Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1864

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: 37599
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:8181 original size:3 final size:3

Alignment explanation


    Indices: 8173--8205  Score: 66
    Period size: 3  Copynumber: 11.0  Consensus size: 3

       8163 GTCATAGATT

                                                       
       8173 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

       8206 AACAATGAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
TAA

Found at i:8318 original size:17 final size:17

Alignment explanation


    Indices: 8280--8318  Score: 60
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       8270 ATTCTTATAC

                      *  *   
       8280 AAAAAGGAAAGGATAAA
          1 AAAAAGGAAAAGAAAAA

                             
       8297 AAAAAGGAAAAGAAAAA
          1 AAAAAGGAAAAGAAAAA

                 
       8314 AAAAA
          1 AAAAA

       8319 CTAACCCAAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  17   20  1.00

ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03


Consensus pattern (17 bp):   
AAAAAGGAAAAGAAAAA

Found at i:9665 original size:27 final size:26

Alignment explanation


    Indices: 9632--9709  Score: 79
    Period size: 27  Copynumber: 2.9  Consensus size: 26

       9622 TAATTAGACC

                                        
       9632 TAAATTTTAAAATCTAAAAATAAATAAA
          1 TAAATTTTAAAA--TAAAAATAAATAAA

                    *           *     
       9660 T-AATTTTTAAATAAAAATAGATAAA
          1 TAAATTTTAAAATAAAAATAAATAAA

                             *        
       9685 TAAAATTTTAAATATAAGAA-AAATA
          1 T-AAATTTTAAA-ATAAAAATAAATA

       9710 TAAACTTAAA


Statistics
Matches: 42,  Mismatches: 5, Indels: 7
        0.78            0.09        0.13

Matches are distributed among these distances:
  25   14  0.33
  27   21  0.50
  28    7  0.17

ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33


Consensus pattern (26 bp):   
TAAATTTTAAAATAAAAATAAATAAA

Found at i:9683 original size:25 final size:26

Alignment explanation


    Indices: 9646--9698  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 26

       9636 TTTTAAAATC

                              *       
       9646 TAAAAATAAATAAAT-AATTTTTAAA
          1 TAAAAATAAATAAATAAAATTTTAAA

                    *                 
       9671 TAAAAATAGATAAATAAAATTTTAAA
          1 TAAAAATAAATAAATAAAATTTTAAA

              
       9697 TA
          1 TA

       9699 TAAGAAAAAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  25   14  0.56
  26   11  0.44

ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34


Consensus pattern (26 bp):   
TAAAAATAAATAAATAAAATTTTAAA

Found at i:9693 original size:26 final size:25

Alignment explanation


    Indices: 9632--9698  Score: 80
    Period size: 25  Copynumber: 2.5  Consensus size: 25

       9622 TAATTAGACC

                                        
       9632 TAAATTTTAAAATCTAAAAATAAATAAA
          1 TAAATTTT-AAA--TAAAAATAAATAAA

               *               *     
       9660 TAATTTTTAAATAAAAATAGATAAA
          1 TAAATTTTAAATAAAAATAAATAAA

                          
       9685 TAAAATTTTAAATA
          1 T-AAATTTTAAATA

       9699 TAAGAAAAAT


Statistics
Matches: 35,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  25   14  0.40
  26   11  0.31
  27    3  0.09
  28    7  0.20

ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36


Consensus pattern (25 bp):   
TAAATTTTAAATAAAAATAAATAAA

Found at i:33821 original size:17 final size:17

Alignment explanation


    Indices: 33801--33858  Score: 93
    Period size: 17  Copynumber: 3.5  Consensus size: 17

      33791 TTGAGATCAA

                             
      33801 AAATTTTGGCAGATTCT
          1 AAATTTTGGCAGATTCT

                            *
      33818 AAATTTTGG-AGA-TCA
          1 AAATTTTGGCAGATTCT

                             
      33833 AAATTTTGGCAGATTCT
          1 AAATTTTGGCAGATTCT

                     
      33850 AAATTTTGG
          1 AAATTTTGG

      33859 ACTCATTGGA


Statistics
Matches: 37,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
  15   11  0.30
  16    6  0.16
  17   20  0.54

ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40


Consensus pattern (17 bp):   
AAATTTTGGCAGATTCT

Found at i:33841 original size:32 final size:33

Alignment explanation


    Indices: 33793--33859  Score: 127
    Period size: 32  Copynumber: 2.1  Consensus size: 33

      33783 GAATATAGTT

                                             
      33793 GAGATCAAAAATTTTGGCAGATTCTAAATTTTG
          1 GAGATCAAAAATTTTGGCAGATTCTAAATTTTG

                                             
      33826 GAGATC-AAAATTTTGGCAGATTCTAAATTTTG
          1 GAGATCAAAAATTTTGGCAGATTCTAAATTTTG

              
      33858 GA
          1 GA

      33860 CTCATTGGAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  32   28  0.82
  33    6  0.18

ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36


Consensus pattern (33 bp):   
GAGATCAAAAATTTTGGCAGATTCTAAATTTTG

Done.