Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold225

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: 857989
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


File 5 of 5

Found at i:850534 original size:33 final size:33

Alignment explanation


    Indices: 850492--850558  Score: 98
    Period size: 33  Copynumber: 2.0  Consensus size: 33

     850482 GCCAAGAAAA

                         ***                 
     850492 TGTATCGATACATTTTTCTGTGTATCGATACAT
          1 TGTATCGATACATGGATCTGTGTATCGATACAT

                               *             
     850525 TGTATCGATACATGGATCTTTGTATCGATACAT
          1 TGTATCGATACATGGATCTGTGTATCGATACAT

             
     850558 T
          1 T

     850559 TGGAAATTTT


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   30  1.00

ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43


Consensus pattern (33 bp):   
TGTATCGATACATGGATCTGTGTATCGATACAT

Found at i:852986 original size:27 final size:28

Alignment explanation


    Indices: 852953--853028  Score: 102
    Period size: 27  Copynumber: 2.8  Consensus size: 28

     852943 ATTTTCTATA

                              *         
     852953 ATCGGGGATACTCCAACCTCGTTA-ATC
          1 ATCGGGGATACTCCAACCCCGTTATATC

                                     *  
     852980 ATCGGGGATACTCCAACCCCGTTATTTC
          1 ATCGGGGATACTCCAACCCCGTTATATC

               *                  
     853008 -TGAGGGGATACTCCAACCCCG
          1 AT-CGGGGATACTCCAACCCCG

     853029 ACTTTATTTC


Statistics
Matches: 44,  Mismatches: 3, Indels: 3
        0.88            0.06        0.06

Matches are distributed among these distances:
  27   24  0.55
  28   20  0.45

ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24


Consensus pattern (28 bp):   
ATCGGGGATACTCCAACCCCGTTATATC

Found at i:853186 original size:53 final size:53

Alignment explanation


    Indices: 853011--853233  Score: 240
    Period size: 52  Copynumber: 4.3  Consensus size: 53

     853001 TTATTTCTGA

                               *              * ***      *       
     853011 GGGGATACTCCAACCCCGACTTTATTTCC-AAAATATTGATTT-TTCATAATC
          1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTCTCCATAATC

                              *        * *       *     *    *    
     853062 GGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCACAATC
          1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTCTCCATAATC

                                       *                    *     
     853114 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTCTCCTTTAATC
          1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTCTCC-ATAATC

                          *                              *  *    
     853167 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTT-TTCACAATC
          1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTCTCCATAATC

             *             
     853219 GAGGATACTCCAACC
          1 GGGGATACTCCAACC

     853234 TCGTTATTTC


Statistics
Matches: 146,  Mismatches: 21, Indels: 9
        0.83            0.12        0.05

Matches are distributed among these distances:
  50    3  0.02
  51   32  0.22
  52   62  0.42
  53   36  0.25
  54   13  0.09

ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31


Consensus pattern (53 bp):   
GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTCTCCATAATC

Found at i:853216 original size:105 final size:103

Alignment explanation


    Indices: 853011--853233  Score: 286
    Period size: 105  Copynumber: 2.1  Consensus size: 103

     853001 TTATTTCTGA

                                             * ***     *                     
     853011 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATCGGGGATACTCCAAC
          1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTCCATAATCGGGGATACTCCAAC

                *       * *       *               
     853076 CCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
         66 CCCGATTTTATTCCAAAAACACCAATTTTTCCACAATC

                               *       *                   *                 
     853114 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGATACTCCA
          1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTT-TCC-ATAATCGGGGATACTCCA

              *                                      
     853179 ACTCCGATTTTATTTCCAAAAACACCAATTTTT-CACAATC
         64 ACCCCGATTTTA-TTCCAAAAACACCAATTTTTCCACAATC

             *             
     853219 GAGGATACTCCAACC
          1 GGGGATACTCCAACC

     853234 TCGTTATTTC


Statistics
Matches: 103,  Mismatches: 14, Indels: 4
        0.85            0.12        0.03

Matches are distributed among these distances:
 103   36  0.35
 104    2  0.02
 105   48  0.47
 106   17  0.17

ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31


Consensus pattern (103 bp):   
GGGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTCCATAATCGGGGATACTCCAAC
CCCGATTTTATTCCAAAAACACCAATTTTTCCACAATC

Found at i:853248 original size:28 final size:28

Alignment explanation


    Indices: 853216--853297  Score: 105
    Period size: 28  Copynumber: 2.9  Consensus size: 28

     853206 ATTTTTCACA

                              *         
     853216 ATCGAGGATACTCCAACCTCGTTATTTC
          1 ATCGAGGATACTCCAACCCCGTTATTTC

                                    *   
     853244 ATCGAGGATACTCCAACCCCGTTACTTC
          1 ATCGAGGATACTCCAACCCCGTTATTTC

                      *                 
     853272 --CGAGGGAACACTCCAACCCCGTTATT
          1 ATCGA-GG-ATACTCCAACCCCGTTATT

     853298 ATCTCCAAAA


Statistics
Matches: 48,  Mismatches: 4, Indels: 4
        0.86            0.07        0.07

Matches are distributed among these distances:
  26    3  0.06
  27    2  0.04
  28   43  0.90

ACGTcount: A:0.26, C:0.33, G:0.16, T:0.26


Consensus pattern (28 bp):   
ATCGAGGATACTCCAACCCCGTTATTTC

Done.