Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007400.1 Corchorus capsularis cultivar CVL-1 contig07421, 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: 17069
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31


Found at i:12270 original size:12 final size:12

Alignment explanation


    Indices: 12255--12279  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      12245 CCACTTGACC

                        
      12255 GGCCATCGCATG
          1 GGCCATCGCATG

                        
      12267 GGCCATCGCATG
          1 GGCCATCGCATG

             
      12279 G
          1 G

      12280 AGCAACCGGC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16


Consensus pattern (12 bp):   
GGCCATCGCATG

Found at i:12302 original size:30 final size:30

Alignment explanation


    Indices: 12267--12327  Score: 104
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      12257 CCATCGCATG

                                   *      
      12267 GGCCATCGCATGGAGCAACCGGCTACAACC
          1 GGCCATCGCATGGAGCAACCGGCCACAACC

                               *          
      12297 GGCCATCGCATGGAGCAACTGGCCACAACC
          1 GGCCATCGCATGGAGCAACCGGCCACAACC

             
      12327 G
          1 G

      12328 ACCAATGGAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.26, C:0.36, G:0.28, T:0.10


Consensus pattern (30 bp):   
GGCCATCGCATGGAGCAACCGGCCACAACC

Found at i:13176 original size:23 final size:23

Alignment explanation


    Indices: 13117--13181  Score: 94
    Period size: 23  Copynumber: 2.8  Consensus size: 23

      13107 GAACTAAATT

                                   
      13117 GCTTGGCGCCCGACCACTTCCAA
          1 GCTTGGCGCCCGACCACTTCCAA

              * *                  
      13140 GCCTAGCGCCCGACCACTTCCAA
          1 GCTTGGCGCCCGACCACTTCCAA

                  *  *         
      13163 GCTTGGTGCTCGACCACTT
          1 GCTTGGCGCCCGACCACTT

      13182 GCAAACAAAG


Statistics
Matches: 36,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   36  1.00

ACGTcount: A:0.17, C:0.42, G:0.22, T:0.20


Consensus pattern (23 bp):   
GCTTGGCGCCCGACCACTTCCAA

Found at i:13356 original size:26 final size:26

Alignment explanation


    Indices: 13270--13386  Score: 94
    Period size: 26  Copynumber: 4.5  Consensus size: 26

      13260 AGCTGGCACA

                                     *
      13270 CCACACGTGACCTCCAACGGACAACT
          1 CCACACGTGACCTCCAACGGACAACC

             **       *   *    *  *  *
      13296 CTTCACGTGATCTCTAAC-TACGACT
          1 CCACACGTGACCTCCAACGGACAACC

              * *                     
      13321 CCTCGCGTGACCTCCAACGGAC-ACC
          1 CCACACGTGACCTCCAACGGACAACC

                  *         *   *      
      13346 TCCACATGTGACCTCCGACGTACAACC
          1 -CCACACGTGACCTCCAACGGACAACC

                          
      13373 CCACACGTGACCTC
          1 CCACACGTGACCTC

      13387 GCGCGTGCGT


Statistics
Matches: 70,  Mismatches: 18, Indels: 6
        0.74            0.19        0.06

Matches are distributed among these distances:
  25   21  0.30
  26   46  0.66
  27    3  0.04

ACGTcount: A:0.25, C:0.42, G:0.15, T:0.18


Consensus pattern (26 bp):   
CCACACGTGACCTCCAACGGACAACC
Done.