Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_4468

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: 14712
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.34


Found at i:1443 original size:13 final size:13

Alignment explanation


    Indices: 1425--1449  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       1415 TATTTTAATA

                         
       1425 TTATTTTGTGTGT
          1 TTATTTTGTGTGT

                        
       1438 TTATTTTGTGTG
          1 TTATTTTGTGTG

       1450 CATTTGATTG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68


Consensus pattern (13 bp):   
TTATTTTGTGTGT

Found at i:2871 original size:41 final size:40

Alignment explanation


    Indices: 2747--2897  Score: 218
    Period size: 41  Copynumber: 3.8  Consensus size: 40

       2737 GAATGTAATA

                  *                                  
       2747 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACA-TT
          1 CAGACTATAAGTCTAGCAGGC-TAATGCCGGTGATACATTT

                  *                                 
       2787 CAGACTTTAAGTCTAGCAGGCTAATGCCGGTG--ACATTT
          1 CAGACTATAAGTCTAGCAGGCTAATGCCGGTGATACATTT

                     *                               
       2825 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
          1 CAGACTATAAGTCTAGCAGGC-TAATGCCGGTGATACATTT

                     *                      
       2866 CAGACTATATGTCTAGCAGGCTAAGTGCCGGT
          1 CAGACTATAAGTCTAGCAGGCTAA-TGCCGGT

       2898 ATGAATCAGG


Statistics
Matches: 104,  Mismatches: 2, Indels: 9
        0.90            0.02        0.08

Matches are distributed among these distances:
  37    3  0.03
  38   21  0.20
  39   22  0.21
  40   24  0.23
  41   34  0.33

ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29


Consensus pattern (40 bp):   
CAGACTATAAGTCTAGCAGGCTAATGCCGGTGATACATTT

Found at i:10263 original size:32 final size:34

Alignment explanation


    Indices: 10222--10358  Score: 131
    Period size: 40  Copynumber: 3.9  Consensus size: 34

      10212 GAATGTAATA

                                              
      10222 CAGACTTAGTCTAGCAGGCTAATGCGGTGATATT
          1 CAGACTTAGTCTAGCAGGCTAATGCGGTGATATT

                                           *   
      10256 C-GA-TTAGTCTAG-A-G-TAATGCCGGTGACATT
          1 CAGACTTAGTCTAGCAGGCTAATG-CGGTGATATT

                                                    
      10286 CAGACTATATGTCTAGCAGGCTTAATGCGGTGATACATTT
          1 CAGACT-TA-GTCTAGCAGGC-TAATGCGGTGAT--A-TT

                                             
      10326 CAGACTATATGTCTAGCAGGCTAAGTGCCGGTG
          1 CAGACT-TA-GTCTAGCAGGCTAA-TG-CGGTG

      10359 TACTGAATCA


Statistics
Matches: 87,  Mismatches: 2, Indels: 21
        0.79            0.02        0.19

Matches are distributed among these distances:
  29    5  0.06
  30   11  0.13
  31    3  0.03
  32   10  0.11
  33    4  0.05
  34    7  0.08
  35    1  0.01
  36    1  0.01
  37    6  0.07
  38    5  0.06
  39    4  0.05
  40   25  0.29
  41    5  0.06

ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29


Consensus pattern (34 bp):   
CAGACTTAGTCTAGCAGGCTAATGCGGTGATATT

Found at i:12504 original size:21 final size:22

Alignment explanation


    Indices: 12465--12510  Score: 60
    Period size: 21  Copynumber: 2.1  Consensus size: 22

      12455 TCTGGATGTG

                 *                
      12465 ATTTTTTAATAATCATTAAA-A
          1 ATTTTATAATAATCATTAAATA

                                   
      12486 ATTTTATAATAAT-ATTTAAATA
          1 ATTTTATAATAATCA-TTAAATA

               
      12508 ATT
          1 ATT

      12511 ATGCAGCCAC


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  20    1  0.05
  21   17  0.77
  22    4  0.18

ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50


Consensus pattern (22 bp):   
ATTTTATAATAATCATTAAATA
Done.