Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold605

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: 21236
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29


Found at i:11341 original size:29 final size:28

Alignment explanation


    Indices: 11275--11374  Score: 155
    Period size: 28  Copynumber: 3.5  Consensus size: 28

      11265 TATAGTAAGT

                          *    *   *    
      11275 CCGCACACTTAGTGTTATATAATCGAAC
          1 CCGCACACTTAGTGCTATACAATTGAAC

            *                            
      11303 TCGCACACTTAGTGCTATACAACTTGAAC
          1 CCGCACACTTAGTGCTATACAA-TTGAAC

                                        
      11332 CCGCACACTTAGTGCTATACAATTGAAC
          1 CCGCACACTTAGTGCTATACAATTGAAC

                           
      11360 CCGCACACTTAGTGC
          1 CCGCACACTTAGTGC

      11375 CAATTTCATG


Statistics
Matches: 66,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  28   40  0.61
  29   26  0.39

ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26


Consensus pattern (28 bp):   
CCGCACACTTAGTGCTATACAATTGAAC

Found at i:15429 original size:93 final size:93

Alignment explanation


    Indices: 15301--15471  Score: 288
    Period size: 93  Copynumber: 1.8  Consensus size: 93

      15291 GCCCATAAGT

                 *                      * *               *                  
      15301 GAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTTAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

            *                           
      15366 TGAGTTCGGATGCCTAGTTACATTTCAC
         66 CGAGTTCGGATGCCTAGTTACATTTCAC

                                   *                                         
      15394 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                         
      15459 CGAGTTCGGATGC
         66 CGAGTTCGGATGC

      15472 TCAACCATCC


Statistics
Matches: 72,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  93   72  1.00

ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23


Consensus pattern (93 bp):   
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC

Found at i:15468 original size:46 final size:46

Alignment explanation


    Indices: 15293--15468  Score: 189
    Period size: 46  Copynumber: 3.8  Consensus size: 46

      15283 TGTAACCCGC

                         *                 *    * *       
      15293 CCATAAGTGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                    *                  *                   *   
      15339 CCATAAGTTAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT

              * *  *                                      
      15389 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                                                 
      15432 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA

      15469 TGCTCAACCA


Statistics
Matches: 105,  Mismatches: 16, Indels: 18
        0.76            0.12        0.13

Matches are distributed among these distances:
  42    2  0.02
  43    4  0.04
  44    1  0.01
  45    2  0.02
  46   61  0.58
  47   27  0.26
  48    2  0.02
  49    1  0.01
  50    3  0.03
  51    2  0.02

ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23


Consensus pattern (46 bp):   
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

Done.