Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3508

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: 28910
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30


Found at i:1715 original size:39 final size:39

Alignment explanation


    Indices: 1623--1737  Score: 142
    Period size: 39  Copynumber: 2.9  Consensus size: 39

       1613 CCGGACATAT

                     *                     * *      
       1623 TTCCAGCACGTAGCCTGCGAACCTTAAGTCCGGTTATAAA
          1 TTCCAGCACATAGCCTGCG-ACCTTAAGTCCAGATATAAA

               *                          *         
       1663 TTCTAGCACATAGCCTGCAGACCTTAAGTCTAGATAT-AA
          1 TTCCAGCACATAGCCTGC-GACCTTAAGTCCAGATATAAA

                                   *            
       1702 TTCCAGCACATAGCCTGCGGACCCTAAGTCCAGATA
          1 TTCCAGCACATAGCCTGC-GACCTTAAGTCCAGATA

       1738 AACATCACTG


Statistics
Matches: 65,  Mismatches: 9, Indels: 3
        0.84            0.12        0.04

Matches are distributed among these distances:
  39   34  0.52
  40   30  0.46
  41    1  0.02

ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24


Consensus pattern (39 bp):   
TTCCAGCACATAGCCTGCGACCTTAAGTCCAGATATAAA

Found at i:8616 original size:40 final size:40

Alignment explanation


    Indices: 8546--8843  Score: 279
    Period size: 40  Copynumber: 7.5  Consensus size: 40

       8536 AAATCACGTA

                   * *           *            *      
       8546 CCTTCGGAATTTAA-CCGGATATAGCT-ACTCGTTCAAATG
          1 CCTTCGGGACTTAACCCGGATTTAG-TAACTCGTACAAATG

                      *  *                           
       8585 CCTTCGGGACATAGCCCGG-TTATAGTAACTCGTACAAATG
          1 CCTTCGGGACTTAACCCGGATT-TAGTAACTCGTACAAATG

                                            *       
       8625 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAACCCGGATTTAGTAACTCGTACAAATG

                             *              *       
       8665 CCTTCGGGACTTAACCCAGATTTAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAACCCGGATTTAGTAACTCGTACAAATG

                          **                         
       8705 CCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTACAAATG
          1 CCTTCGGGA-CTTAACCCGGATTTAGTAACTCGTACAAATG

                         *  *           *    *       
       8745 CCTTCGGG-CTTAGCCTGGAATTT-GTATCTCGCACAAATG
          1 CCTTCGGGACTTAACCCGG-ATTTAGTAACTCGTACAAATG

                          **      * *  *    * *       
       8784 CCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-G
          1 CCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGTACAAATG

                         *      
       8824 CCTTCGGGACTTAGCCCGGA
          1 CCTTCGGGACTTAACCCGGA

       8844 CATCATTCAA


Statistics
Matches: 222,  Mismatches: 25, Indels: 23
        0.82            0.09        0.09

Matches are distributed among these distances:
  38    2  0.01
  39   45  0.20
  40  160  0.72
  41   15  0.07

ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28


Consensus pattern (40 bp):   
CCTTCGGGACTTAACCCGGATTTAGTAACTCGTACAAATG

Found at i:8691 original size:80 final size:79

Alignment explanation


    Indices: 8579--8841  Score: 327
    Period size: 80  Copynumber: 3.3  Consensus size: 79

       8569 GCTACTCGTT

                            *       *             *                     **   
       8579 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGTACAAATGCCTTCGGGA-CTTAACCCG
          1 CAAATGCCTTCGGGACTTAGCCCGATT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG

                            
       8643 GATTTAGTAACTCGCA
         64 GATTTAGTAACTCGCA

                               *                                             
       8659 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
          1 CAAATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG

                         * 
       8724 ATTTAGTAACTCGTA
         65 ATTTAGTAACTCGCA

                                   *          *                              
       8739 CAAATGCCTTCGGG-CTTAGCCTGGAATTT-GTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
          1 CAAATGCCTTCGGGACTTAGCC-CG-ATTTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG

               * *  *    *   
       8802 GATATGGTCACTTAGCA
         64 GATTTAGTAAC-TCGCA

                                    
       8819 CAAA-GCCTTCGGGACTTAGCCCG
          1 CAAATGCCTTCGGGACTTAGCCCG

       8842 GACATCATTC


Statistics
Matches: 161,  Mismatches: 16, Indels: 13
        0.85            0.08        0.07

Matches are distributed among these distances:
  79   61  0.38
  80   97  0.60
  81    3  0.02

ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27


Consensus pattern (79 bp):   
CAAATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
TTTAGTAACTCGCA

Found at i:16667 original size:39 final size:40

Alignment explanation


    Indices: 16561--16689  Score: 187
    Period size: 40  Copynumber: 3.3  Consensus size: 40

      16551 GCTACTCGTT

                            *  *                     
      16561 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA

                                                    
      16601 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                                  * 
      16641 CAAATGCCTTC-GGACTTAACCCGGA-TTAGTAACTC-TA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                         
      16678 C-AATGCCTTCGG
          1 CAAATGCCTTCGG

      16690 ATCTTAGCCG


Statistics
Matches: 84,  Mismatches: 3, Indels: 7
        0.89            0.03        0.07

Matches are distributed among these distances:
  36    9  0.11
  37    3  0.04
  38   10  0.12
  39   14  0.17
  40   46  0.55
  41    2  0.02

ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Done.