Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2836

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: 27924
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:15664 original size:41 final size:41

Alignment explanation


    Indices: 15607--15691  Score: 170
    Period size: 41  Copynumber: 2.1  Consensus size: 41

      15597 AATGCTCCAG

                                                     
      15607 CTACATTCATGAATCTAATAAATCAAGTATTTCAGTCATAT
          1 CTACATTCATGAATCTAATAAATCAAGTATTTCAGTCATAT

                                                     
      15648 CTACATTCATGAATCTAATAAATCAAGTATTTCAGTCATAT
          1 CTACATTCATGAATCTAATAAATCAAGTATTTCAGTCATAT

               
      15689 CTA
          1 CTA

      15692 GATCAGTTTG


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  41   44  1.00

ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36


Consensus pattern (41 bp):   
CTACATTCATGAATCTAATAAATCAAGTATTTCAGTCATAT

Found at i:20990 original size:3 final size:3

Alignment explanation


    Indices: 20906--20981  Score: 107
    Period size: 3  Copynumber: 25.3  Consensus size: 3

      20896 GTACTTTTGC

                                         *                                 
      20906 TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                    *    *    *           *      
      20954 TAT TAT CAT TTT TAC TAT TAT TAG TAT T
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T

      20982 GGTATTATTG


Statistics
Matches: 63,  Mismatches: 10, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   3   63  1.00

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


Consensus pattern (3 bp):   
TAT

Found at i:21161 original size:29 final size:34

Alignment explanation


    Indices: 21095--21162  Score: 78
    Period size: 29  Copynumber: 2.2  Consensus size: 34

      21085 GTACATATTT

                                              
      21095 TACATA-TAATTTGTTTAATATATATACGTATAC
          1 TACATATTAATTTGTTTAATATATATACGTATAC

                    *                         
      21128 T-CATATTTATTT-TTT-ATATATAT-C-TATA-
          1 TACATATTAATTTGTTTAATATATATACGTATAC

                   
      21156 TACATAT
          1 TACATAT

      21163 ACATATTTTT


Statistics
Matches: 32,  Mismatches: 1, Indels: 8
        0.78            0.02        0.20

Matches are distributed among these distances:
  28    1  0.03
  29    9  0.28
  30    1  0.03
  31    8  0.25
  32    7  0.22
  33    6  0.19

ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51


Consensus pattern (34 bp):   
TACATATTAATTTGTTTAATATATATACGTATAC

Found at i:21181 original size:18 final size:18

Alignment explanation


    Indices: 21166--21217  Score: 50
    Period size: 20  Copynumber: 2.7  Consensus size: 18

      21156 TACATATACA

                 *            
      21166 TATTTTTATTTTTATAAG
          1 TATTTATATTTTTATAAG

                           *  * 
      21184 TATTTATATTTATATGTATG
          1 TATTTATATTT-T-TATAAG

                          
      21204 TATTTATATATTTT
          1 TATTTATAT-TTTT

      21218 TGTATATCTT


Statistics
Matches: 28,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  18   10  0.36
  19    2  0.07
  20   14  0.50
  21    2  0.07

ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65


Consensus pattern (18 bp):   
TATTTATATTTTTATAAG
Done.