Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004280.1 Corchorus capsularis cultivar CVL-1 contig04288, 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, 628

Length: 1047
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28


Found at i:157 original size:14 final size:14

Alignment explanation


    Indices: 138--168  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

        128 TGTACAATAT

                          
        138 ATAAGAATTATACG
          1 ATAAGAATTATACG

                          
        152 ATAAGAATTATACG
          1 ATAAGAATTATACG

               
        166 ATA
          1 ATA

        169 TATATCCATC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29


Consensus pattern (14 bp):   
ATAAGAATTATACG

Found at i:886 original size:17 final size:17

Alignment explanation


    Indices: 864--922  Score: 73
    Period size: 17  Copynumber: 3.2  Consensus size: 17

        854 CCTCTTTTCG

                             * 
        864 TTTATATATAAATATATTT
          1 TTTATATATAAAT-T-TAT

                               
        883 TATATATATATAAATTTAT
          1 T-T-TATATATAAATTTAT

                             
        902 TTTATATATAAATTTAT
          1 TTTATATATAAATTTAT

                
        919 TTTA
          1 TTTA

        923 AAAATTTATA


Statistics
Matches: 37,  Mismatches: 1, Indels: 6
        0.84            0.02        0.14

Matches are distributed among these distances:
  17   19  0.51
  18    1  0.03
  19    4  0.11
  20    2  0.05
  21   11  0.30

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (17 bp):   
TTTATATATAAATTTAT

Found at i:892 original size:21 final size:21

Alignment explanation


    Indices: 866--911  Score: 83
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        856 TCTTTTCGTT

                                 
        866 TATATATAAATATATTTTATA
          1 TATATATAAATATATTTTATA

                       *         
        887 TATATATAAATTTATTTTATA
          1 TATATATAAATATATTTTATA

                
        908 TATA
          1 TATA

        912 AATTTATTTT


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

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (21 bp):   
TATATATAAATATATTTTATA

Found at i:920 original size:21 final size:20

Alignment explanation


    Indices: 864--920  Score: 57
    Period size: 21  Copynumber: 2.9  Consensus size: 20

        854 CCTCTTTTCG

                                
        864 TTTATATATAAA-TA--TAT
          1 TTTATATATAAATTATTTAT

                      *   *      
        881 TTTATATATATATAAATTTAT
          1 TTTATATATAAAT-TATTTAT

                               
        902 TTTATATATAAATTTATTT
          1 TTTATATATAAA-TTATTT

        921 TAAAAATTTA


Statistics
Matches: 31,  Mismatches: 4, Indels: 6
        0.76            0.10        0.15

Matches are distributed among these distances:
  17   11  0.35
  19    1  0.03
  21   18  0.58
  22    1  0.03

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (20 bp):   
TTTATATATAAATTATTTAT
Done.