Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020523.1 Corchorus olitorius cultivar O-4 contig20556, 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: 4146
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:2125 original size:14 final size:15

Alignment explanation


    Indices: 2106--2135  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2096 CAATCAAAGC

                           
       2106 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       2120 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       2135 A
          1 A

       2136 TTAAAGAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:2515 original size:21 final size:21

Alignment explanation


    Indices: 2491--2563  Score: 65
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       2481 GGCTTGGAAT

                                 
       2491 GGTGATGGCACGGGCATGGCC
          1 GGTGATGGCACGGGCATGGCC

                *          * **  
       2512 GGTGGTGGCACGGGCTTAACC
          1 GGTGATGGCACGGGCATGGCC

                *  *       *      
       2533 GGTGGTGTCACGGTGAATGGCC
          1 GGTGATGGCACGG-GCATGGCC

               *     
       2555 GGTAATGGC
          1 GGTGATGGC

       2564 TTGGTAGTGG


Statistics
Matches: 39,  Mismatches: 12, Indels: 1
        0.75            0.23        0.02

Matches are distributed among these distances:
  21   29  0.74
  22   10  0.26

ACGTcount: A:0.15, C:0.21, G:0.45, T:0.19


Consensus pattern (21 bp):   
GGTGATGGCACGGGCATGGCC
Done.