Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000662.1 Corchorus olitorius cultivar O-4 contig00662, 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, 618

Length: 1030
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34


Found at i:324 original size:10 final size:10

Alignment explanation


    Indices: 300--334  Score: 61
    Period size: 10  Copynumber: 3.4  Consensus size: 10

        290 GGTCCATTCA

                      
        300 TTTTCTTTTT
          1 TTTTCTTTTT

                       
        310 CTTTTCTTTTT
          1 -TTTTCTTTTT

                      
        321 TTTTCTTTTT
          1 TTTTCTTTTT

                
        331 TTTT
          1 TTTT

        335 AAAAAACTTG


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

Matches are distributed among these distances:
  10   14  0.58
  11   10  0.42

ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89


Consensus pattern (10 bp):   
TTTTCTTTTT

Found at i:419 original size:19 final size:18

Alignment explanation


    Indices: 394--456  Score: 65
    Period size: 19  Copynumber: 3.4  Consensus size: 18

        384 CCGCGCACCA

                              
        394 GGCCTGGGCGCTTGGGCC
          1 GGCCTGGGCGCTTGGGCC

                      * *  *   
        412 GTGCCT-GGCCCGTGCGCC
          1 G-GCCTGGGCGCTTGGGCC

                               
        430 AGGCCTGGGCGCTTGGGCC
          1 -GGCCTGGGCGCTTGGGCC

                    
        449 GCGCCTGG
          1 G-GCCTGG

        457 CCCGCGCGCC


Statistics
Matches: 35,  Mismatches: 6, Indels: 7
        0.73            0.12        0.15

Matches are distributed among these distances:
  18   15  0.43
  19   20  0.57

ACGTcount: A:0.02, C:0.37, G:0.46, T:0.16


Consensus pattern (18 bp):   
GGCCTGGGCGCTTGGGCC

Found at i:466 original size:37 final size:37

Alignment explanation


    Indices: 379--466  Score: 149
    Period size: 37  Copynumber: 2.4  Consensus size: 37

        369 GGGCCATACG

                       *                      *  
        379 CTGGCCCGCGCACCAGGCCTGGGCGCTTGGGCCGTGC
          1 CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC

                    *                            
        416 CTGGCCCGTGCGCCAGGCCTGGGCGCTTGGGCCGCGC
          1 CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC

                          
        453 CTGGCCCGCGCGCC
          1 CTGGCCCGCGCGCC

        467 TGGCTGGCCC


Statistics
Matches: 47,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  37   47  1.00

ACGTcount: A:0.03, C:0.43, G:0.41, T:0.12


Consensus pattern (37 bp):   
CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC
Done.