Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000530.1 Corchorus olitorius cultivar O-4 contig00530, 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: 2564
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:378 original size:27 final size:26

Alignment explanation


    Indices: 348--403  Score: 60
    Period size: 26  Copynumber: 2.1  Consensus size: 26

        338 ATAATTTTCG

                          *             
        348 TAAGAACGTAAATTCCCGTT-TTACCCA
          1 TAAG-ACGTAAATTACC-TTATTACCCA

                **                    
        375 TAAGTGGTAAATTACCTTATTACCCA
          1 TAAGACGTAAATTACCTTATTACCCA

               
        401 TAA
          1 TAA

        404 TTAGTAAAAG


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  25    2  0.08
  26   19  0.76
  27    4  0.16

ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32


Consensus pattern (26 bp):   
TAAGACGTAAATTACCTTATTACCCA

Found at i:410 original size:26 final size:26

Alignment explanation


    Indices: 355--411  Score: 71
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        345 TCGTAAGAAC

                   *                 *
        355 GTAAATTCCCGTTTTACCCATAAGTG
          1 GTAAATTACCGTTTTACCCATAAGTA

                                    *  
        381 GTAAATTACC-TTATTACCCATAATTA
          1 GTAAATTACCGTT-TTACCCATAAGTA

                 
        407 GTAAA
          1 GTAAA

        412 AGCGTACTAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  25    2  0.07
  26   25  0.93

ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35


Consensus pattern (26 bp):   
GTAAATTACCGTTTTACCCATAAGTA
Done.