Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014656.1 Corchorus capsularis cultivar CVL-1 contig14677, 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: 7097
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28


Found at i:2539 original size:1 final size:1

Alignment explanation


    Indices: 2533--2569  Score: 74
    Period size: 1  Copynumber: 37.0  Consensus size: 1

       2523 ACACACAAGG

                                                 
       2533 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       2570 GCTAATAGAC


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   36  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:3609 original size:33 final size:33

Alignment explanation


    Indices: 3572--3635  Score: 85
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       3562 ATCAAGGCAG

                               *       *      
       3572 AAAATGAGGGAT-AAAGTCGAAAAGCAGCAGCAC
          1 AAAATG-GGGATGAAAGTCAAAAAGCAACAGCAC

                     *                     
       3605 AAAATGGGGGTGAAAGTCAAAAAGCAACAGC
          1 AAAATGGGGATGAAAGTCAAAAAGCAACAGC

       3636 GGCAATCGTG


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  32    4  0.15
  33   23  0.85

ACGTcount: A:0.48, C:0.14, G:0.28, T:0.09


Consensus pattern (33 bp):   
AAAATGGGGATGAAAGTCAAAAAGCAACAGCAC

Found at i:6446 original size:27 final size:27

Alignment explanation


    Indices: 6416--6495  Score: 115
    Period size: 27  Copynumber: 3.0  Consensus size: 27

       6406 GCATTAGGGT

                  *   *                
       6416 CACCCAAGGGTATTTTGGTCATTTTTG
          1 CACCCAGGGGCATTTTGGTCATTTTTG

                                       
       6443 CACCCAGGGGCATTTTGGTCATTTTTG
          1 CACCCAGGGGCATTTTGGTCATTTTTG

            *  *            *         
       6470 TACTCAGGGGCATTTTAGTCATTTTT
          1 CACCCAGGGGCATTTTGGTCATTTTT

       6496 AGGTTCACCT


Statistics
Matches: 48,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   48  1.00

ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41


Consensus pattern (27 bp):   
CACCCAGGGGCATTTTGGTCATTTTTG
Done.