Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold994

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: 12082
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26


Found at i:10285 original size:13 final size:12

Alignment explanation


    Indices: 10263--10298  Score: 63
    Period size: 13  Copynumber: 2.9  Consensus size: 12

      10253 CGTTACACAC

                        
      10263 CAAAAAAAAAAA
          1 CAAAAAAAAAAA

                         
      10275 CAAACAAAAAAAA
          1 CAAA-AAAAAAAA

                       
      10288 CAAAAAAAAAA
          1 CAAAAAAAAAA

      10299 GAAAAAATAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  12   11  0.48
  13   12  0.52

ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00


Consensus pattern (12 bp):   
CAAAAAAAAAAA

Found at i:10292 original size:20 final size:20

Alignment explanation


    Indices: 10264--10315  Score: 61
    Period size: 20  Copynumber: 2.6  Consensus size: 20

      10254 GTTACACACC

                        *       
      10264 AAAAA-AAAAAACAAACAAA
          1 AAAAACAAAAAAAAAACAAA

                            *   
      10283 AAAAACAAAAAAAAAAGAAA
          1 AAAAACAAAAAAAAAACAAA

                 *       
      10303 AAATAGCAAAAAA
          1 AAA-AACAAAAAA

      10316 TAGAAGGGTC


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  19    5  0.18
  20   15  0.54
  21    8  0.29

ACGTcount: A:0.87, C:0.08, G:0.04, T:0.02


Consensus pattern (20 bp):   
AAAAACAAAAAAAAAACAAA

Found at i:11575 original size:29 final size:29

Alignment explanation


    Indices: 11533--12079  Score: 671
    Period size: 29  Copynumber: 18.6  Consensus size: 29

      11523 AATGTTCATC

                                         
      11533 CCTTTCAAAGCCCACAAGTCAGTGGCACT
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

                             *           
      11562 CCTTTCAAAGCCCACAAATCAGTGGCACT
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

             *                           
      11591 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

                                         
      11619 CCTTTCAAAGCCCACAAGTCAGTGGCACT
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

                        *      *     *   
      11648 CCTTTCAAAGCCTACAAGTTAGTGGTACT
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

             *               *           
      11677 CTTTTCAAAGCCCACAAATCAGTGGCACT
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

             *   *                       
      11706 CTTTTTAAAGCCCACAAGTCAGTGGCACT
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

                                         
      11735 CCTTTCAAAGCCCACAAGTCAGTGGCACT
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

                             *           
      11764 CCTTTCAAAGCCCACAAATCAGTGGCACT
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

             *                           
      11793 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

                             *   *       
      11821 CCTTTCAAAGCCCACAACTCATTGGCA-T
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

                                         
      11849 CCTTTCAAAGCCCACAAGTCAGTGGCACT
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

                              *          
      11878 CCTTTCAAAGCCCACAAGCCAGTGGCACT
          1 CCTTTCAAAGCCCACAAGTCAGTGGCACT

                   *            *         
      11907 -CTTTCAGAGCCCACAAGTCGGTGGCAAC-
          1 CCTTTCAAAGCCCACAAGTCAGTGGC-ACT

                                   *         
      11935 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC-
          1 CC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACT

                 *                 *         
      11967 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC-
          1 CC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACT

                 *                 *         
      11999 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC-
          1 CC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACT

                 *                           
      12031 CCATTCCAAAGCCCACACAAGTCAGTGGCAAC-
          1 CC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACT

                             
      12063 CCATTTCAAAGCCCACA
          1 CC-TTTCAAAGCCCACA

      12080 CAA


Statistics
Matches: 478,  Mismatches: 32, Indels: 15
        0.91            0.06        0.03

Matches are distributed among these distances:
  28   98  0.21
  29  244  0.51
  30   11  0.02
  31    4  0.01
  32  121  0.25

ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20


Consensus pattern (29 bp):   
CCTTTCAAAGCCCACAAGTCAGTGGCACT

Done.