Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold366

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: 36252
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30


Found at i:4065 original size:21 final size:21

Alignment explanation


    Indices: 4027--4066  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       4017 ATTACTCCAA

                       *         
       4027 AGAAGCCGATTGATCCATCTC
          1 AGAAGCCGATTCATCCATCTC

                                
       4048 AGAAGCCGGATTCA-CCATC
          1 AGAAGCC-GATTCATCCATC

       4067 AAGACTGAAC


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  21   12  0.71
  22    5  0.29

ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20


Consensus pattern (21 bp):   
AGAAGCCGATTCATCCATCTC

Found at i:22027 original size:39 final size:40

Alignment explanation


    Indices: 21982--22205  Score: 242
    Period size: 40  Copynumber: 5.7  Consensus size: 40

      21972 GCTCCTCGTT

                            *  *     *           *  
      21982 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                          *         
      22022 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

             *                                      
      22061 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                *         *                   *      
      22100 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA

                                **      *  * *    *   
      22140 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA

                               *      
      22181 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAACCCGGA

      22206 CAGCATTCAA


Statistics
Matches: 157,  Mismatches: 20, Indels: 14
        0.82            0.10        0.07

Matches are distributed among these distances:
  39   70  0.45
  40   76  0.48
  41   11  0.07

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


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

Found at i:22085 original size:79 final size:77

Alignment explanation


    Indices: 21982--22205  Score: 252
    Period size: 79  Copynumber: 2.8  Consensus size: 77

      21972 GCTCCTCGTT

                            *        *                 *                     
      21982 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCACACAAAGCCTTCGGGACTTAACCCGGA

                          
      22047 TTTAATAACTCGCA
         65 TTT-ATAACTCGCA

             *                 *                *                *           
      22061 CGAATGCCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCACACAAA-GCCTTCGGGACTTAACCCGG-

                *  *      
      22126 ATTTGTATCTCGCA
         64 ATTTATAACTCGCA

                                 *      *  *     *                      *    
      22140 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
          1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-ACTCA-CACAAAGCCTTCGGGACTTAACCCG

              
      22204 GA
         63 GA

      22206 CAGCATTCAA


Statistics
Matches: 122,  Mismatches: 18, Indels: 10
        0.81            0.12        0.07

Matches are distributed among these distances:
  78   12  0.10
  79   79  0.65
  80   25  0.20
  81    6  0.05

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


Consensus pattern (77 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCACACAAAGCCTTCGGGACTTAACCCGGAT
TTATAACTCGCA

Found at i:22214 original size:41 final size:41

Alignment explanation


    Indices: 22137--22214  Score: 97
    Period size: 40  Copynumber: 1.9  Consensus size: 41

      22127 TTTGTATCTC

                                   *     * *         
      22137 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
          1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA

                                                   
      22178 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
          1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA

      22215 ATTAATCATG


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  40   17  0.53
  41   15  0.47

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


Consensus pattern (41 bp):   
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA

Found at i:29970 original size:39 final size:40

Alignment explanation


    Indices: 29925--30147  Score: 242
    Period size: 39  Copynumber: 5.7  Consensus size: 40

      29915 GCTCCTCGTT

                            *  *     *           *  
      29925 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                          *         
      29965 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

             *                                      
      30004 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                *                             *      
      30043 CAAAGGCCTTCGGG-CTTAACCCGGAATTT-GTATCTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA

                                **      *  * *    *   
      30082 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA

                               *      
      30123 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAACCCGGA

      30148 CAGCATTCAA


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

Matches are distributed among these distances:
  38   14  0.09
  39   76  0.48
  40   56  0.36
  41   11  0.07

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


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

Found at i:30156 original size:41 final size:41

Alignment explanation


    Indices: 30079--30156  Score: 97
    Period size: 40  Copynumber: 1.9  Consensus size: 41

      30069 TTTGTATCTC

                                   *     * *         
      30079 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
          1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA

                                                   
      30120 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
          1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA

      30157 ATTAATCATG


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  40   17  0.53
  41   15  0.47

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


Consensus pattern (41 bp):   
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.