

      16980 TGCTAGGAGA

                                  
      16990 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                    *        *   
      17011 TCATTGGACAAGGTTCCTAGC
          1 TCATTGGAGAAGGTTCCAAGC

              *                  
      17032 TCCTTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
      17053 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
      17074 TCATTGGA
          1 TCATTGGA

      17082 ATTGCCTAAG


Statistics
Matches: 63,  Mismatches: 7, Indels: 2
        0.88            0.10        0.03

Matches are distributed among these distances:
  20    2  0.03
  21   61  0.97

ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:22095 original size:20 final size:21

Alignment explanation


    Indices: 22072--22114  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      22062 ATCTTGAAGA

                                 
      22072 ATTTAAAG-CCATCGGAGATC
          1 ATTTAAAGCCCATCGGAGATC

                *        *       
      22092 ATTTGAAGCCCATTGGAGATC
          1 ATTTAAAGCCCATCGGAGATC

              
      22113 AT
          1 AT

      22115 CAACAAAGGA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    7  0.35
  21   13  0.65

ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28


Consensus pattern (21 bp):   
ATTTAAAGCCCATCGGAGATC

Done.