Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3041

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: 5656
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29


Found at i:4226 original size:40 final size:40

Alignment explanation


    Indices: 4057--4279  Score: 242
    Period size: 39  Copynumber: 5.7  Consensus size: 40

       4047 TTGAATGCTG

                                          *   * *  * 
       4057 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA

                 *                           *       
       4097 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
          1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA

                   *              *                  
       4136 TTCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAG-TACTAAA
          1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA

                  *                 *          *    
       4175 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA

                  *                     *           
       4215 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA

            *        *                
       4254 ACCGGGCTATGTCCCGAAGGCATTTG
          1 TCCGGGCTAAGTCCCGAAGGCATTTG

       4280 AACGAGGAGC


Statistics
Matches: 157,  Mismatches: 18, Indels: 16
        0.82            0.09        0.08

Matches are distributed among these distances:
  38   14  0.09
  39   74  0.47
  40   61  0.39
  41    8  0.05

ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26


Consensus pattern (40 bp):   
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA

Found at i:4270 original size:118 final size:119

Alignment explanation


    Indices: 4057--4312  Score: 263
    Period size: 118  Copynumber: 2.2  Consensus size: 119

       4047 TTGAATGCTG

                  *                *              *                          
       4057 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATTT
          1 TCCGGGTTAAGTCCCGAAGGCTTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATTT

                           *     *             *    **    *       
       4122 GTGCGAGATACAAATTCCGGGTTAAGCCCGAAGGCCTTTGTGCGAGTA-CTAAA
         66 GTGCGAGATACAAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGGAGCTAAA

                                          *   * *         **                 
       4175 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCA-
          1 TCCGGGTTAAGTCCCGAAGGC-TTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT

                 *   *                 *                            * 
       4237 TTGTGTGAGTTACTAAA-ACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTATA
         64 TTGTGCGAGATAC-AAATACCGGGCTAAG-CCCGAAGGCATTTGAACGAGGAGCTAAA

                      *         
       4294 TCC-GGTTAAATCCCGAAGG
          1 TCCGGGTTAAGTCCCGAAGG

       4313 TACGTGATTT


Statistics
Matches: 114,  Mismatches: 19, Indels: 10
        0.80            0.13        0.07

Matches are distributed among these distances:
 117   20  0.18
 118   81  0.71
 119   13  0.11

ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25


Consensus pattern (119 bp):   
TCCGGGTTAAGTCCCGAAGGCTTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACAAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGGAGCTAAA

Found at i:4297 original size:79 final size:79

Alignment explanation


    Indices: 4137--4312  Score: 198
    Period size: 79  Copynumber: 2.3  Consensus size: 79

       4127 AGATACAAAT

                                  *                *     *                   
       4137 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
          1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG

            **     * *    
       4201 TGCGAGTTATTAAA
         66 AACGAGTGACTAAA

                                        *                    *              *
       4215 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
          1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAG-TACTAAAACCGGGCTAAGTCCCGAAGGCATTC

                          * 
       4279 GAACGAG-GAGCTATA
         65 GAACGAGTGA-CTAAA

                      *         
       4294 TCC-GGTTAAATCCCGAAGG
          1 TCCGGGTTAAGTCCCGAAGG

       4313 TACGTGATTT


Statistics
Matches: 83,  Mismatches: 12, Indels: 6
        0.82            0.12        0.06

Matches are distributed among these distances:
  78   36  0.43
  79   47  0.57

ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24


Consensus pattern (79 bp):   
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
AACGAGTGACTAAA
Done.