Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003487.1 Corchorus capsularis cultivar CVL-1 contig03495, 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, 717

Length: 1196
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37


Found at i:934 original size:14 final size:14

Alignment explanation


    Indices: 898--927  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

        888 AAGGTTTTCA

                          
        898 AAAATTCAAAAATC
          1 AAAATTCAAAAATC

                          
        912 AAAATTCAAAAATC
          1 AAAATTCAAAAATC

              
        926 AA
          1 AA

        928 GAATCAAGTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20


Consensus pattern (14 bp):   
AAAATTCAAAAATC

Found at i:935 original size:7 final size:7

Alignment explanation


    Indices: 895--934  Score: 53
    Period size: 7  Copynumber: 5.6  Consensus size: 7

        885 AAAAAGGTTT

                   
        895 TCAAAAA
          1 TCAAAAA

                    
        902 TTCAAAAA
          1 -TCAAAAA

                  *
        910 TCAAAAT
          1 TCAAAAA

                   
        917 TCAAAAA
          1 TCAAAAA

                *  
        924 TCAAGAA
          1 TCAAAAA

                
        931 TCAA
          1 TCAA

        935 GTTTTCAAAG


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
   7   22  0.76
   8    7  0.24

ACGTcount: A:0.62, C:0.15, G:0.03, T:0.20


Consensus pattern (7 bp):   
TCAAAAA

Found at i:1008 original size:36 final size:37

Alignment explanation


    Indices: 930--1039  Score: 150
    Period size: 37  Copynumber: 3.0  Consensus size: 37

        920 AAAATCAAGA

                                    **           
        930 ATCAAGTTTTCAAAGTTTTCAAATAAGGAAAGTTCCC
          1 ATCAAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCC

                                  *              
        967 ATCAAGTTTTCAAAGTTTTC-ATTTGGGAAAGTTCCC
          1 ATCAAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCC

            *            *   *    *              
       1003 CTCAAGTTTTCAAGGTTGTCAAGTTGGGAAAGTTCCC
          1 ATCAAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCC

       1040 GTTAGGTTTC


Statistics
Matches: 65,  Mismatches: 7, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  36   30  0.46
  37   35  0.54

ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Consensus pattern (37 bp):   
ATCAAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCC
Done.