Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_926 ID=scaffold_926-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: 4026
ACGTcount: A:0.18, C:0.12, G:0.11, T:0.18

Warning! 1650 characters in sequence are not A, C, G, or T


Found at i:62 original size:32 final size:32

Alignment explanation


    Indices: 21--81  Score: 122
    Period size: 32  Copynumber: 1.9  Consensus size: 32

         11 ATAGTATTAC

                                            
         21 TCACTACAGCAAAACAGGCTTTTCGCGGCTAT
          1 TCACTACAGCAAAACAGGCTTTTCGCGGCTAT

                                         
         53 TCACTACAGCAAAACAGGCTTTTCGCGGC
          1 TCACTACAGCAAAACAGGCTTTTCGCGGC

         82 GCTTTTTTAG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   29  1.00

ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23


Consensus pattern (32 bp):   
TCACTACAGCAAAACAGGCTTTTCGCGGCTAT

Found at i:199 original size:21 final size:21

Alignment explanation


    Indices: 139--199  Score: 51
    Period size: 21  Copynumber: 3.0  Consensus size: 21

        129 AGCGGCGCTT

                                 
        139 ACTATAGCGGCGCTTCTTCTA
          1 ACTATAGCGGCGCTTCTTCTA

                      *        *   
        160 A-TA-ATGACTGCGC--C-GCTA
          1 ACTATA-G-CGGCGCTTCTTCTA

                                 
        178 ACTATAGCGGCGCTTCTTCTA
          1 ACTATAGCGGCGCTTCTTCTA

             
        199 A
          1 A

        200 TAAACGCCGC


Statistics
Matches: 29,  Mismatches: 4, Indels: 14
        0.62            0.09        0.30

Matches are distributed among these distances:
  18    9  0.31
  19    5  0.17
  20    5  0.17
  21   10  0.34

ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30


Consensus pattern (21 bp):   
ACTATAGCGGCGCTTCTTCTA

Found at i:463 original size:43 final size:42

Alignment explanation


    Indices: 246--682  Score: 225
    Period size: 43  Copynumber: 10.1  Consensus size: 42

        236 TCTTTTGCCG

                             *   *            * * *    
        246 CGCCACTATAGATGTGGCTCTTTAGCGGCGCTTAGATACAAAA
          1 CGCCACTATAGATG-GGTTCTATAGCGGCGCTTATACAAAAAA

                 *        * **   *             * *     
        289 CGCCATTATAGATCAGCCTCTCTAGCGGCGCTTATCCGAAAAA
          1 CGCCACTATAGAT-GGGTTCTATAGCGGCGCTTATACAAAAAA

            *                        **     *      **    
        332 TGCCACTATAGA-GGGTGGGTCTATTCCGGCGGTTATACTCAAAA
          1 CGCCACTATAGATGGGT---TCTATAGCGGCGCTTATACAAAAAA

                          * *                          
        376 CGCCACTATAGATGTGATCTATAGCGGCGCTTATACAAAAAAA
          1 CGCCACTATAGATGGGTTCTATAGCGGCGCTTATAC-AAAAAA

                        *                    *     *   
        419 CGCCACTATAGCTTGGGTTCTATAGCGGCGCTTGTACAACAAA
          1 CGCCACTATAG-ATGGGTTCTATAGCGGCGCTTATACAAAAAA

                    *    *       * **              *   
        462 CGCCACTAGAGAGAGGGTTCTTTTCCGGCGCTTATACAAGAAA
          1 CGCCACTATAGA-TGGGTTCTATAGCGGCGCTTATACAAAAAA

                                 *  **            * **   
        505 CGCCACTATAGATAGGGTT-TTTCTCCGGCGCTTCA-ATAGGAAA
          1 CGCCACTATAGAT-GGGTTCTAT-AGCGGCGCTT-ATACAAAAAA

                  *       *      * **          *   *   
        548 CGCCACGATAGATAAGGTTCTTTTCCGGCGCTTATGCAAGAAA
          1 CGCCACTATAGAT-GGGTTCTATAGCGGCGCTTATACAAAAAA

             *    *              * *              *     
        591 CACCACGATAGATAGGGTTCTTTTGCGGCGCTTAGT-CTAAAAA
          1 CGCCACTATAGAT-GGGTTCTATAGCGGCGCTTA-TACAAAAAA

                    *    *   *   * *           *        
        634 CGCCACTACAGACGGGGATCTTTCGCGGCGCTTATGCAAAAAAA
          1 CGCCACTATAGA-TGGGTTCTATAGCGGCGCTTATAC-AAAAAA

                 
        678 CGCCA
          1 CGCCA

        683 TAATAGGCTG


Statistics
Matches: 314,  Mismatches: 63, Indels: 33
        0.77            0.15        0.08

Matches are distributed among these distances:
  41    1  0.00
  42   21  0.07
  43  225  0.72
  44   65  0.21
  45    2  0.01

ACGTcount: A:0.28, C:0.24, G:0.23, T:0.24


Consensus pattern (42 bp):   
CGCCACTATAGATGGGTTCTATAGCGGCGCTTATACAAAAAA

Found at i:523 original size:86 final size:86

Alignment explanation


    Indices: 400--682  Score: 272
    Period size: 86  Copynumber: 3.3  Consensus size: 86

        390 TGATCTATAG

                                          * *       * *                      
        400 CGGCGCTTATACAAAAAAACGCCACTATAGCTTGGGTTCTATAGCGGCGCTTGTACAACAAACGC
          1 CGGCGCTTATACAAAAAAACGCCACTATAGATAGGGTTCTTTTGCGGCGCTTGTACAA-AAACGC

                 *                
        465 CACTAGAGAGAGGGTTCTTTTC
         65 CACTACAGAGAGGGTTCTTTTC

                           *                            *        ** *  *     
        487 CGGCGCTTATAC-AAGAAACGCCACTATAGATAGGGTT-TTTCTCCGGCGCTTCAATAGGAAACG
          1 CGGCGCTTATACAAAAAAACGCCACTATAGATAGGGTTCTTT-TGCGGCGCTTGTACA-AAAACG

                * *   * *          
        550 CCACGATAGATAAGGTTCTTTTC
         64 CCACTACAGAGAGGGTTCTTTTC

                      *    *    *    *                                       
        573 CGGCGCTTATGC-AAGAAACACCACGATAGATAGGGTTCTTTTGCGGCGCTTAGT-CTAAAAACG
          1 CGGCGCTTATACAAAAAAACGCCACTATAGATAGGGTTCTTTTGCGGCGCTT-GTAC-AAAAACG

                            *       
        636 CCACTACAGACG-GGGATC-TTTC
         64 CCACTACAGA-GAGGGTTCTTTTC

                       *             
        658 GCGGCGCTTATGCAAAAAAACGCCA
          1 -CGGCGCTTATACAAAAAAACGCCA

        683 TAATAGGCTG


Statistics
Matches: 159,  Mismatches: 29, Indels: 16
        0.78            0.14        0.08

Matches are distributed among these distances:
  85    6  0.04
  86  128  0.81
  87   25  0.16

ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24


Consensus pattern (86 bp):   
CGGCGCTTATACAAAAAAACGCCACTATAGATAGGGTTCTTTTGCGGCGCTTGTACAAAAACGCC
ACTACAGAGAGGGTTCTTTTC
Done.