Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018661.1 Corchorus olitorius cultivar O-4 contig18694, 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: 4566
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34


Found at i:2334 original size:54 final size:55

Alignment explanation


    Indices: 2232--2339  Score: 130
    Period size: 54  Copynumber: 2.0  Consensus size: 55

       2222 AAAAGTGGCC

                     *     *                  *     *  *     *     
       2232 AAAATGCCCTTGAATGTAAAAAATGACCAAAATATCCCTGGACGTGCAATTGACT
          1 AAAATGCCCCTGAATATAAAAAATGACCAAAATAGCCCTGAACATGCAAATGACT

                                       *                           
       2287 AAAATGCCCCTGAATAT-AAAAATGACTAAAAT-GCCCTTGAACATGCAAATGAC
          1 AAAATGCCCCTGAATATAAAAAATGACCAAAATAGCCC-TGAACATGCAAATGAC

       2340 CCAAAATCCC


Statistics
Matches: 45,  Mismatches: 7, Indels: 3
        0.82            0.13        0.05

Matches are distributed among these distances:
  53    3  0.07
  54   27  0.60
  55   15  0.33

ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22


Consensus pattern (55 bp):   
AAAATGCCCCTGAATATAAAAAATGACCAAAATAGCCCTGAACATGCAAATGACT

Found at i:2336 original size:27 final size:27

Alignment explanation


    Indices: 2252--2339  Score: 86
    Period size: 27  Copynumber: 3.3  Consensus size: 27

       2242 TGAATGTAAA

                   *     **     *  *   
       2252 AAATGACCAAAATATCCCTGGACGTGC
          1 AAATGACTAAAATGCCCCTGAACATGC

              *                   *  **
       2279 AATTGACTAAAATGCCCCTGAATATAA
          1 AAATGACTAAAATGCCCCTGAACATGC

                             *         
       2306 AAATGACTAAAATGCCCTTGAACATGC
          1 AAATGACTAAAATGCCCCTGAACATGC

                   
       2333 AAATGAC
          1 AAATGAC

       2340 CCAAAATCCC


Statistics
Matches: 47,  Mismatches: 14, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  27   47  1.00

ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22


Consensus pattern (27 bp):   
AAATGACTAAAATGCCCCTGAACATGC

Found at i:2346 original size:55 final size:55

Alignment explanation


    Indices: 2230--2352  Score: 133
    Period size: 55  Copynumber: 2.2  Consensus size: 55

       2220 GTAAAAGTGG

                       *     *                  *     *  *     *   
       2230 CCAAAATGCCCTTGAATGTAAAAAATGACCAAAATATCCCTGGACGTGCAATTGA
          1 CCAAAATGCCCCTGAATATAAAAAATGACCAAAATAGCCCTGAACATGCAAATGA

             *                           *                          
       2285 CTAAAATGCCCCTGAATAT-AAAAATGACTAAAAT-GCCCTTGAACATGCAAATGA
          1 CCAAAATGCCCCTGAATATAAAAAATGACCAAAATAGCCC-TGAACATGCAAATGA

                    *     
       2339 CCCAAAATCCCCCT
          1 -CCAAAATGCCCCT

       2353 AGGTGATCCT


Statistics
Matches: 56,  Mismatches: 10, Indels: 4
        0.80            0.14        0.06

Matches are distributed among these distances:
  53    3  0.05
  54   26  0.46
  55   27  0.48

ACGTcount: A:0.41, C:0.25, G:0.13, T:0.21


Consensus pattern (55 bp):   
CCAAAATGCCCCTGAATATAAAAAATGACCAAAATAGCCCTGAACATGCAAATGA
Done.