Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold277

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: 24683
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.33


Found at i:15233 original size:41 final size:41

Alignment explanation


    Indices: 15188--15314  Score: 218
    Period size: 41  Copynumber: 3.1  Consensus size: 41

      15178 CCGAAATGTA

                      *             *                
      15188 TCACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATAATT
          1 TCACCGGCATCAAGCCTGCTAGACATATAGTCTGAATAATT

                                                     
      15229 TCACCGGCATCAAGCCTGCTAGACATATAGTCTGAATAATT
          1 TCACCGGCATCAAGCCTGCTAGACATATAGTCTGAATAATT

                                       *         *   
      15270 TCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAATTATT
          1 TCACCGGCATCAAGCCTGCTAGACATATAGTCTGAATAATT

                
      15311 TCAC
          1 TCAC

      15315 TGACAATAAA


Statistics
Matches: 82,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  41   82  1.00

ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28


Consensus pattern (41 bp):   
TCACCGGCATCAAGCCTGCTAGACATATAGTCTGAATAATT

Found at i:15346 original size:82 final size:82

Alignment explanation


    Indices: 15188--15346  Score: 196
    Period size: 82  Copynumber: 1.9  Consensus size: 82

      15178 CCGAAATGTA

                      *             *  *                   *      *    *     
      15188 TCACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATAATTTCACCGGCATCAAGCCTGCTAGAC
          1 TCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAATAATTTCACCGACATCAAACCTGATAGAC

                  *          
      15253 ATATAGTCTGAATAATT
         66 ATATAGCCTGAATAATT

                                                 *       *                  *
      15270 TCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAATTATTTCACTGACAAT-AAACCTGATAGG
          1 TCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAATAATTTCACCGAC-ATCAAACCTGATAGA

                          
      15334 CACTA-AGCCTGAA
         65 CA-TATAGCCTGAA

      15347 AATCTCAATT


Statistics
Matches: 65,  Mismatches: 10, Indels: 4
        0.82            0.13        0.05

Matches are distributed among these distances:
  82   61  0.94
  83    4  0.06

ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26


Consensus pattern (82 bp):   
TCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAATAATTTCACCGACATCAAACCTGATAGAC
ATATAGCCTGAATAATT

Found at i:16285 original size:21 final size:21

Alignment explanation


    Indices: 16261--16302  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      16251 AATAAGCTAG

                                 
      16261 TTTAAATATAATTACATTCAA
          1 TTTAAATATAATTACATTCAA

                          *      
      16282 TTTAAATATAATTATATTCAA
          1 TTTAAATATAATTACATTCAA

      16303 AATAAACTAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45


Consensus pattern (21 bp):   
TTTAAATATAATTACATTCAA

Found at i:16308 original size:21 final size:21

Alignment explanation


    Indices: 16263--16308  Score: 65
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      16253 TAAGCTAGTT

                               **
      16263 TAAATATAATTACATTCAATT
          1 TAAATATAATTACATTCAAAA

                        *        
      16284 TAAATATAATTATATTCAAAA
          1 TAAATATAATTACATTCAAAA

                
      16305 TAAA
          1 TAAA

      16309 CTAGTTCTTG


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39


Consensus pattern (21 bp):   
TAAATATAATTACATTCAAAA

Found at i:20219 original size:25 final size:25

Alignment explanation


    Indices: 20189--20295  Score: 142
    Period size: 25  Copynumber: 4.3  Consensus size: 25

      20179 TCAGCTTTTC

                              *  *   
      20189 CGAGCTGAATAACGGGAATCTTATG
          1 CGAGCTGAATAACGGGAAGCTCATG

                                     
      20214 CGAGCTGAATAACGGGAAGCTCATG
          1 CGAGCTGAATAACGGGAAGCTCATG

                  *      *           
      20239 CGAGCTAAATAACAGGAAGCTCATG
          1 CGAGCTGAATAACGGGAAGCTCATG

                    *  * *           
      20264 CGAGCTGAGTATCAGGAAGCTCATG
          1 CGAGCTGAATAACGGGAAGCTCATG

             *     
      20289 CAAGCTG
          1 CGAGCTG

      20296 TGGTGTGTCC


Statistics
Matches: 74,  Mismatches: 8, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  25   74  1.00

ACGTcount: A:0.33, C:0.20, G:0.29, T:0.19


Consensus pattern (25 bp):   
CGAGCTGAATAACGGGAAGCTCATG

Done.