Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010934.1 Corchorus olitorius cultivar O-4 contig10966, 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: 10932
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33


Found at i:1955 original size:20 final size:20

Alignment explanation


    Indices: 1930--1971  Score: 75
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       1920 GCGGCTGGTG

                                
       1930 TGTGCTTTTGGCGATTATCT
          1 TGTGCTTTTGGCGATTATCT

                       *        
       1950 TGTGCTTTTGGTGATTATCT
          1 TGTGCTTTTGGCGATTATCT

              
       1970 TG
          1 TG

       1972 AACCATTGCT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.10, C:0.12, G:0.26, T:0.52


Consensus pattern (20 bp):   
TGTGCTTTTGGCGATTATCT

Found at i:3131 original size:3 final size:3

Alignment explanation


    Indices: 3123--3148  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       3113 GTAATTAAAT

                                              
       3123 TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TT

       3149 TAAGAAAATA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTA

Found at i:9917 original size:31 final size:31

Alignment explanation


    Indices: 9882--9940  Score: 91
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       9872 GGTTAATTAA

                         *     *           
       9882 GTCCCTAACATTGTAAAATTGGCTCAAAAAT
          1 GTCCCTAACATTGCAAAATCGGCTCAAAAAT

                     *                  
       9913 GTCCCTAACGTTGCAAAATCGGCTCAAA
          1 GTCCCTAACATTGCAAAATCGGCTCAAA

       9941 TTAGTCCCTG


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  31   25  1.00

ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25


Consensus pattern (31 bp):   
GTCCCTAACATTGCAAAATCGGCTCAAAAAT

Found at i:9948 original size:31 final size:31

Alignment explanation


    Indices: 9876--9949  Score: 87
    Period size: 31  Copynumber: 2.4  Consensus size: 31

       9866 TAATTTGGTT

                               *     *      
       9876 AATTAAGTCCCTAACATTGTAAAATTGGCTCA
          1 AATT-AGTCCCTAACATTGCAAAATCGGCTCA

               *           *                
       9908 AA-AATGTCCCTAACGTTGCAAAATCGGCTCA
          1 AATTA-GTCCCTAACATTGCAAAATCGGCTCA

                       
       9939 AATTAGTCCCT
          1 AATTAGTCCCT

       9950 GAAATCAATT


Statistics
Matches: 35,  Mismatches: 5, Indels: 5
        0.78            0.11        0.11

Matches are distributed among these distances:
  30    1  0.03
  31   31  0.89
  32    3  0.09

ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28


Consensus pattern (31 bp):   
AATTAGTCCCTAACATTGCAAAATCGGCTCA
Done.