Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010544.1 Corchorus capsularis cultivar CVL-1 contig10565, 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: 25024
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:989 original size:31 final size:30

Alignment explanation


    Indices: 921--989  Score: 79
    Period size: 31  Copynumber: 2.3  Consensus size: 30

        911 TGCCATAAAT

                           *            * 
        921 CTCAAATAAGGGCCTGAACTTTAGAAAATG
          1 CTCAAATAAGGGCCTCAACTTTAGAAAAGG

                                             
        951 -TCAAAATAAGGG-CTCCAACTTTTAGAAAAGG
          1 CTC-AAATAAGGGCCT-CAAC-TTTAGAAAAGG

                    
        982 CTCAAATA
          1 CTCAAATA

        990 GGTCCAATCC


Statistics
Matches: 33,  Mismatches: 2, Indels: 7
        0.79            0.05        0.17

Matches are distributed among these distances:
  29    4  0.12
  30   12  0.36
  31   15  0.45
  32    2  0.06

ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23


Consensus pattern (30 bp):   
CTCAAATAAGGGCCTCAACTTTAGAAAAGG

Found at i:2704 original size:18 final size:17

Alignment explanation


    Indices: 2672--2710  Score: 62
    Period size: 18  Copynumber: 2.3  Consensus size: 17

       2662 CAAATAAGAA

                             
       2672 AAAT-GAAAAAGAAATT
          1 AAATAGAAAAAGAAATT

                              
       2688 AAATAGAAAATAGAAATT
          1 AAATAGAAAA-AGAAATT

                 
       2706 AAATA
          1 AAATA

       2711 AAATGAAAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  16    4  0.19
  17    5  0.24
  18   12  0.57

ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21


Consensus pattern (17 bp):   
AAATAGAAAAAGAAATT
Done.