Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010093.1 Corchorus capsularis cultivar CVL-1 contig10114, 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: 12953
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:8076 original size:12 final size:12

Alignment explanation


    Indices: 8059--8092  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       8049 TATGGAGTAA

                       *
       8059 TTAATAATAATT
          1 TTAATAATAATC

                        
       8071 TTAATAATAATC
          1 TTAATAATAATC

            *         
       8083 ATAATAATAA
          1 TTAATAATAA

       8093 GTTGTTTAAC


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41


Consensus pattern (12 bp):   
TTAATAATAATC

Found at i:10217 original size:22 final size:22

Alignment explanation


    Indices: 10191--10237  Score: 85
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      10181 ATTTATTCAT

                                  
      10191 TATTAATTAACTATTAATTAGA
          1 TATTAATTAACTATTAATTAGA

                     *            
      10213 TATTAATTAGCTATTAATTAGA
          1 TATTAATTAACTATTAATTAGA

               
      10235 TAT
          1 TAT

      10238 ATAGTATAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47


Consensus pattern (22 bp):   
TATTAATTAACTATTAATTAGA

Found at i:10233 original size:11 final size:11

Alignment explanation


    Indices: 10191--10233  Score: 68
    Period size: 11  Copynumber: 3.9  Consensus size: 11

      10181 ATTTATTCAT

                     * 
      10191 TATTAATTAAC
          1 TATTAATTAGC

                      *
      10202 TATTAATTAGA
          1 TATTAATTAGC

                       
      10213 TATTAATTAGC
          1 TATTAATTAGC

                      
      10224 TATTAATTAG
          1 TATTAATTAG

      10234 ATATATAGTA


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  11   29  1.00

ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47


Consensus pattern (11 bp):   
TATTAATTAGC

Found at i:10733 original size:2 final size:2

Alignment explanation


    Indices: 10716--10751  Score: 54
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      10706 GTTTGTTTAT

                         *                                       
      10716 TA TA GTA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      10752 TTAAATCTTA


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   2   29  0.94
   3    2  0.06

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


Consensus pattern (2 bp):   
TA

Done.