Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011848.1 Corchorus capsularis cultivar CVL-1 contig11869, 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: 11024
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30


Found at i:188 original size:20 final size:20

Alignment explanation


    Indices: 163--200  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        153 GTCCCTCACC

                    *           
        163 ATTTTTTTTAAAAATTATAT
          1 ATTTTTTTAAAAAATTATAT

                              
        183 ATTTTTTTAAAAAATTAT
          1 ATTTTTTTAAAAAATTAT

        201 TTTTTAATAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (20 bp):   
ATTTTTTTAAAAAATTATAT

Found at i:214 original size:18 final size:16

Alignment explanation


    Indices: 165--205  Score: 55
    Period size: 19  Copynumber: 2.4  Consensus size: 16

        155 CCCTCACCAT

                               
        165 TTTTTTTAAAAATTATATA
          1 TTTTTTTAAAAA--AT-TA

                            
        184 TTTTTTTAAAAAATTA
          1 TTTTTTTAAAAAATTA

                  
        200 TTTTTT
          1 TTTTTT

        206 AATAAAAAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    8  0.36
  17    2  0.09
  19   12  0.55

ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63


Consensus pattern (16 bp):   
TTTTTTTAAAAAATTA

Found at i:6903 original size:45 final size:43

Alignment explanation


    Indices: 6836--6929  Score: 129
    Period size: 45  Copynumber: 2.2  Consensus size: 43

       6826 AAGGATCGCA

                            *                   *       
       6836 TGGCC-GGTTGTGCATGGGCATGGCC-GAGTCATGTGGCCGGTG
          1 TGGCCGGGTTGTGCATCGGCATGGCCTGA-TCATGTAGCCGGTG

                                                         
       6878 TGGCCGGGCTTGTGCGATCGGCATGGCCTGATCATGTAGCCGGTG
          1 TGGCCGGG-TTGTGC-ATCGGCATGGCCTGATCATGTAGCCGGTG

                   
       6923 TGGCCGG
          1 TGGCCGG

       6930 TCAACTGCTT


Statistics
Matches: 46,  Mismatches: 2, Indels: 5
        0.87            0.04        0.09

Matches are distributed among these distances:
  42    5  0.11
  43    2  0.04
  44    6  0.13
  45   31  0.67
  46    2  0.04

ACGTcount: A:0.10, C:0.23, G:0.44, T:0.23


Consensus pattern (43 bp):   
TGGCCGGGTTGTGCATCGGCATGGCCTGATCATGTAGCCGGTG
Done.