Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3782

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, 396

Length: 660
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:267 original size:12 final size:12

Alignment explanation


    Indices: 250--275  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

        240 CAAAACAGGC

                        
        250 TTTTAGCGGCGT
          1 TTTTAGCGGCGT

                        
        262 TTTTAGCGGCGT
          1 TTTTAGCGGCGT

              
        274 TT
          1 TT

        276 GGATAAAAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46


Consensus pattern (12 bp):   
TTTTAGCGGCGT

Found at i:309 original size:41 final size:38

Alignment explanation


    Indices: 264--355  Score: 94
    Period size: 40  Copynumber: 2.3  Consensus size: 38

        254 AGCGGCGTTT

                                      *     *  *  *  
        264 TTAGCGGCGTTTGGATAAAAAACGCCGCTAAAGATTGATCA
          1 TTAGCGGCGTTT--ATAAAAAACGCCACTAAAAATAG-GCA

                           **                      
        305 TTAGCGGCGCTTTATGGAAAACGCCACTAAAAATAGGCA
          1 TTAGCGGCG-TTTATAAAAAACGCCACTAAAAATAGGCA

                        
        344 TTAGCGGCGTTT
          1 TTAGCGGCGTTT

        356 TCCAGAAAGC


Statistics
Matches: 44,  Mismatches: 6, Indels: 5
        0.80            0.11        0.09

Matches are distributed among these distances:
  38    3  0.07
  39   11  0.25
  40   18  0.41
  41    9  0.20
  42    3  0.07

ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25


Consensus pattern (38 bp):   
TTAGCGGCGTTTATAAAAAACGCCACTAAAAATAGGCA

Found at i:542 original size:113 final size:114

Alignment explanation


    Indices: 344--660  Score: 460
    Period size: 113  Copynumber: 2.8  Consensus size: 114

        334 AAAATAGGCA

                         **         *         *              *               
        344 TTAGCGGCGTTTTCCAGAAAGCGCTGC-AAAAAATCTAAGCCCAACGACGCCGTTTTTTGAGCTT
          1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTTTGAGCTT

              *                            *   *             
        408 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGTCGCTAATGCTCAGGGCT
         66 TCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCGAATGCTCAGGGCT

                                                      *                  *   
        457 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACACCGTTTTTTGAACTT
          1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTTTGAGCTT

                            *                             *  
        522 TC-GGGATTTAGCGGCTTTTTTAAGAAAGCGCCGCGAATGCTCAGGTCT
         66 TCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCGAATGCTCAGGGCT

                              *                               *        *     
        570 TTAGCGGCGTTTTTG-GTGAAGCGCCGCAAAAAAACCTAAGCCCAACGTAAACCGTTTTCTGAGC
          1 TTAGCGGCGTTTTTGAG-AAAGCGCCGCAAAAAAACCTAAGCCCAACG-ACACCGTTTTTTGAGC

                                       
        634 TTTCAGGGATTTAGCGGCGTTTTTAAG
         64 TTTCAGGGATTTAGCGGCGTTTTTAAG


Statistics
Matches: 183,  Mismatches: 17, Indels: 6
        0.89            0.08        0.03

Matches are distributed among these distances:
 112    1  0.01
 113  109  0.60
 114   52  0.28
 115   21  0.11

ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27


Consensus pattern (114 bp):   
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTTTGAGCTT
TCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCGAATGCTCAGGGCT
Done.