Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002870.1 Corchorus capsularis cultivar CVL-1 contig02878, 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, 664

Length: 1108
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.34


Found at i:814 original size:78 final size:77

Alignment explanation


    Indices: 732--935  Score: 205
    Period size: 78  Copynumber: 2.6  Consensus size: 77

        722 CAAGAAATAT

                             *                               *               
        732 ATTTAAAAAAACTAATATATCAAGTTGTT-TTAACTAAAATAGTAAAATTGTAAAATATAATAGT
          1 ATTTAAAAAAA-TAA-AAATCAAGTTGTTATTAACTAAAATAGTAAAATGGTAAAATATAATAGT

                          
        796 TATAAGGATATTAG
         64 TATAAGGATATTAG

                  ** *        **    *      * *                               
        810 ATTTAATTATATAAAAATTGAGTTTTTAGTTGAGTAAAATAGTAAAATGGTAAAATATAATAGTT
          1 ATTTAAAAAAATAAAAATCAAGTTGTTA-TTAACTAAAATAGTAAAATGGTAAAATATAATAGTT

                         
        875 ATAAGGATATTAG
         65 ATAAGGATATTAG

                  ** *               *      * *              
        888 ATTTAATTATATAAAAAT-AGAGTTTTTAGTTGAGTAAAATAGTAAAAT
          1 ATTTAAAAAAATAAAAATCA-AGTTGTTA-TTAACTAAAATAGTAAAAT

        936 AAAATAATTA


Statistics
Matches: 112,  Mismatches: 11, Indels: 6
        0.87            0.09        0.05

Matches are distributed among these distances:
  76    9  0.08
  77    3  0.03
  78  100  0.89

ACGTcount: A:0.48, C:0.01, G:0.13, T:0.38


Consensus pattern (77 bp):   
ATTTAAAAAAATAAAAATCAAGTTGTTATTAACTAAAATAGTAAAATGGTAAAATATAATAGTTA
TAAGGATATTAG

Found at i:847 original size:70 final size:70

Alignment explanation


    Indices: 772--996  Score: 315
    Period size: 70  Copynumber: 3.1  Consensus size: 70

        762 TAACTAAAAT

                                                                    *        
        772 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
          1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT

                 
        837 AGTTG
         66 AGTTG

                                                                             
        842 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
          1 AGT-AAA-A-T----T-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA

                         
        907 GAGTTTTTAGTTG
         58 GAGTTTTTAGTTG

                    *        *    *      *       *         *                 
        920 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
          1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT

                 
        985 AGTTG
         66 AGTTG

                   
        990 AGTAAAA
          1 AGTAAAA

        997 CTATAAAAAC


Statistics
Matches: 140,  Mismatches: 7, Indels: 16
        0.86            0.04        0.10

Matches are distributed among these distances:
  70   66  0.47
  71    3  0.02
  72    1  0.01
  73    1  0.01
  75    1  0.01
  76    1  0.01
  77    4  0.03
  78   63  0.45

ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38


Consensus pattern (70 bp):   
AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG

Done.