Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2389

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: 20168
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29


Found at i:15125 original size:39 final size:38

Alignment explanation


    Indices: 14982--15232  Score: 253
    Period size: 37  Copynumber: 6.6  Consensus size: 38

      14972 AGTCCTCGTT

                           **     *                 
      14982 CAAATGCCTTCGGGAAATAGCCCGATTATAGTAACTCGCA
          1 CAAATGCCTTC-GGACTTAGCCGGATT-TAGTAACTCGCA

                            * *                 * 
      15022 CAAATGCCTTCGGACTAACCCGGATTTA--AACTCGTA
          1 CAAATGCCTTCGGACTTAGCCGGATTTAGTAACTCGCA

                                    *      *      
      15058 CAAATGCCTTCGG-CTTAGCCGGAATTAGTATCTCGCA
          1 CAAATGCCTTCGGACTTAGCCGGATTTAGTAACTCGCA

                                                    
      15095 CAAATGCCTTCGGATCTTAGTCC-GATTTAGTAACTCGCA
          1 CAAATGCCTTCGGA-CTTAG-CCGGATTTAGTAACTCGCA

                         *          *      *      
      15134 CAAATG-CTTCGGGCTTAGCCGGAATTAGTATCTCGCA
          1 CAAATGCCTTCGGACTTAGCCGGATTTAGTAACTCGCA

                      *                * *       *   
      15171 CAAATGCCTTTGGATCTTAGTCCGGATATGGTAACTTAGCA
          1 CAAATGCCTTCGGA-CTTAG-CCGGATTTAGTAAC-TCGCA

                                  
      15212 CAAA-GCCTTCGGGACTTAGCC
          1 CAAATGCCTTC-GGACTTAGCC

      15233 CGGACATCAT


Statistics
Matches: 176,  Mismatches: 24, Indels: 23
        0.79            0.11        0.10

Matches are distributed among these distances:
  35   11  0.06
  36   22  0.12
  37   44  0.25
  38   13  0.07
  39   42  0.24
  40   33  0.19
  41   11  0.06

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


Consensus pattern (38 bp):   
CAAATGCCTTCGGACTTAGCCGGATTTAGTAACTCGCA

Found at i:15138 original size:76 final size:78

Alignment explanation


    Indices: 14982--15232  Score: 302
    Period size: 76  Copynumber: 3.3  Consensus size: 78

      14972 AGTCCTCGTT

                           **     *  *       *                         **    
      14982 CAAATGCCTTCGGGAAATAGCCCGATTATAGTAACTCGCACAAATGCCTTCGGA-C-TAACCCGG
          1 CAAATGCCTTCGGG-CTTAGCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG

                         * 
      15045 ATTTA--AACTCGTA
         64 ATTTAGTAACTCGCA

                                                                             
      15058 CAAATGCCTTC-GGCTTAGCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCC-GAT
          1 CAAATGCCTTCGGGCTTAGCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGAT

                         
      15121 TTAGTAACTCGCA
         66 TTAGTAACTCGCA

                                                            *                
      15134 CAAATG-CTTCGGGCTTAGCCGGAATTAGTATCTCGCACAAATGCCTTTGGATCTTAGTCCGGAT
          1 CAAATGCCTTCGGGCTTAGCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGAT

            * *       *   
      15198 ATGGTAACTTAGCA
         66 TTAGTAAC-TCGCA

                                  
      15212 CAAA-GCCTTCGGGACTTAGCC
          1 CAAATGCCTTCGGG-CTTAGCC

      15233 CGGACATCAT


Statistics
Matches: 154,  Mismatches: 12, Indels: 15
        0.85            0.07        0.08

Matches are distributed among these distances:
  73   25  0.16
  74   15  0.10
  75   10  0.06
  76   72  0.47
  77   10  0.06
  78   15  0.10
  79    7  0.05

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


Consensus pattern (78 bp):   
CAAATGCCTTCGGGCTTAGCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
TTAGTAACTCGCA

Done.