Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold109

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: 651366
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


File 3 of 3

Found at i:614185 original size:27 final size:27

Alignment explanation


    Indices: 614155--614214  Score: 102
    Period size: 27  Copynumber: 2.2  Consensus size: 27

     614145 ACCCCTATTA

                                       
     614155 GGTAAAAAGACCGTAAAGCCCCTGTAG
          1 GGTAAAAAGACCGTAAAGCCCCTGTAG

                  **                   
     614182 GGTAAAGTGACCGTAAAGCCCCTGTAG
          1 GGTAAAAAGACCGTAAAGCCCCTGTAG

                  
     614209 GGTAAA
          1 GGTAAA

     614215 GTGACTATAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  27   31  1.00

ACGTcount: A:0.35, C:0.20, G:0.28, T:0.17


Consensus pattern (27 bp):   
GGTAAAAAGACCGTAAAGCCCCTGTAG

Found at i:614215 original size:27 final size:27

Alignment explanation


    Indices: 614163--614246  Score: 116
    Period size: 27  Copynumber: 3.1  Consensus size: 27

     614153 TAGGTAAAAA

                                       
     614163 GACCGTAAAGCCCCTGTAGGGTAAAGT
          1 GACCGTAAAGCCCCTGTAGGGTAAAGT

                                       
     614190 GACCGTAAAGCCCCTGTAGGGTAAAGT
          1 GACCGTAAAGCCCCTGTAGGGTAAAGT

               **              *      * 
     614217 GACTATAATA-CCCCTGTATGGTAAAAT
          1 GACCGTAA-AGCCCCTGTAGGGTAAAGT

               
     614244 GAC
          1 GAC

     614247 GAATATGCGC


Statistics
Matches: 52,  Mismatches: 4, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  27   51  0.98
  28    1  0.02

ACGTcount: A:0.32, C:0.21, G:0.25, T:0.21


Consensus pattern (27 bp):   
GACCGTAAAGCCCCTGTAGGGTAAAGT

Found at i:615146 original size:25 final size:26

Alignment explanation


    Indices: 615049--615146  Score: 162
    Period size: 26  Copynumber: 3.8  Consensus size: 26

     615039 GAGGAAGTGC

                                      
     615049 AAAAGGGCTTATGCCCCAGTTTACCG
          1 AAAAGGGCTTATGCCCCAGTTTACCG

                                   ** 
     615075 AAAAGGGCTTATGCCCCAGTTTATTG
          1 AAAAGGGCTTATGCCCCAGTTTACCG

                                      
     615101 AAAAGGGCTTATGCCCCAGTTTACCG
          1 AAAAGGGCTTATGCCCCAGTTTACCG

                            *    
     615127 AAAAGGGCTT-TGCCCTAGTT
          1 AAAAGGGCTTATGCCCCAGTT

     615147 ATTAAAGAGG


Statistics
Matches: 67,  Mismatches: 5, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  25    9  0.13
  26   58  0.87

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


Consensus pattern (26 bp):   
AAAAGGGCTTATGCCCCAGTTTACCG

Found at i:615350 original size:42 final size:42

Alignment explanation


    Indices: 615291--615382  Score: 148
    Period size: 42  Copynumber: 2.2  Consensus size: 42

     615281 TAGTCTCCCC

                              *     **   *            
     615291 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
          1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG

                                                      
     615333 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
          1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG

                    
     615375 AAATGGGC
          1 AAATGGGC

     615383 CTATAGGCCA


Statistics
Matches: 46,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  42   46  1.00

ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35


Consensus pattern (42 bp):   
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG

Found at i:615451 original size:31 final size:31

Alignment explanation


    Indices: 615406--615484  Score: 113
    Period size: 31  Copynumber: 2.5  Consensus size: 31

     615396 CGTTTACAGT

                 *   *                     
     615406 AAAGGCTTCAGCCCAGTGAAATGATTTATGA
          1 AAAGGATTCGGCCCAGTGAAATGATTTATGA

                    *          *           
     615437 AAAGGATTTGGCCCAGTGATATGATTTATGA
          1 AAAGGATTCGGCCCAGTGAAATGATTTATGA

                 *           
     615468 AAAGGCTTCGGCCCAGT
          1 AAAGGATTCGGCCCAGT

     615485 AACCGTTAAA


Statistics
Matches: 42,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  31   42  1.00

ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27


Consensus pattern (31 bp):   
AAAGGATTCGGCCCAGTGAAATGATTTATGA

Found at i:626190 original size:29 final size:30

Alignment explanation


    Indices: 626153--626211  Score: 84
    Period size: 30  Copynumber: 2.0  Consensus size: 30

     626143 TTACCGAGCC

                       *                  
     626153 TAGGGG-AAAAGTGTAATTATGCAAAAGTT
          1 TAGGGGAAAAAATGTAATTATGCAAAAGTT

                               *   *      
     626182 TAGGGGAAAAAATGTAATTTTGCCAAAGTT
          1 TAGGGGAAAAAATGTAATTATGCAAAAGTT

     626212 CGCATTAAAT


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  29    6  0.23
  30   20  0.77

ACGTcount: A:0.41, C:0.05, G:0.25, T:0.29


Consensus pattern (30 bp):   
TAGGGGAAAAAATGTAATTATGCAAAAGTT


Done.