Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014855.1 Corchorus olitorius cultivar O-4 contig14888, 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: 2472
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36


Found at i:862 original size:6 final size:6

Alignment explanation


    Indices: 851--905  Score: 51
    Period size: 6  Copynumber: 9.5  Consensus size: 6

        841 TTTTATTTTA

                                      *  *   *      *        *     
        851 TTTTCT TTTTCT TTTTCT TTTTCC TCTTCC TTTTCC TTTTC- CTTT-T
          1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT

                      
        897 TTTTCT TTT
          1 TTTTCT TTT

        906 CCTGGCTTGG


Statistics
Matches: 42,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
   5    6  0.14
   6   36  0.86

ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76


Consensus pattern (6 bp):   
TTTTCT

Found at i:868 original size:12 final size:12

Alignment explanation


    Indices: 851--905  Score: 60
    Period size: 12  Copynumber: 4.8  Consensus size: 12

        841 TTTTATTTTA

                       *
        851 TTTTCTTTTTCT
          1 TTTTCTTTTTCC

                        
        863 TTTTCTTTTTCC
          1 TTTTCTTTTTCC

             *   *      
        875 TCTTCCTTTTCC
          1 TTTTCTTTTTCC

                 *      
        887 TTTTCCTTTT--
          1 TTTTCTTTTTCC

                     
        897 TTTTCTTTT
          1 TTTTCTTTT

        906 CCTGGCTTGG


Statistics
Matches: 38,  Mismatches: 5, Indels: 2
        0.84            0.11        0.04

Matches are distributed among these distances:
  10    8  0.21
  12   30  0.79

ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76


Consensus pattern (12 bp):   
TTTTCTTTTTCC

Found at i:969 original size:25 final size:23

Alignment explanation


    Indices: 941--992  Score: 68
    Period size: 24  Copynumber: 2.2  Consensus size: 23

        931 AGCCTGGCCT

                                     
        941 GGCCCGCGCGCCTGGGCCACGCACA
          1 GGCCCGCGCG-CTGGGCCACGC-CA

                  *          *     
        966 GGCCCGTGCGCTGGGCCGCGCCA
          1 GGCCCGCGCGCTGGGCCACGCCA

                
        989 GGCC
          1 GGCC

        993 GGCCCAGCAG


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  23    6  0.24
  24   10  0.40
  25    9  0.36

ACGTcount: A:0.08, C:0.46, G:0.40, T:0.06


Consensus pattern (23 bp):   
GGCCCGCGCGCTGGGCCACGCCA
Done.