Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2819

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: 28609
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31


Found at i:4306 original size:40 final size:40

Alignment explanation


    Indices: 4269--4492  Score: 287
    Period size: 40  Copynumber: 5.7  Consensus size: 40

       4259 GCTACTCGTT

                            *  *                     
       4269 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA

                                                    
       4309 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                                    
       4349 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                      *      *      
       4389 CAAATGCCTTCGGG-CTT-ACCCGGAATTAGTATCTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                **      * *  *    *   
       4427 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA

                               *      
       4468 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAACCCGGA

       4493 CATCATTCGA


Statistics
Matches: 165,  Mismatches: 13, Indels: 12
        0.87            0.07        0.06

Matches are distributed among these distances:
  37    2  0.01
  38   30  0.18
  39    6  0.04
  40  114  0.69
  41   13  0.08

ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

Found at i:4452 original size:118 final size:120

Alignment explanation


    Indices: 4269--4492  Score: 296
    Period size: 118  Copynumber: 1.9  Consensus size: 120

       4259 GCTACTCGTT

                                     *                                       
       4269 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
          1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG

              *         *                                           
       4334 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
         66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                            *                 *                          **  
       4389 CAAATGCCTTCGGG-CTTA-CCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
          1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC

                  *  *                          *      
       4450 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
         64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA

       4493 CATCATTCGA


Statistics
Matches: 91,  Mismatches: 10, Indels: 8
        0.83            0.09        0.07

Matches are distributed among these distances:
 117    4  0.04
 118   62  0.68
 119   11  0.12
 120   14  0.15

ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25


Consensus pattern (120 bp):   
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

Found at i:12420 original size:40 final size:40

Alignment explanation


    Indices: 12383--12607  Score: 287
    Period size: 40  Copynumber: 5.7  Consensus size: 40

      12373 GCTACTCGTT

                            *  *                     
      12383 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA

                                                    
      12423 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                                    
      12463 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                               *      *      *      
      12503 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                **      * *  *    *   
      12542 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA

                               *      
      12583 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAACCCGGA

      12608 CATCATTCGA


Statistics
Matches: 167,  Mismatches: 13, Indels: 10
        0.88            0.07        0.05

Matches are distributed among these distances:
  38    2  0.01
  39   33  0.20
  40  119  0.71
  41   13  0.08

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


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

Found at i:12567 original size:119 final size:120

Alignment explanation


    Indices: 12383--12607  Score: 305
    Period size: 119  Copynumber: 1.9  Consensus size: 120

      12373 GCTACTCGTT

                                     *                                       
      12383 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
          1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG

              *         *                                           
      12448 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
         66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                            *                 *                          **  
      12503 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
          1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC

                  *  *                          *      
      12565 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
         64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA

      12608 CATCATTCGA


Statistics
Matches: 92,  Mismatches: 10, Indels: 7
        0.84            0.09        0.06

Matches are distributed among these distances:
 118    4  0.04
 119   66  0.72
 120   22  0.24

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


Consensus pattern (120 bp):   
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Done.