Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004963.1 Corchorus capsularis cultivar CVL-1 contig04981, 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: 3220
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:707 original size:59 final size:59

Alignment explanation


    Indices: 615--732  Score: 236
    Period size: 59  Copynumber: 2.0  Consensus size: 59

        605 AAAATGAGCC

                                                                       
        615 CATTGCAGGGCCATGATAAGGCCCATCATTAGAAGCCTAATCTTGCTATGTTTTGAATG
          1 CATTGCAGGGCCATGATAAGGCCCATCATTAGAAGCCTAATCTTGCTATGTTTTGAATG

                                                                       
        674 CATTGCAGGGCCATGATAAGGCCCATCATTAGAAGCCTAATCTTGCTATGTTTTGAATG
          1 CATTGCAGGGCCATGATAAGGCCCATCATTAGAAGCCTAATCTTGCTATGTTTTGAATG

        733 TTGATTATTC


Statistics
Matches: 59,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  59   59  1.00

ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31


Consensus pattern (59 bp):   
CATTGCAGGGCCATGATAAGGCCCATCATTAGAAGCCTAATCTTGCTATGTTTTGAATG

Found at i:891 original size:43 final size:45

Alignment explanation


    Indices: 806--895  Score: 148
    Period size: 43  Copynumber: 2.0  Consensus size: 45

        796 ATGGTAATCT

                                                         
        806 ATAAGTTCCCTATGTAACCAAAGAGAGATTGAGAGATTGGATCGA
          1 ATAAGTTCCCTATGTAACCAAAGAGAGATTGAGAGATTGGATCGA

                   *               *                     
        851 ATAAGTTGCCTATGTAACC-AA-CGAGATTGAGAGATTGGATCGA
          1 ATAAGTTCCCTATGTAACCAAAGAGAGATTGAGAGATTGGATCGA

              
        894 AT
          1 AT

        896 GCTAAGCAAC


Statistics
Matches: 43,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
  43   23  0.53
  44    2  0.05
  45   18  0.42

ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26


Consensus pattern (45 bp):   
ATAAGTTCCCTATGTAACCAAAGAGAGATTGAGAGATTGGATCGA

Found at i:2837 original size:49 final size:50

Alignment explanation


    Indices: 2534--2956  Score: 576
    Period size: 50  Copynumber: 8.4  Consensus size: 50

       2524 TGTCACTATG

                                          *        *          
       2534 CTAATTACTAAATTTTTTAAATGTTTGGAGAGACAGCTCTCATCGGTCTC
          1 CTAATTACTAAATTTTTTAAATGTTTGGAGGGACAGCTCCCATCGGTCTC

                                                          *     
       2584 CTAATTACTAAATTTTTTAAAATGTTTGGAGGGACAGC-CCTCATCAGTCTC
          1 CTAATTACTAAATTTTTT-AAATGTTTGGAGGGACAGCTCC-CATCGGTCTC

                                                               
       2635 CTAATTACTAAATTTTTTAAATGTTTGGAGGGACAGC-CCTCATCGGTCTC
          1 CTAATTACTAAATTTTTTAAATGTTTGGAGGGACAGCTCC-CATCGGTCTC

                                                                  
       2685 CTAATTACTAAATTTTTTTAAAATGTTTGGAGGGACAGC-CCTCATCGGTCTCC
          1 CTAATTACTAAA-TTTTTT-AAATGTTTGGAGGGACAGCTCC-CATCGGTCT-C

                                                     *          
       2738 CTAATTACTAAAATTTTTTAAAATGTTTGGAGGGACAGCTCTCAT--GTCTC
          1 CTAATTACT-AAATTTTTT-AAATGTTTGGAGGGACAGCTCCCATCGGTCTC

                               *                               
       2788 CTAATTACTAAA-TTTTTAGATGTTTGG-GGAGACAGCTCCCATCGGTCTC
          1 CTAATTACTAAATTTTTTAAATGTTTGGAGG-GACAGCTCCCATCGGTCTC

                               *          * *                 
       2837 CTAATTACTAAATTTTTTAGATGTTTGG-GAGTCAGCTCCCATCGGTCTC
          1 CTAATTACTAAATTTTTTAAATGTTTGGAGGGACAGCTCCCATCGGTCTC

                               *             *                 
       2886 CTAATTACTAAATTTTTTAGATGTTTGG-GGAGGCAGCTCCCATCGGTCTC
          1 CTAATTACTAAATTTTTTAAATGTTTGGAGG-GACAGCTCCCATCGGTCTC

                        **       
       2936 CTAATTACTAAAAATTTTAAA
          1 CTAATTACTAAATTTTTTAAA

       2957 CTTTTTAAAT


Statistics
Matches: 347,  Mismatches: 14, Indels: 24
        0.90            0.04        0.06

Matches are distributed among these distances:
  46    2  0.01
  47   20  0.06
  48    5  0.01
  49   67  0.19
  50  124  0.36
  51   55  0.16
  52   31  0.09
  53   39  0.11
  54    4  0.01

ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37


Consensus pattern (50 bp):   
CTAATTACTAAATTTTTTAAATGTTTGGAGGGACAGCTCCCATCGGTCTC
Done.