Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_248 ID=scaffold_248-JGI_221_v2.0

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: 11353
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.26

Warning! 2355 characters in sequence are not A, C, G, or T


Found at i:10139 original size:46 final size:46

Alignment explanation


    Indices: 10068--10312  Score: 364
    Period size: 46  Copynumber: 5.3  Consensus size: 46

      10058 TACCCTGTTT

                                       *     *             
      10068 TGGACAGCATTTATACATCAAATTGGATAGCATTAATATGCTCAAAA
          1 TGGACAGCA-TTATACATCAAATTGGACAGCATCAATATGCTCAAAA

             **                                 *         
      10115 TAAACAGCATTATACATCAAATTGGACAGCATCAATTTGCTCAAAA
          1 TGGACAGCATTATACATCAAATTGGACAGCATCAATATGCTCAAAA

             *  *                     *   * *            *
      10161 TTGATAGCATTATACATCAAATTGGATAGCTTTAATATGCTCAAAT
          1 TGGACAGCATTATACATCAAATTGGACAGCATCAATATGCTCAAAA

                                                  *       
      10207 TGGACAGCATTATACATCAAATTGGACAGCATCAATATACTCAAAA
          1 TGGACAGCATTATACATCAAATTGGACAGCATCAATATGCTCAAAA

                  *                                       
      10253 TGGACAACATTATACATCAAATTGGACAGCATCAATATGCTCAAAA
          1 TGGACAGCATTATACATCAAATTGGACAGCATCAATATGCTCAAAA

                          
      10299 TGGACAGCATTATA
          1 TGGACAGCATTATA

      10313 ACATATAAAA


Statistics
Matches: 175,  Mismatches: 23, Indels: 1
        0.88            0.12        0.01

Matches are distributed among these distances:
  46  168  0.96
  47    7  0.04

ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28


Consensus pattern (46 bp):   
TGGACAGCATTATACATCAAATTGGACAGCATCAATATGCTCAAAA

Found at i:10206 original size:24 final size:24

Alignment explanation


    Indices: 10085--10310  Score: 145
    Period size: 24  Copynumber: 9.8  Consensus size: 24

      10075 CATTTATACA

                                    
      10085 TCAAATTGGATAGCATTAATATGC
          1 TCAAATTGGATAGCATTAATATGC

                 * ** *             
      10109 TCAAAATAAACAGCATT-ATA--C
          1 TCAAATTGGATAGCATTAATATGC

                       *     *   *   
      10130 ATCAAATTGGACAGCATCAATTTGC
          1 -TCAAATTGGATAGCATTAATATGC

                                     
      10155 TCAAAATT-GATAGCATT-ATA--C
          1 TC-AAATTGGATAGCATTAATATGC

                           *         
      10176 ATCAAATTGGATAGCTTTAATATGC
          1 -TCAAATTGGATAGCATTAATATGC

                      *             
      10201 TCAAATTGGACAGCATT-ATA--C
          1 TCAAATTGGATAGCATTAATATGC

                       *     *     * 
      10222 ATCAAATTGGACAGCATCAATATAC
          1 -TCAAATTGGATAGCATTAATATGC

                 *    * *           
      10247 TCAAAATGGACAACATT-ATA--C
          1 TCAAATTGGATAGCATTAATATGC

                       *     *       
      10268 ATCAAATTGGACAGCATCAATATGC
          1 -TCAAATTGGATAGCATTAATATGC

                 *    *       
      10293 TCAAAATGGACAGCATTA
          1 TCAAATTGGATAGCATTA

      10311 TAACATATAA


Statistics
Matches: 160,  Mismatches: 24, Indels: 36
        0.73            0.11        0.16

Matches are distributed among these distances:
  21    9  0.06
  22   53  0.33
  23   22  0.14
  24   67  0.42
  25    9  0.06

ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28


Consensus pattern (24 bp):   
TCAAATTGGATAGCATTAATATGC

Done.