Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_4163

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: 15796
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30


Found at i:725 original size:93 final size:94

Alignment explanation


    Indices: 613--784  Score: 310
    Period size: 93  Copynumber: 1.8  Consensus size: 94

        603 GCCCATAAGT

                                        * *                                  
        613 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                                         
        678 CGAG-TCGGATGCCTAGTTACATCTTCAC
         66 CGAGTTCGGATGCCTAGTTACATCTTCAC

                                   *                                         
        706 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                          
        771 CGAGTTCGGATGCC
         66 CGAGTTCGGATGCC

        785 AACCATCCTA


Statistics
Matches: 75,  Mismatches: 3, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  93   66  0.88
  94    9  0.12

ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21


Consensus pattern (94 bp):   
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTTCAC

Found at i:780 original size:46 final size:46

Alignment explanation


    Indices: 605--780  Score: 216
    Period size: 46  Copynumber: 3.8  Consensus size: 46

        595 TGTAACCCGC

                                           *    * *       
        605 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                                                           *   
        651 CCATAAGTGAACTCGGACTCAACTCAACGAG-TCGGATGCCTAGTT-ACAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT

              * *  *                                      
        700 -CTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                                                 
        744 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA

        781 TGCCAACCAT


Statistics
Matches: 111,  Mismatches: 10, Indels: 18
        0.80            0.07        0.13

Matches are distributed among these distances:
  43    2  0.02
  44    4  0.04
  45    8  0.07
  46   60  0.54
  47   23  0.21
  48    9  0.08
  49    3  0.03
  50    2  0.02

ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21


Consensus pattern (46 bp):   
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

Found at i:3125 original size:15 final size:14

Alignment explanation


    Indices: 3068--3134  Score: 64
    Period size: 14  Copynumber: 4.7  Consensus size: 14

       3058 CAAGAAAACC

                         * 
       3068 GAATAAAGAAATCAA
          1 GAATAAAG-AATCCA

                 *    *  *
       3083 G-ATAGAGAAACCG
          1 GAATAAAGAATCCA

                          
       3096 GAATAAAGAATCCA
          1 GAATAAAGAATCCA

                           
       3110 GAATAAAGAGATCCA
          1 GAATAAAGA-ATCCA

             *        
       3125 GGATAAAGAA
          1 GAATAAAGAA

       3135 ACCCAAGATA


Statistics
Matches: 42,  Mismatches: 8, Indels: 5
        0.76            0.15        0.09

Matches are distributed among these distances:
  13    4  0.10
  14   24  0.57
  15   14  0.33

ACGTcount: A:0.57, C:0.10, G:0.21, T:0.12


Consensus pattern (14 bp):   
GAATAAAGAATCCA

Found at i:6028 original size:46 final size:46

Alignment explanation


    Indices: 5961--6089  Score: 240
    Period size: 46  Copynumber: 2.8  Consensus size: 46

       5951 TGTAACCCGC

                                           *    *         
       5961 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                                                          
       6007 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                                                 
       6053 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA

       6090 TGCTCAACCA


Statistics
Matches: 81,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  46   81  1.00

ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20


Consensus pattern (46 bp):   
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

Done.