Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3317

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: 16198
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31


Found at i:12609 original size:26 final size:26

Alignment explanation


    Indices: 12580--12693  Score: 120
    Period size: 27  Copynumber: 4.2  Consensus size: 26

      12570 TGCCTGGCTG

                             *    **  
      12580 CCAGAACAGATATTGTGACAGAATCA
          1 CCAGAACAGATATTGTGGCAGAGCCA

                   *                   
      12606 CCAGATATAGATATTGTGGCAGAGCCA
          1 CCAGA-ACAGATATTGTGGCAGAGCCA

            *     *              *     
      12633 TCAGAATAGATATTTGTGGCATAGCCA
          1 CCAGAACAGATA-TTGTGGCAGAGCCA

                                  *     
      12660 CCAGAAACAGATATTTGTGGCATAGCCA
          1 CCAG-AACAGATA-TTGTGGCAGAGCCA

                  
      12688 CCAGAA
          1 CCAGAA

      12694 TGCTTCCTCC


Statistics
Matches: 77,  Mismatches: 8, Indels: 5
        0.86            0.09        0.06

Matches are distributed among these distances:
  26   12  0.16
  27   39  0.51
  28   26  0.34

ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22


Consensus pattern (26 bp):   
CCAGAACAGATATTGTGGCAGAGCCA

Found at i:12680 original size:28 final size:28

Alignment explanation


    Indices: 12604--12693  Score: 130
    Period size: 28  Copynumber: 3.3  Consensus size: 28

      12594 GTGACAGAAT

                   *                *   
      12604 CACCAGATATAGATA-TTGTGGCAGAGC
          1 CACCAGAAATAGATATTTGTGGCATAGC

              *                         
      12631 CATCAG-AATAGATATTTGTGGCATAGC
          1 CACCAGAAATAGATATTTGTGGCATAGC

                     *                  
      12658 CACCAGAAACAGATATTTGTGGCATAGC
          1 CACCAGAAATAGATATTTGTGGCATAGC

                    
      12686 CACCAGAA
          1 CACCAGAA

      12694 TGCTTCCTCC


Statistics
Matches: 56,  Mismatches: 5, Indels: 3
        0.88            0.08        0.05

Matches are distributed among these distances:
  26    7  0.12
  27   21  0.38
  28   28  0.50

ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22


Consensus pattern (28 bp):   
CACCAGAAATAGATATTTGTGGCATAGC

Found at i:13243 original size:27 final size:27

Alignment explanation


    Indices: 13214--13326  Score: 181
    Period size: 27  Copynumber: 4.2  Consensus size: 27

      13204 GGGTATCTTG

                                      *
      13214 ATAATTCTACCCTACAGGGGTATTTCG
          1 ATAATTCTACCCTACAGGGGTATTTCA

               *            *          
      13241 ATATTTCTACCCTACAAGGGTATTTCA
          1 ATAATTCTACCCTACAGGGGTATTTCA

                                       
      13268 ATAATTCTACCCTACAGGGGTATTTCA
          1 ATAATTCTACCCTACAGGGGTATTTCA

            *                    *     
      13295 GTAATTCTACCCTACAGGGGTTTTTCA
          1 ATAATTCTACCCTACAGGGGTATTTCA

                 
      13322 ATAAT
          1 ATAAT

      13327 GTTATAAATC


Statistics
Matches: 78,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   78  1.00

ACGTcount: A:0.28, C:0.21, G:0.15, T:0.35


Consensus pattern (27 bp):   
ATAATTCTACCCTACAGGGGTATTTCA

Found at i:13259 original size:54 final size:54

Alignment explanation


    Indices: 13191--13326  Score: 190
    Period size: 54  Copynumber: 2.6  Consensus size: 54

      13181 CAAAATGGAA

                                     *                              
      13191 ATTT-TACCC-ACAAGGGTATCTT-GATAATTCTACCCTACAGGGGTATTTC-GAT
          1 ATTTCTACCCTACAAGGGTAT-TTCAATAATTCTACCCTACAGGGGTATTTCAG-T

                                                                  
      13243 ATTTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGT
          1 ATTTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGT

             *            *    *          
      13297 AATTCTACCCTACAGGGGTTTTTCAATAAT
          1 ATTTCTACCCTACAAGGGTATTTCAATAAT

      13327 GTTATAAATC


Statistics
Matches: 76,  Mismatches: 4, Indels: 6
        0.88            0.05        0.07

Matches are distributed among these distances:
  52    4  0.05
  53    7  0.09
  54   64  0.84
  55    1  0.01

ACGTcount: A:0.28, C:0.21, G:0.15, T:0.35


Consensus pattern (54 bp):   
ATTTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGT

Found at i:15850 original size:28 final size:27

Alignment explanation


    Indices: 15818--15883  Score: 73
    Period size: 28  Copynumber: 2.4  Consensus size: 27

      15808 CTGGAGGAAA

                                         
      15818 TACTG-TATTAGTGGCTCTGCCACGTAAT
          1 TACTGCTATTAGTGGCTCTGCCACGT--T

                    *        *         
      15846 TACTGCT-CTAGTGGCTTTGCCACGTT
          1 TACTGCTATTAGTGGCTCTGCCACGTT

                 *      
      15872 TACTGTTATTAG
          1 TACTGCTATTAG

      15884 CAGCATTGCT


Statistics
Matches: 32,  Mismatches: 4, Indels: 5
        0.78            0.10        0.12

Matches are distributed among these distances:
  26    7  0.22
  27    3  0.09
  28   21  0.66
  29    1  0.03

ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39


Consensus pattern (27 bp):   
TACTGCTATTAGTGGCTCTGCCACGTT

Found at i:15990 original size:21 final size:21

Alignment explanation


    Indices: 15961--16002  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      15951 AATCCCTACA

                     *           
      15961 TGGTATGTTTGTTGGTACGGG
          1 TGGTATGTTGGTTGGTACGGG

                *           *    
      15982 TGGTGTGTTGGTTGGTTCGGG
          1 TGGTATGTTGGTTGGTACGGG

      16003 ATGGGATAGG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.05, C:0.05, G:0.48, T:0.43


Consensus pattern (21 bp):   
TGGTATGTTGGTTGGTACGGG
Done.