Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2836

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, 503

Length: 839
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.25

Warning! 276 characters in sequence are not A, C, G, or T


Found at i:100 original size:9 final size:9

Alignment explanation


    Indices: 86--201  Score: 72
    Period size: 9  Copynumber: 11.6  Consensus size: 9

         76 ATTAATATTA

                     
         86 TACATAAAT
          1 TACATAAAT

                      
         95 TACATAAAAT
          1 TACAT-AAAT

                        
        105 TA-ATTAATATT
          1 TACA-TAA-A-T

                      
        116 ATACATAAAT
          1 -TACATAAAT

                   * 
        126 TACATAACT
          1 TACATAAAT

                        
        135 TACATTAATATT
          1 TACA-TAA-A-T

                      
        147 ATACATAAAT
          1 -TACATAAAT

             *     * 
        157 TGCATAACT
          1 TACATAAAT

                        
        166 TACATTAATATT
          1 TACA-TAA-A-T

                      
        178 ATACATAAAT
          1 -TACATAAAT

                   * 
        188 TACATAACT
          1 TACATAAAT

                 
        197 TACAT
          1 TACAT

        202 TAATATTATA


Statistics
Matches: 86,  Mismatches: 7, Indels: 28
        0.71            0.06        0.23

Matches are distributed among these distances:
   9   43  0.50
  10   17  0.20
  11    4  0.05
  12   13  0.15
  13    9  0.10

ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38


Consensus pattern (9 bp):   
TACATAAAT

Found at i:108 original size:31 final size:31

Alignment explanation


    Indices: 28--219  Score: 296
    Period size: 31  Copynumber: 6.0  Consensus size: 31

         18 ATTCATATTA

                                            
         28 TACATAACTTACATTAATATTATACATAAATT
          1 TACATAACTTACATTAATATTATACATAAA-T

                           *                   
         60 ATACATAACTTAATTAATTAATATTATACATAAAT
          1 -TACATAACTT-A--CATTAATATTATACATAAAT

                    *                       
         95 TACATAAAATTA-ATTAATATTATACATAAAT
          1 TACAT-AACTTACATTAATATTATACATAAAT

                                           
        126 TACATAACTTACATTAATATTATACATAAAT
          1 TACATAACTTACATTAATATTATACATAAAT

             *                             
        157 TGCATAACTTACATTAATATTATACATAAAT
          1 TACATAACTTACATTAATATTATACATAAAT

                                           
        188 TACATAACTTACATTAATATTATACATAAAT
          1 TACATAACTTACATTAATATTATACATAAAT

             
        219 T
          1 T

        220 NNNNNNNNNN


Statistics
Matches: 149,  Mismatches: 5, Indels: 12
        0.90            0.03        0.07

Matches are distributed among these distances:
  30    5  0.03
  31  104  0.70
  33   10  0.07
  34    7  0.05
  35    5  0.03
  36   18  0.12

ACGTcount: A:0.49, C:0.11, G:0.01, T:0.40


Consensus pattern (31 bp):   
TACATAACTTACATTAATATTATACATAAAT

Found at i:110 original size:25 final size:24

Alignment explanation


    Indices: 54--107  Score: 63
    Period size: 25  Copynumber: 2.1  Consensus size: 24

         44 ATATTATACA

                          *     *   
         54 TAAATTATACATAACTTAATTAAT
          1 TAAATTATACATAAATTAATAAAT

                                       
         78 TAATATTATACATAAATTACATAAAAT
          1 TAA-ATTATACATAAATTA-AT-AAAT

               
        105 TAA
          1 TAA

        108 TTAATATTAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  24    3  0.12
  25   14  0.56
  26    2  0.08
  27    6  0.24

ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39


Consensus pattern (24 bp):   
TAAATTATACATAAATTAATAAAT

Done.