Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3017

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, 486

Length: 810
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31


Found at i:463 original size:44 final size:44

Alignment explanation


    Indices: 281--476  Score: 125
    Period size: 43  Copynumber: 4.5  Consensus size: 44

        271 CTTTGATCTG

                                                        
        281 CTCCACTACTGATTAGGGTGACAGAATCTGCAATC-TCAACCTA
          1 CTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTA

                       *    **   *  *              *  *  *
        324 CTCCACTACTGCTTAGAATGATAGGA-CT--AATGGCTTAAATCTG
          1 CTCCACTACTGATTAGGGTGACAGAATCTGCAAT--CTTCAACCTA

              * * *             *   *   *   * *      * *  *
        367 CTTCTCCACTGTATT-GGGAAGATAAGATTC-ACCATCTTCGATCTG
          1 CTCCACTACTG-ATTAGGG-TGA-CAGAATCTGCAATCTTCAACCTA

                                                        
        412 CTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTA
          1 CTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTA

                       *         
        456 CTCCACTACTGCTTAGGGTGA
          1 CTCCACTACTGATTAGGGTGA

        477 TAGGACTAAT


Statistics
Matches: 109,  Mismatches: 33, Indels: 21
        0.67            0.20        0.13

Matches are distributed among these distances:
  40    3  0.03
  42    3  0.03
  43   40  0.37
  44   39  0.36
  45   21  0.19
  46    1  0.01
  47    2  0.02

ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29


Consensus pattern (44 bp):   
CTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTA

Found at i:523 original size:132 final size:132

Alignment explanation


    Indices: 1--810  Score: 1279
    Period size: 132  Copynumber: 6.2  Consensus size: 132

                                        *            *    *                  
          1 TTCACCATCTTCGATCTGCTCCACTACTAATTAGGGTGACAAAATCGGCAATCTTC-ACCTACTC
          1 TTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTC

              *                           *                        *         
         65 CAGTACTGCTTAGGGTGATAGGACTAATGGTTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
         66 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAA

              
        130 GA
        131 GA

                                       *                                     
        132 TTCACCATCTTCGATCTGCTCCACTACCGATTAGGGTGACAGAATCTGCAATC-TCAACCTACTC
          1 TTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTC

                         **                                                  
        196 CACTACTGCTTAGAATGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAA
         66 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAA

              
        261 GA
        131 GA

              *        *                                                     
        263 TTAACCATCTTTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATC-TCAACCTACTC
          1 TTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTC

                         **                                        *         
        327 CACTACTGCTTAGAATGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
         66 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAA

              
        392 GA
        131 GA

                                                                             
        394 TTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTC
          1 TTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTC

                                                             *    *    *     
        459 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACCGTATAAGGAGGATAA
         66 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAA

              
        524 GA
        131 GA

              *        *        *                                         *  
        526 TTAACCATCTTTGATCTGCTTCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTAATC
          1 TTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTC

                   *                                         *    *    *     
        591 CACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACCGTATAAGGAGGATAA
         66 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAA

              
        656 GA
        131 GA

              *        *        *                            *               
        658 TTAACCATCTTTGATCTGCTTCACTACTGATTTAGGGTGAC-GAATCTGTAATCTTCAACCTACT
          1 TTCACCATCTTCGATCTGCTCCACTACTGA-TTAGGGTGACAGAATCTGCAATCTTCAACCTACT

                    *                      *               *                 
        722 CCACTACTACTTAGGGTGATAGGACTAATGGATTAAATCTGCTTCTCTACTGTATT-GAGAAGAT
         65 CCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAG-GAAGAT

                
        786 AAGA
        129 AAGA

                                 
        790 TTCACCATCTTCGATCTGCTC
          1 TTCACCATCTTCGATCTGCTC


Statistics
Matches: 639,  Mismatches: 36, Indels: 7
        0.94            0.05        0.01

Matches are distributed among these distances:
 130    2  0.00
 131  298  0.47
 132  329  0.51
 133   10  0.02

ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31


Consensus pattern (132 bp):   
TTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTC
CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAA
GA

Done.