Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1527

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: 10885
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.30


Found at i:668 original size:39 final size:38

Alignment explanation


    Indices: 609--939  Score: 178
    Period size: 39  Copynumber: 8.5  Consensus size: 38

        599 AGCAGCGTTT

                    *    *                         
        609 TTTAAAAAGCGCCGCTAAAGACCTGACCTTTAGCGGCGC
          1 TTTAAAAAACGCCACTAAAGACCTGA-CTTTAGCGGCGC

                           *       *  *        * * 
        648 TTTAAAAAACGCCACCAAAGACCAG-GTTTAGCGTACTC
          1 TTTAAAAAACGCCACTAAAGACCTGACTTTAGCG-GCGC

               *          *       * *               *
        686 TTAAAAAAAACGCCGC-AAAGATCAGACTTT-GC-GCGTTT
          1 TT-TAAAAAACGCCACTAAAGACCTGACTTTAGCGGCG--C

                *         *          *              
        724 TTTATAAAA-GCGCGCTAAAGACCAGGACTTTAGCGGCGC
          1 TTTAAAAAACGC-CACTAAAGACC-TGACTTTAGCGGCGC

                               *             *       
        763 TTTATAAAAAACGCCACTATAGACCTGTACTTTTGCGGCGC
          1 -TT-TAAAAAACGCCACTAAAGACCTG-ACTTTAGCGGCGC

                            *  *       *             
        804 TTTTATAAAAACGCC-GTATAGACCT-TCTTTTAGCGGCGC
          1 -TTTA-AAAAACGCCACTAAAGACCTGAC-TTTAGCGGCGC

                          *   *                     
        843 TTTTAAAAAACG-CGCTATAGA-C-GAACTTTAGCGGCGC
          1 -TTTAAAAAACGCCACTAAAGACCTG-ACTTTAGCGGCGC

               *     *       *                       *
        880 TTTTAAAAATGCCACTATAGACCTGTACTTTTAGCGGCGTTT
          1 TTTAAAAAACGCCACTAAAGACCTG-AC-TTTAGCGGCG--C

                         *    
        922 TTTAAAAAACGCCGCTAA
          1 TTTAAAAAACGCCACTAA

        940 TTTGCCCAGT


Statistics
Matches: 229,  Mismatches: 38, Indels: 47
        0.73            0.12        0.15

Matches are distributed among these distances:
  36   12  0.05
  37   36  0.16
  38   38  0.17
  39   59  0.26
  40   26  0.11
  41   42  0.18
  42   16  0.07

ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26


Consensus pattern (38 bp):   
TTTAAAAAACGCCACTAAAGACCTGACTTTAGCGGCGC

Found at i:744 original size:115 final size:123

Alignment explanation


    Indices: 565--779  Score: 315
    Period size: 115  Copynumber: 1.8  Consensus size: 123

        555 CGCGGCGTTT

                        *                                                    
        565 TTAAGAAAAAACTCCGCTAAAGACCACGATCTTTAGCAGCGTTTTTTAAAAAGCGCCGCTAAAGA
          1 TTAAGAAAAAACGCCGCTAAAGACCACGATCTTTAGCAGCGTTTTTTAAAAAGCGCCGCTAAAGA

               *                                                       
        630 CC-TGACCTTTAGCGGCGC-TT-TAAAAAACGCCACCAAAGACCAGGTTTAGCGTACTC
         66 CCAGGA-CTTTAGCGGCGCTTTATAAAAAACGCCACCAAAGACCAGGTTTAGCGTACTC

                                   *                                         
        686 TTAA-AAAAAACGCCGC-AAAGATCA-GA-CTTT-GC-GCGTTTTTTATAAAAGCG-CGCTAAAG
          1 TTAAGAAAAAACGCCGCTAAAGACCACGATCTTTAGCAGCGTTTTTTA-AAAAGCGCCGCTAAAG

                                                
        744 ACCAGGACTTTAGCGGCGCTTTATAAAAAACGCCAC
         65 ACCAGGACTTTAGCGGCGCTTTATAAAAAACGCCAC

        780 TATAGACCTG


Statistics
Matches: 87,  Mismatches: 3, Indels: 12
        0.85            0.03        0.12

Matches are distributed among these distances:
 115   33  0.38
 116   13  0.15
 117   17  0.20
 118    2  0.02
 119    7  0.08
 120   11  0.13
 121    4  0.05

ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22


Consensus pattern (123 bp):   
TTAAGAAAAAACGCCGCTAAAGACCACGATCTTTAGCAGCGTTTTTTAAAAAGCGCCGCTAAAGA
CCAGGACTTTAGCGGCGCTTTATAAAAAACGCCACCAAAGACCAGGTTTAGCGTACTC

Found at i:1264 original size:20 final size:19

Alignment explanation


    Indices: 1229--1276  Score: 71
    Period size: 20  Copynumber: 2.5  Consensus size: 19

       1219 ATTTCCTGTT

                               
       1229 CTGCT-CGCCTCCTCGCTG
          1 CTGCTCCGCCTCCTCGCTG

                                
       1247 CTGCTCCGCCTCCCTCGCTG
          1 CTGCTCCGCCT-CCTCGCTG

                      
       1267 CTGCCTCCGC
          1 CTG-CTCCGC

       1277 TCTAAGTTGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  18    5  0.19
  19    5  0.19
  20   11  0.41
  21    6  0.22

ACGTcount: A:0.00, C:0.54, G:0.21, T:0.25


Consensus pattern (19 bp):   
CTGCTCCGCCTCCTCGCTG

Found at i:1862 original size:18 final size:18

Alignment explanation


    Indices: 1830--1867  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       1820 TACAATATAG

                               
       1830 TAGTAAAAATATTATTTAA
          1 TAGTAAAAATATTA-TTAA

                      *       
       1849 TAGTAAAAA-GTTATTAA
          1 TAGTAAAAATATTATTAA

              
       1866 TA
          1 TA

       1868 CTTGATAGAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  17    6  0.33
  18    3  0.17
  19    9  0.50

ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39


Consensus pattern (18 bp):   
TAGTAAAAATATTATTAA
Done.