Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022664.1 Corchorus olitorius cultivar O-4 contig22697, 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: 7695
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34


Found at i:6912 original size:29 final size:30

Alignment explanation


    Indices: 6844--6922  Score: 88
    Period size: 29  Copynumber: 2.6  Consensus size: 30

       6834 TAAATACCAA

                *                    *     
       6844 AAAAAAATCCCTTATGTTTTGCTTTTGGGAC
          1 AAAATAATCCCTTATGTTTT-CTTTCGGGAC

                      *                  *
       6875 AAAATAATCCATTATGTTTT-TTTCGGGAT
          1 AAAATAATCCCTTATGTTTTCTTTCGGGAC

               *          *    
       6904 AAATTAATCCCTTACGTTT
          1 AAAATAATCCCTTATGTTT

       6923 CAAAAATGAG


Statistics
Matches: 41,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  29   23  0.56
  31   18  0.44

ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42


Consensus pattern (30 bp):   
AAAATAATCCCTTATGTTTTCTTTCGGGAC

Found at i:7081 original size:31 final size:31

Alignment explanation


    Indices: 7046--7143  Score: 142
    Period size: 32  Copynumber: 3.1  Consensus size: 31

       7036 AAGGGACTGA

                                           
       7046 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
          1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT

                   *            *           
       7077 TTTGTCCAAAAAGAAAAACAAAAGGGATTTTT
          1 TTTGTCCCAAAAGAAAAACATAAGGGA-TTTT

                              *       *     
       7109 TTTGTCCCAAAAGAAAAATATAAGAGAATTTT
          1 TTTGTCCCAAAAGAAAAACATAAG-GGATTTT

               
       7141 TTT
          1 TTT

       7144 AGTATTTAGT


Statistics
Matches: 59,  Mismatches: 6, Indels: 3
        0.87            0.09        0.04

Matches are distributed among these distances:
  31   25  0.42
  32   32  0.54
  33    2  0.03

ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32


Consensus pattern (31 bp):   
TTTGTCCCAAAAGAAAAACATAAGGGATTTT

Found at i:7114 original size:32 final size:31

Alignment explanation


    Indices: 7046--7126  Score: 135
    Period size: 31  Copynumber: 2.6  Consensus size: 31

       7036 AAGGGACTGA

                                *          
       7046 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
          1 TTTGTCCCAAAAGAAAAACAAAAGGGATTTT

                   *                        
       7077 TTTGTCCAAAAAGAAAAACAAAAGGGATTTTT
          1 TTTGTCCCAAAAGAAAAACAAAAGGGA-TTTT

                              
       7109 TTTGTCCCAAAAGAAAAA
          1 TTTGTCCCAAAAGAAAAA

       7127 TATAAGAGAA


Statistics
Matches: 46,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  31   25  0.54
  32   21  0.46

ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27


Consensus pattern (31 bp):   
TTTGTCCCAAAAGAAAAACAAAAGGGATTTT

Done.