Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001764.1 Corchorus capsularis cultivar CVL-1 contig01764, 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, 762

Length: 1271
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27


Found at i:173 original size:17 final size:17

Alignment explanation


    Indices: 151--209  Score: 73
    Period size: 17  Copynumber: 3.2  Consensus size: 17

        141 CCTCTTTTCG

                             * 
        151 TTTATATATAAATATATTT
          1 TTTATATATAAAT-T-TAT

                               
        170 TATATATATATAAATTTAT
          1 T-T-TATATATAAATTTAT

                             
        189 TTTATATATAAATTTAT
          1 TTTATATATAAATTTAT

                
        206 TTTA
          1 TTTA

        210 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:179 original size:21 final size:21

Alignment explanation


    Indices: 153--198  Score: 83
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        143 TCTTTTCGTT

                                 
        153 TATATATAAATATATTTTATA
          1 TATATATAAATATATTTTATA

                       *         
        174 TATATATAAATTTATTTTATA
          1 TATATATAAATATATTTTATA

                
        195 TATA
          1 TATA

        199 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:207 original size:21 final size:20

Alignment explanation


    Indices: 151--207  Score: 57
    Period size: 21  Copynumber: 2.9  Consensus size: 20

        141 CCTCTTTTCG

                                
        151 TTTATATATAAA-TA--TAT
          1 TTTATATATAAATTATTTAT

                      *   *      
        168 TTTATATATATATAAATTTAT
          1 TTTATATATAAAT-TATTTAT

                               
        189 TTTATATATAAATTTATTT
          1 TTTATATATAAA-TTATTT

        208 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.