Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2582

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: 26567
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29


Found at i:17966 original size:3 final size:3

Alignment explanation


    Indices: 17885--17957  Score: 69
    Period size: 3  Copynumber: 24.3  Consensus size: 3

      17875 GTACTTTTGC

                                     *                                       
      17885 TAT TAT TA- TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT T-T ATATT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TA-T

                *    *    *           *      
      17933 TAT CAT TTT TAC TAT TAT TAG TAT T
          1 TAT TAT TAT TAT TAT TAT TAT TAT T

      17958 GGTATTATTG


Statistics
Matches: 56,  Mismatches: 10, Indels: 8
        0.76            0.14        0.11

Matches are distributed among these distances:
   2    3  0.05
   3   50  0.89
   4    2  0.04
   5    1  0.02

ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64


Consensus pattern (3 bp):   
TAT

Found at i:17993 original size:21 final size:23

Alignment explanation


    Indices: 17968--18012  Score: 67
    Period size: 22  Copynumber: 2.0  Consensus size: 23

      17958 GGTATTATTG

                     *             
      17968 ACTTA-TTTGTTTTATAT-TCTT
          1 ACTTATTTTCTTTTATATGTCTT

                                   
      17989 ACTTATTTTCTTTTATATGTCTT
          1 ACTTATTTTCTTTTATATGTCTT

             
      18012 A
          1 A

      18013 ATATCATCAT


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

Matches are distributed among these distances:
  21    5  0.24
  22   11  0.52
  23    5  0.24

ACGTcount: A:0.20, C:0.11, G:0.04, T:0.64


Consensus pattern (23 bp):   
ACTTATTTTCTTTTATATGTCTT

Found at i:23835 original size:27 final size:27

Alignment explanation


    Indices: 23805--23880  Score: 104
    Period size: 27  Copynumber: 2.9  Consensus size: 27

      23795 CCATTTATAA

                                        
      23805 ATAT-TATATATTTATTTTTAAACTGTT
          1 ATATATATATATTTATTTTTAAA-TGTT

                *                      
      23832 ATATGTAT-TATTTATTTTTAAAT-TT
          1 ATATATATATATTTATTTTTAAATGTT

                            *       
      23857 ATATATATATATTTATCTTTAAAT
          1 ATATATATATATTTATTTTTAAAT

      23881 TGTTTTGTAT


Statistics
Matches: 45,  Mismatches: 2, Indels: 5
        0.87            0.04        0.10

Matches are distributed among these distances:
  25    9  0.20
  26   15  0.33
  27   18  0.40
  28    3  0.07

ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59


Consensus pattern (27 bp):   
ATATATATATATTTATTTTTAAATGTT

Found at i:23878 original size:53 final size:52

Alignment explanation


    Indices: 23805--23912  Score: 137
    Period size: 53  Copynumber: 2.0  Consensus size: 52

      23795 CCATTTATAA

                           *               *                     
      23805 ATATTATATATTTATTTTTAAACTGTTATATGTATTATT-TATTTTTAAATTT
          1 ATATTATATATTTATCTTTAAACTGTTATATATATTATTATA-TTTTAAATTT

                                   *    * *                       
      23857 ATATATATATATTTATCTTTAAATTGTTTTGTATATTATTATCATTTTAAATTT
          1 ATAT-TATATATTTATCTTTAAACTGTTATATATATTATTAT-ATTTTAAATTT

              
      23911 AT
          1 AT

      23913 TTCTACATAA


Statistics
Matches: 48,  Mismatches: 5, Indels: 4
        0.84            0.09        0.07

Matches are distributed among these distances:
  52    4  0.08
  53   30  0.62
  54   13  0.27
  55    1  0.02

ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60


Consensus pattern (52 bp):   
ATATTATATATTTATCTTTAAACTGTTATATATATTATTATATTTTAAATTT

Found at i:23891 original size:26 final size:26

Alignment explanation


    Indices: 23809--23909  Score: 82
    Period size: 26  Copynumber: 3.8  Consensus size: 26

      23799 TTATAAATAT

                       *      *         
      23809 TATATATTTATTTTTAAACTGTTATATG
          1 TATATATTTATCTTTAAATTGTT-T-TG

                       *            * *
      23837 TAT-TATTTATTTTTAAATT-TATATA
          1 TATATATTTATCTTTAAATTGT-TTTG

                                      
      23862 TATATATTTATCTTTAAATTGTTTTG
          1 TATATATTTATCTTTAAATTGTTTTG

                                   
      23888 TATAT-TATTATCATTTTAAATT
          1 TATATAT-TTATC--TTTAAATT

      23910 TATTTCTACA


Statistics
Matches: 61,  Mismatches: 6, Indels: 12
        0.77            0.08        0.15

Matches are distributed among these distances:
  25    5  0.08
  26   28  0.46
  27   17  0.28
  28   11  0.18

ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60


Consensus pattern (26 bp):   
TATATATTTATCTTTAAATTGTTTTG
Done.