Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3149

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: 3389
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28


Found at i:3123 original size:40 final size:40

Alignment explanation


    Indices: 3025--3312  Score: 361
    Period size: 40  Copynumber: 7.3  Consensus size: 40

       3015 TCCTCGTTCA

                          *  *     *    *      *    
       3025 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

                          *              *          
       3064 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

             *                                      
       3104 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

                                                    
       3144 AATGCCTTC-GGACTTAACCCGGATTTAATAACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

                                        *  *       *
       3183 AATGCCTTCGGGACTT-A-CCGGATTTAGTATCTCGCACA
          1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

              *                *      *              
       3221 AAGGCCTTC-GGATCTTAATCCGGATATAATAACTCGCACG
          1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAACTCGCACG

                                         *  *       *
       3261 AATGCCTTCGGGACTTAACCCGGATTTTAGTATCTCGCACA
          1 AATGCCTTCGGGACTTAACCCGGA-TTTAATAACTCGCACG

              *        
       3302 AAGGCCTTCGG
          1 AATGCCTTCGG

       3313 ATCTTAATTC


Statistics
Matches: 218,  Mismatches: 24, Indels: 12
        0.86            0.09        0.05

Matches are distributed among these distances:
  37    3  0.01
  38   29  0.13
  39   75  0.34
  40   86  0.39
  41   25  0.11

ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25


Consensus pattern (40 bp):   
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG

Found at i:3126 original size:79 final size:79

Alignment explanation


    Indices: 3025--3319  Score: 398
    Period size: 79  Copynumber: 3.7  Consensus size: 79

       3015 TCCTCGTTCA

                          *  *     *           *      *           *          
       3025 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGAT
          1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAAGGCCTTC-GGACTTAACCCGGAT

                *          
       3089 TTAACAACTCGCACG
         65 TTAATAACTCGCACG

             *                          *          *  *                      
       3104 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGACTTAACCCGGATT
          1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAAGGCCTTCGGACTTAACCCGGATT

                          
       3169 TAATAACTCGCACG
         66 TAATAACTCGCACG

                                           *                          *      
       3183 AATGCCTTCGGGACTT-A-CCGGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAATCCGGAT
          1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAAGGCCTTCGGA-CTTAACCCGGAT

            *              
       3246 ATAATAACTCGCACG
         65 TTAATAACTCGCACG

                                            *                          
       3261 AATGCCTTCGGGACTTAACCCGGATTTTAGTATCTCGCACAAAGGCCTTCGGATCTTAA
          1 AATGCCTTCGGGACTTAACCCGGA-TTTAGTAACTCGCACAAAGGCCTTCGGA-CTTAA

       3320 TTCGGATATA


Statistics
Matches: 196,  Mismatches: 15, Indels: 8
        0.89            0.07        0.04

Matches are distributed among these distances:
  77   29  0.15
  78   42  0.21
  79   77  0.39
  80   14  0.07
  81   34  0.17

ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26


Consensus pattern (79 bp):   
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAAGGCCTTCGGACTTAACCCGGATT
TAATAACTCGCACG
Done.