Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021383.1 Corchorus olitorius cultivar O-4 contig21416, 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: 2978
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:641 original size:52 final size:52

Alignment explanation


    Indices: 541--718  Score: 252
    Period size: 52  Copynumber: 3.4  Consensus size: 52

        531 TTTTTTTAAG

                *                   *                           
        541 TTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGCATTCAATCTAGCTC
          1 TTTTTAAATTGGGAAAGTTCCCATCCAGTTTTCAAAGCATTCAATCTAGCTC

                                                    *            
        593 TTTTTCAAATTGGGAAAGTTCCCA-CCAGTTTTCAAAGCAATCAATCTAGCT-
          1 TTTTT-AAATTGGGAAAGTTCCCATCCAGTTTTCAAAGCATTCAATCTAGCTC

                                     *     *     *       *      
        644 TTTTTAAATTGGGAAAGTTCCCATCAAGTTTCCAAAGTATTCAATTTAGCTC
          1 TTTTTAAATTGGGAAAGTTCCCATCCAGTTTTCAAAGCATTCAATCTAGCTC

                   *               
        696 TTTTTAATTTAGGGAAAGTTCCC
          1 TTTTTAAATT-GGGAAAGTTCCC

        719 GTCATTTTCG


Statistics
Matches: 113,  Mismatches: 9, Indels: 7
        0.88            0.07        0.05

Matches are distributed among these distances:
  50   18  0.16
  51   27  0.24
  52   38  0.34
  53   30  0.27

ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37


Consensus pattern (52 bp):   
TTTTTAAATTGGGAAAGTTCCCATCCAGTTTTCAAAGCATTCAATCTAGCTC

Found at i:1695 original size:22 final size:21

Alignment explanation


    Indices: 1651--1696  Score: 58
    Period size: 22  Copynumber: 2.1  Consensus size: 21

       1641 AAAATCTCCT

                                  
       1651 AATTCAACCTCTAGAGAGGTCG
          1 AATTCAACCTCTAGAGA-GTCG

                                   
       1673 AATTCAACCTTCGTAGAGA-TCG
          1 AATTCAACC-TC-TAGAGAGTCG

              
       1695 AA
          1 AA

       1697 ACAACAACTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  22   14  0.64
  23    2  0.09
  24    6  0.27

ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24


Consensus pattern (21 bp):   
AATTCAACCTCTAGAGAGTCG
Done.