Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1365

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: 8275
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30


Found at i:5823 original size:27 final size:27

Alignment explanation


    Indices: 5793--5969  Score: 196
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       5783 ATATTGAGTC

                    *       *   *      
       5793 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAGTCAACT

                             *  *      
       5820 CGCACACTTAGTGCTACGTAATCAA-T
          1 CGCACACTTAGTGCTACATAGTCAACT

                                        
       5846 CGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAGTC-AACT

                          **   *     * 
       5874 CGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTACATAGTCAACT

                                 *   ** 
       5901 CGCACACTTAGTGC-ATCATATTCATTT
          1 CGCACACTTAGTGCTA-CATAGTCAACT

                          *          * 
       5928 CGCACACTTAGTGCAACATAGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAACT

                           
       5955 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       5970 GTACAATTTA


Statistics
Matches: 129,  Mismatches: 17, Indels: 8
        0.84            0.11        0.05

Matches are distributed among these distances:
  26   22  0.17
  27   85  0.66
  28   22  0.17

ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACATAGTCAACT

Found at i:5958 original size:81 final size:81

Alignment explanation


    Indices: 5814--5968  Score: 233
    Period size: 81  Copynumber: 1.9  Consensus size: 81

       5804 TGCTATATAA

                                   *                      *                  
       5814 TCAACTCGCACACTTAGTGCTACGTAATCAATCGCACACTTAGTGCTACATAGTCAAACTCGCAC
          1 TCAACTCGCACACTTAGTGCTACATAATCAATCGCACACTTAGTGCAACATAGTCAAACTCGCAC

                            
       5879 ACTTAGTGCCGCATGG
         66 ACTTAGTGCCGCATGG

                *                      *    *                                
       5895 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAA-TCGC
          1 TCAACTCGCACACTTAGTGCTA-CATAATCA-ATCGCACACTTAGTGCAACATAGTCAAACTCGC

                       
       5958 ACACTTAGTGC
         64 ACACTTAGTGC

       5969 TGTACAATTT


Statistics
Matches: 67,  Mismatches: 5, Indels: 4
        0.88            0.07        0.05

Matches are distributed among these distances:
  80    1  0.01
  81   40  0.60
  82   26  0.39

ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27


Consensus pattern (81 bp):   
TCAACTCGCACACTTAGTGCTACATAATCAATCGCACACTTAGTGCAACATAGTCAAACTCGCAC
ACTTAGTGCCGCATGG
Done.