Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012106.1 Corchorus capsularis cultivar CVL-1 contig12127, 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: 10898
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31


Found at i:5846 original size:2 final size:2

Alignment explanation


    Indices: 5841--5887  Score: 57
    Period size: 2  Copynumber: 25.5  Consensus size: 2

       5831 AATTTCAGGC

                                                 *                        
       5841 TA TA TA TA -A TA TA TA TA TA TA T- TC TA TA TA -A TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                         
       5880 TA TA -A TA T
          1 TA TA TA TA T

       5888 TTTTAAAATT


Statistics
Matches: 40,  Mismatches: 1, Indels: 8
        0.82            0.02        0.16

Matches are distributed among these distances:
   1    4  0.10
   2   36  0.90

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:5857 original size:11 final size:11

Alignment explanation


    Indices: 5841--5911  Score: 58
    Period size: 11  Copynumber: 6.5  Consensus size: 11

       5831 AATTTCAGGC

                       
       5841 TATATATAATA
          1 TATATATAATA

                       
       5852 TATATAT-ATA
          1 TATATATAATA

              *         
       5862 TTCTATATAATA
          1 -TATATATAATA

                        
       5874 TATATAT-ATAA
          1 TATATATAAT-A

               * *   * 
       5885 TATTTTTAAAA
          1 TATATATAATA

                   *   
       5896 T-TATATTATA
          1 TATATATAATA

                  
       5906 TATATA
          1 TATATA

       5912 GTCAGTCGGT


Statistics
Matches: 46,  Mismatches: 9, Indels: 10
        0.71            0.14        0.15

Matches are distributed among these distances:
  10   11  0.24
  11   31  0.67
  12    4  0.09

ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51


Consensus pattern (11 bp):   
TATATATAATA

Found at i:5876 original size:24 final size:24

Alignment explanation


    Indices: 5840--5911  Score: 76
    Period size: 24  Copynumber: 2.9  Consensus size: 24

       5830 CAATTTCAGG

                                     
       5840 CTATAT-ATAATATATATATATATT
          1 CTATATAAT-ATATATATATATATT

                                     
       5864 CTATATAATATATATATATAATATT
          1 CTATATAATATATATATAT-ATATT

              *  *                  
       5889 -TTTAAAATTATATTATATATATA
          1 CTATATAA-TATA-TATATATATA

       5912 GTCAGTCGGT


Statistics
Matches: 42,  Mismatches: 2, Indels: 7
        0.82            0.04        0.14

Matches are distributed among these distances:
  24   21  0.50
  25   14  0.33
  26    7  0.17

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (24 bp):   
CTATATAATATATATATATATATT
Done.