Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_212 ID=scaffold_212-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: 9290
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38


Found at i:93 original size:22 final size:21

Alignment explanation


    Indices: 55--111  Score: 60
    Period size: 22  Copynumber: 2.6  Consensus size: 21

         45 CCCTTTTACC

                                *  
         55 TTTTCTTATTTTCTTTTCTTTTA
          1 TTTT-TTATTTT-TTTTCTTATA

                            *     
         78 TTTTTTATATTTTTTTGTTATA
          1 TTTTTTAT-TTTTTTTCTTATA

              *         
        100 TTATTTATTTTT
          1 TTTTTTATTTTT

        112 ATTTGAATAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  21    4  0.13
  22   19  0.63
  23    7  0.23

ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79


Consensus pattern (21 bp):   
TTTTTTATTTTTTTTCTTATA

Found at i:4781 original size:41 final size:41

Alignment explanation


    Indices: 4724--4878  Score: 220
    Period size: 41  Copynumber: 3.8  Consensus size: 41

       4714 TTGTAAGTTT

                                                     
       4724 AGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATATC
          1 AGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATATC

                                   *    *            
       4765 AGGCTTTATGCCTAGCAGGCTTTGTGCCAGTGAATTATATC
          1 AGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATATC

              *       *            *   *      * *    
       4806 AGACTTTATGTCTAGCAGGCTTTGTGCGGGTGAAATGTATC
          1 AGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATATC

            *      *                        
       4847 GGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
          1 AGGCTTTATGCCTAGCAGGCTTTATGCCGGTG

       4879 TTTTATACAA


Statistics
Matches: 100,  Mismatches: 14, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  41  100  1.00

ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34


Consensus pattern (41 bp):   
AGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATATC

Found at i:6950 original size:20 final size:21

Alignment explanation


    Indices: 6925--6968  Score: 63
    Period size: 22  Copynumber: 2.1  Consensus size: 21

       6915 TAAATATATA

                     *           
       6925 TATACATG-TATATTTATTTT
          1 TATACATGACATATTTATTTT

                                  
       6945 TATACATGCACATATTTATTTT
          1 TATACATG-ACATATTTATTTT

              
       6967 TA
          1 TA

       6969 ACTAATATTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20    8  0.38
  22   13  0.62

ACGTcount: A:0.32, C:0.09, G:0.05, T:0.55


Consensus pattern (21 bp):   
TATACATGACATATTTATTTT

Found at i:8208 original size:24 final size:23

Alignment explanation


    Indices: 8175--8375  Score: 84
    Period size: 24  Copynumber: 8.7  Consensus size: 23

       8165 AACACTGCCC

                 *                 
       8175 ATTTGTTGTATATATGCTGTTAA
          1 ATTTGGTGTATATATGCTGTTAA

                       * *      * * 
       8198 ATTTTGGTGTAAAAATGCTGCTCA
          1 A-TTTGGTGTATATATGCTGTTAA

                   ***          ***
       8222 ATTTGGTACGTATATGCTG-CCC
          1 ATTTGGTGTATATATGCTGTTAA

                 *                 
       8244 ATTTGTTGTATATATGCTGTTAA
          1 ATTTGGTGTATATATGCTGTTAA

                       * *     ** * 
       8267 ATTTTGGTGTAAAAATGCTACTCA
          1 A-TTTGGTGTATATATGCTGTTAA

                  ** *     *    ***
       8291 ATTTGGCATGTATATCCTG-CCC
          1 ATTTGGTGTATATATGCTGTTAA

                 *                 
       8313 ATTTGTTGTATATATGCTGTTAA
          1 ATTTGGTGTATATATGCTGTTAA

                         *    *      
       8336 ATTTTGGTGTA-AAAGTGTTGTTAA
          1 A-TTTGGTGTATATA-TGCTGTTAA

                   * *      
       8360 ATTTGGTATGTATATG
          1 ATTTGGTGTATATATG

       8376 TTGCCCATTT


Statistics
Matches: 123,  Mismatches: 48, Indels: 14
        0.66            0.26        0.08

Matches are distributed among these distances:
  22   31  0.25
  23   38  0.31
  24   54  0.44

ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44


Consensus pattern (23 bp):   
ATTTGGTGTATATATGCTGTTAA

Found at i:8250 original size:69 final size:69

Alignment explanation


    Indices: 8169--8401  Score: 376
    Period size: 69  Copynumber: 3.4  Consensus size: 69

       8159 GGTTTCAACA

                                                                         *   
       8169 CTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTACGTA
          1 CTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATGTA

                
       8234 TATG
         66 TATG

                                                            *          *     
       8238 CTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTACTCAATTTGGCATGTA
          1 CTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATGTA

               *
       8303 TATC
         66 TATG

                                                       *  *  * *             
       8307 CTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGTTGTTAAATTTGGTATGTA
          1 CTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATGTA

                
       8372 TATG
         66 TATG

            *                   *     
       8376 TTGCCCATTTGTTGTATATAAGCTGT
          1 CTGCCCATTTGTTGTATATATGCTGT

       8402 CCAAATTGAT


Statistics
Matches: 151,  Mismatches: 13, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  69  151  1.00

ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44


Consensus pattern (69 bp):   
CTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTATGTA
TATG

Done.