Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold231

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: 25507
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30


Found at i:12311 original size:40 final size:40

Alignment explanation


    Indices: 12227--12410  Score: 196
    Period size: 40  Copynumber: 4.6  Consensus size: 40

      12217 TTGAATGCTG

                  *                       *   * *    
      12227 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
          1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT

                  **              *                   
      12266 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
          1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT

                                 *          *  *    
      12307 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
          1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT

                                    *               *
      12347 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
          1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT

                                    
      12387 TCCGGGTTAAGTCCCGAAGGCATT
          1 TCCGGGTTAAGTCCCGAAGGCATT

      12411 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:12364 original size:80 final size:81

Alignment explanation


    Indices: 12227--12407  Score: 221
    Period size: 80  Copynumber: 2.3  Consensus size: 81

      12217 TTGAATGCTG

                  *                      *                               *   
      12227 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
          1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT

            *               *
      12291 TGTGCGAGTTATT-AAT
         66 CGTGCGAGTT-TTAAAA

                                                            **               
      12307 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
          1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC

                               
      12368 ATTCGTGCGAGTTTTAAAA
         63 ATTCGTGCGAGTTTTAAAA

                                 
      12387 TCCGGGTTAAGTCCCGAAGGC
          1 TCCGGGTTAAGTCCCGAAGGC

      12408 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

Found at i:20165 original size:40 final size:40

Alignment explanation


    Indices: 20081--20264  Score: 196
    Period size: 40  Copynumber: 4.6  Consensus size: 40

      20071 TTGAATGCTG

                  *                       *   * *    
      20081 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
          1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT

                  **              *                   
      20120 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
          1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT

                                 *          *  *    
      20161 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
          1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT

                                    *               *
      20201 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
          1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT

                                    
      20241 TCCGGGTTAAGTCCCGAAGGCATT
          1 TCCGGGTTAAGTCCCGAAGGCATT

      20265 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:20218 original size:80 final size:81

Alignment explanation


    Indices: 20081--20261  Score: 221
    Period size: 80  Copynumber: 2.3  Consensus size: 81

      20071 TTGAATGCTG

                  *                      *                               *   
      20081 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
          1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT

            *               *
      20145 TGTGCGAGTTATT-AAT
         66 CGTGCGAGTT-TTAAAA

                                                            **               
      20161 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
          1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC

                               
      20222 ATTCGTGCGAGTTTTAAAA
         63 ATTCGTGCGAGTTTTAAAA

                                 
      20241 TCCGGGTTAAGTCCCGAAGGC
          1 TCCGGGTTAAGTCCCGAAGGC

      20262 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

Found at i:20285 original size:39 final size:38

Alignment explanation


    Indices: 20162--20311  Score: 131
    Period size: 40  Copynumber: 3.8  Consensus size: 38

      20152 GTTATTAATT

                                 *   **    *       *
      20162 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
          1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A

                                     **       *     
      20202 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
          1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA

                                       *            
      20241 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
          1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA

                 *  *                      
      20281 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
          1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG

      20312 GAGCTAAATC


Statistics
Matches: 93,  Mismatches: 11, Indels: 12
        0.80            0.09        0.10

Matches are distributed among these distances:
  39   30  0.32
  40   63  0.68

ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25


Consensus pattern (38 bp):   
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Done.