Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002806.1 Corchorus capsularis cultivar CVL-1 contig02814, 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: 2390
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.38


Found at i:377 original size:13 final size:14

Alignment explanation


    Indices: 357--388  Score: 55
    Period size: 14  Copynumber: 2.3  Consensus size: 14

        347 TTGGATTTAA

                  *       
        357 ATTTTTTATAAATT
          1 ATTTTTAATAAATT

                          
        371 ATTTTTAATAAATT
          1 ATTTTTAATAAATT

                
        385 ATTT
          1 ATTT

        389 AATTCAACAT


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

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (14 bp):   
ATTTTTAATAAATT

Found at i:865 original size:41 final size:41

Alignment explanation


    Indices: 818--950  Score: 110
    Period size: 41  Copynumber: 3.2  Consensus size: 41

        808 ATGTCTTTAG

                                                *    
        818 GGACTTTGATACAGATGTCTCTGTGTTAAGAATGTGCTTGA
          1 GGACTTTGATACAGATGTCTCTGTGTTAAGAATGTGTTTGA

                     * *         *             *        *
        859 GGACTTTGAGAGAGAAT-TGCCCATGTGTTATA-ATTGTGTTTGG
          1 GGACTTTGATACAG-ATGT-CTC-TGTGTTA-AGAATGTGTTTGA

               *        *     *          *            
        902 GGATTTTGATATTA-ATGCCTCTGTGTTATGAATGTGTTTGA
          1 GGACTTTGATA-CAGATGTCTCTGTGTTAAGAATGTGTTTGA

                    
        943 GGACTTTG
          1 GGACTTTG

        951 GTTATTGGGT


Statistics
Matches: 70,  Mismatches: 15, Indels: 14
        0.71            0.15        0.14

Matches are distributed among these distances:
  41   36  0.51
  42    8  0.11
  43   24  0.34
  44    2  0.03

ACGTcount: A:0.23, C:0.10, G:0.28, T:0.40


Consensus pattern (41 bp):   
GGACTTTGATACAGATGTCTCTGTGTTAAGAATGTGTTTGA

Found at i:2074 original size:15 final size:14

Alignment explanation


    Indices: 2043--2084  Score: 57
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       2033 ACATATATTC

                      *   
       2043 AATGTTATAACATA
          1 AATGTTATAAAATA

                           
       2057 AATGTTATAATAATA
          1 AATGTTATAA-AATA

                  *      
       2072 AATGTTCTAAAAT
          1 AATGTTATAAAAT

       2085 TGTAACCTCT


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

Matches are distributed among these distances:
  14   13  0.52
  15   12  0.48

ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38


Consensus pattern (14 bp):   
AATGTTATAAAATA
Done.