Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_3691

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: 17567
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:873 original size:83 final size:85

Alignment explanation


    Indices: 731--997  Score: 360
    Period size: 88  Copynumber: 3.1  Consensus size: 85

        721 TGTAACCTTT

                                                               *          *  
        731 AACCAGCTCCAATGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTTGCTGTTAATGCAG
          1 AACCAGCTCC-ATGCAACCGATGGAGGCAAGGCTTTG-TTTCGATCTGCTTCGCTGTTAATGTAG

                         **      *
        796 GAAGGCAAGATCTGCT-TCTTT
         64 GAAGGCAAGATCTTTTGTCTTC

                                                                             
        817 AACCAGCTCCACTGCAA-CGATGGA-GCAAGGCTTTGTTTCGATCTGCTTCGCTGTTAATGTAGG
          1 AACCAGCTCCA-TGCAACCGATGGAGGCAAGGCTTTGTTTCGATCTGCTTCGCTGTTAATGTAGG

                                 
        880 AAGGCAAGATCTTTTGTCTTC
         65 AAGGCAAGATCTTTTGTCTTC

                     *   *       **         *                         *      
        901 AACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTA
          1 AACCAGCTCCAT-GCAACCGATGGAGGCAAGGCTT-TGT-TTCGATCTGCTTCGCTGTTAATGTA

                                   
        966 GGAAGGCAAGATCTTTTGTCTTC
         63 GGAAGGCAAGATCTTTTGTCTTC

                     
        989 AACCAGCTC
          1 AACCAGCTC

        998 TATCAAAGTT


Statistics
Matches: 163,  Mismatches: 11, Indels: 12
        0.88            0.06        0.06

Matches are distributed among these distances:
  83   40  0.25
  84   28  0.17
  85   13  0.08
  86   23  0.14
  87    3  0.02
  88   56  0.34

ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30


Consensus pattern (85 bp):   
AACCAGCTCCATGCAACCGATGGAGGCAAGGCTTTGTTTCGATCTGCTTCGCTGTTAATGTAGGA
AGGCAAGATCTTTTGTCTTC

Found at i:931 original size:44 final size:44

Alignment explanation


    Indices: 879--1002  Score: 108
    Period size: 44  Copynumber: 2.8  Consensus size: 44

        869 GTTAATGTAG

                                                         
        879 GAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAA
          1 GAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAA-CGAAA

                     *    *       * * *     ** **   * * *
        924 G-AGGCAAGGT-TTGTGTCTTCGATCTGCTTCGCTGTCAATGTAG
          1 GAAGGCAAGATCTTTTGTCTTCAACCAGC-TCTATCACAACGAAA

                                                
        967 GAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCA
          1 GAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCA

       1003 AAGTTTAATC


Statistics
Matches: 55,  Mismatches: 21, Indels: 7
        0.66            0.25        0.08

Matches are distributed among these distances:
  43   16  0.29
  44   25  0.45
  45   14  0.25

ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30


Consensus pattern (44 bp):   
GAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACGAAA

Found at i:5499 original size:19 final size:19

Alignment explanation


    Indices: 5459--5500  Score: 50
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       5449 GTGAAAATCT

                 *      *      
       5459 ATGCATATGATGCAATGCA
          1 ATGCAAATGATGAAATGCA

                                
       5478 ATGCAAATGCATGAAATG-A
          1 ATGCAAATG-ATGAAATGCA

                
       5497 ATGC
          1 ATGC

       5501 CTAAAAGACG


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  19   13  0.65
  20    7  0.35

ACGTcount: A:0.40, C:0.14, G:0.21, T:0.24


Consensus pattern (19 bp):   
ATGCAAATGATGAAATGCA

Found at i:17277 original size:2 final size:2

Alignment explanation


    Indices: 17270--17294  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      17260 TAACAAAGAG

                                                 
      17270 CT CT CT CT CT CT CT CT CT CT CT CT C
          1 CT CT CT CT CT CT CT CT CT CT CT CT C

      17295 CCTTCCCAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48


Consensus pattern (2 bp):   
CT

Done.