Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold283

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: 4908
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30


Found at i:3353 original size:40 final size:40

Alignment explanation


    Indices: 3269--3452  Score: 196
    Period size: 40  Copynumber: 4.6  Consensus size: 40

       3259 TTGAATGCTG

                  *                       *   * *    
       3269 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
          1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT

                  **              *                   
       3308 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
          1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT

                                 *          *  *    
       3349 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
          1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT

                                    *               *
       3389 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
          1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT

                                    
       3429 TCCGGGTTAAGTCCCGAAGGCATT
          1 TCCGGGTTAAGTCCCGAAGGCATT

       3453 GAATGAGTTA


Statistics
Matches: 123,  Mismatches: 16, Indels: 10
        0.83            0.11        0.07

Matches are distributed among these distances:
  39    2  0.02
  40  111  0.90
  41   10  0.08

ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28


Consensus pattern (40 bp):   
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT

Found at i:3406 original size:80 final size:81

Alignment explanation


    Indices: 3269--3449  Score: 221
    Period size: 80  Copynumber: 2.3  Consensus size: 81

       3259 TTGAATGCTG

                  *                      *                               *   
       3269 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
          1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT

            *               *
       3333 TGTGCGAGTTATT-AAT
         66 CGTGCGAGTT-TTAAAA

                                                            **               
       3349 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
          1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC

                               
       3410 ATTCGTGCGAGTTTTAAAA
         63 ATTCGTGCGAGTTTTAAAA

                                 
       3429 TCCGGGTTAAGTCCCGAAGGC
          1 TCCGGGTTAAGTCCCGAAGGC

       3450 ATTGAATGAG


Statistics
Matches: 89,  Mismatches: 7, Indels: 10
        0.84            0.07        0.09

Matches are distributed among these distances:
  79    4  0.04
  80   76  0.85
  81    9  0.10

ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28


Consensus pattern (81 bp):   
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Done.