Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003069.1 Corchorus capsularis cultivar CVL-1 contig03077, 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, 785

Length: 1309
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:478 original size:27 final size:27

Alignment explanation


    Indices: 418--524  Score: 133
    Period size: 27  Copynumber: 3.9  Consensus size: 27

        408 ATCTTTTAAA

                     *      *       *    
        418 AAAAATGACTAAAATGCCCTCCTGAGTGC
          1 AAAAATGACCAAAAT-ACC-CCTGGGTGC

                      *                
        447 AAAAATGACCGAAATACCCCTGGGTGC
          1 AAAAATGACCAAAATACCCCTGGGTGC

            *              *           
        474 GAAAATGACCAAAATGCCCCTGGGTGC
          1 AAAAATGACCAAAATACCCCTGGGTGC

                               *    
        501 AAAAATGACCAAAATACCCTTGGG
          1 AAAAATGACCAAAATACCCCTGGG

        525 CGACTCTAAT


Statistics
Matches: 68,  Mismatches: 10, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  27   53  0.78
  28    2  0.03
  29   13  0.19

ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17


Consensus pattern (27 bp):   
AAAAATGACCAAAATACCCCTGGGTGC

Found at i:516 original size:54 final size:56

Alignment explanation


    Indices: 419--524  Score: 162
    Period size: 54  Copynumber: 1.9  Consensus size: 56

        409 TCTTTTAAAA

                    *                             *                 
        419 AAAATGACTAAAATGCCCTCCTGAGTGCAAAAATGACCGAAATACCCCTGGGTGCG
          1 AAAATGACCAAAATGCCCTCCTGAGTGCAAAAATGACCAAAATACCCCTGGGTGCG

                                   *                       *    
        475 AAAATGACCAAAATG-CC-CCTGGGTGCAAAAATGACCAAAATACCCTTGGG
          1 AAAATGACCAAAATGCCCTCCTGAGTGCAAAAATGACCAAAATACCCCTGGG

        525 CGACTCTAAT


Statistics
Matches: 46,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  54   30  0.65
  55    2  0.04
  56   14  0.30

ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17


Consensus pattern (56 bp):   
AAAATGACCAAAATGCCCTCCTGAGTGCAAAAATGACCAAAATACCCCTGGGTGCG
Done.