Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_354 ID=scaffold_354-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: 7976
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32


Found at i:801 original size:8 final size:8

Alignment explanation


    Indices: 779--817  Score: 53
    Period size: 8  Copynumber: 4.9  Consensus size: 8

        769 AATACAAATT

                     
        779 TTTTCTTTC
          1 TTTT-TTTC

             *      
        788 TATTTTTC
          1 TTTTTTTC

                    
        796 TTTTTTTC
          1 TTTTTTTC

                    
        804 -TTTTTTC
          1 TTTTTTTC

                   
        811 TTTTTTT
          1 TTTTTTT

        818 GCTGTCGATT


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
   7    7  0.26
   8   17  0.63
   9    3  0.11

ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85


Consensus pattern (8 bp):   
TTTTTTTC

Found at i:810 original size:15 final size:16

Alignment explanation


    Indices: 779--817  Score: 62
    Period size: 15  Copynumber: 2.4  Consensus size: 16

        769 AATACAAATT

                             
        779 TTTTCTTTCTATTTTTC
          1 TTTT-TTTCTATTTTTC

                            
        796 TTTTTTTCT-TTTTTC
          1 TTTTTTTCTATTTTTC

                   
        811 TTTTTTT
          1 TTTTTTT

        818 GCTGTCGATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  15   13  0.59
  16    5  0.23
  17    4  0.18

ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85


Consensus pattern (16 bp):   
TTTTTTTCTATTTTTC

Found at i:1594 original size:44 final size:43

Alignment explanation


    Indices: 1498--1837  Score: 245
    Period size: 44  Copynumber: 7.8  Consensus size: 43

       1488 ACTTGATGCG

                *   *          *  *              *    * 
       1498 ATCTACTCTACTGCAACTTTAGAGAGATAAGATCTATTACTTTA
          1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATGACTTCA

               *        *        *       *              
       1542 ATCCGCTCCACTACAACTTCAAGGAGATAGGATTATCGACTTCA
          1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-GACTTCA

                                    *       *    **    *
       1586 ATCTGCTCCACTGCAACTTCAGGGGGATAAGACT-TGTTTTCTC
          1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATGACTTC-A

             *      *         *               **     * *
       1629 AGCTTGCTTCACTGCAACCTCAGGGAGATAAGA-CCTGA-TACG
          1 ATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTATGACTTCA

               **   *             *              * *  * 
       1671 ATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTTA
          1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATGACTTCA

                    *   *                *        *     
       1715 ATCTGCTCTACTACAACTTCAGGGAGATAGGATTATCGGCTTCA
          1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-GACTTCA

                *            *                     *     
       1759 ATCTACTCCACTGCAACCTCAGGGAGATAAGATTTATCGGCTTCA
          1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAT-GACTTCA

                             *    *           
       1804 ATCTGCTCCACTGCAACCTCAGAGAGATAAGATT
          1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT

       1838 TGCCATCTTC


Statistics
Matches: 231,  Mismatches: 56, Indels: 18
        0.76            0.18        0.06

Matches are distributed among these distances:
  41   23  0.10
  42    6  0.03
  43   13  0.06
  44  147  0.64
  45   42  0.18

ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29


Consensus pattern (43 bp):   
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATGACTTCA

Found at i:1859 original size:45 final size:45

Alignment explanation


    Indices: 1675--1862  Score: 155
    Period size: 45  Copynumber: 4.2  Consensus size: 45

       1665 GATACGATCC

                *        *               *  **  *  *     
       1675 ACTCTACTGCAACTTCAGAGAGATAAGATCTATTA-TTTTAATCT
          1 ACTCCACTGCAACCTCAGAGAGATAAGATTTACCAGCTTCAATCT

            *   *   *    *    *      *      * *          
       1719 GCTCTACTACAACTTCAGGGAGATAGGA-TTATCGGCTTCAATCT
          1 ACTCCACTGCAACCTCAGAGAGATAAGATTTACCAGCTTCAATCT

                              *             * *          
       1763 ACTCCACTGCAACCTCAGGGAGATAAGATTTATCGGCTTCAATCT
          1 ACTCCACTGCAACCTCAGAGAGATAAGATTTACCAGCTTCAATCT

            *                              *   *    *    
       1808 GCTCCACTGCAACCTCAGAGAGATAAGATTTGCCATCTTCGATCT
          1 ACTCCACTGCAACCTCAGAGAGATAAGATTTACCAGCTTCAATCT

             *        
       1853 ATTCCACTGC
          1 ACTCCACTGC

       1863 TGACCAGGGA


Statistics
Matches: 119,  Mismatches: 23, Indels: 3
        0.82            0.16        0.02

Matches are distributed among these distances:
  43    3  0.03
  44   54  0.45
  45   62  0.52

ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30


Consensus pattern (45 bp):   
ACTCCACTGCAACCTCAGAGAGATAAGATTTACCAGCTTCAATCT
Done.