Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000942.1 Corchorus olitorius cultivar O-4 contig00942, 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: 2253
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--58  Score: 61
    Period size: 2  Copynumber: 31.0  Consensus size: 2

                                                               *         *
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A GA TA -A TC
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                   *                     
         40 TA TA TC TA TA T- TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA

         59 AAAGTACGAA


Statistics
Matches: 47,  Mismatches: 5, Indels: 8
        0.78            0.08        0.13

Matches are distributed among these distances:
   1    4  0.09
   2   43  0.91

ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:1848 original size:21 final size:21

Alignment explanation


    Indices: 1822--1898  Score: 100
    Period size: 22  Copynumber: 3.6  Consensus size: 21

       1812 CTTATGGAAT

                  *     *       *
       1822 TTATCACAATTTTATAGGTAA
          1 TTATCAAAATTTAATAGGTAG

                        *         
       1843 TTATCAAAATTTCATATGGTAG
          1 TTATCAAAATTTAATA-GGTAG

                                  
       1865 TTATCAAAATTTAATAGGATAG
          1 TTATCAAAATTTAATAGG-TAG

                        
       1887 TTATCAAAATTT
          1 TTATCAAAATTT

       1899 CATAAAATTA


Statistics
Matches: 50,  Mismatches: 4, Indels: 3
        0.88            0.07        0.05

Matches are distributed among these distances:
  21   16  0.32
  22   34  0.68

ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42


Consensus pattern (21 bp):   
TTATCAAAATTTAATAGGTAG

Found at i:1861 original size:43 final size:44

Alignment explanation


    Indices: 1800--1902  Score: 136
    Period size: 43  Copynumber: 2.4  Consensus size: 44

       1790 CATTGTTAGG

                    *    *       *      *     *         
       1800 TTATCAAAGTTTCTTATGGAATTTATCACAATTTTATAGG-TAA
          1 TTATCAAAATTTCATATGGAAGTTATCAAAATTTAATAGGATAA

                               *                       *
       1843 TTATCAAAATTTCATATGGTAGTTATCAAAATTTAATAGGATAG
          1 TTATCAAAATTTCATATGGAAGTTATCAAAATTTAATAGGATAA

                            
       1887 TTATCAAAATTTCATA
          1 TTATCAAAATTTCATA

       1903 AAATTATTCG


Statistics
Matches: 52,  Mismatches: 7, Indels: 1
        0.87            0.12        0.02

Matches are distributed among these distances:
  43   34  0.65
  44   18  0.35

ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42


Consensus pattern (44 bp):   
TTATCAAAATTTCATATGGAAGTTATCAAAATTTAATAGGATAA
Done.