Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1157

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: 6446
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35


Found at i:493 original size:16 final size:16

Alignment explanation


    Indices: 472--510  Score: 51
    Period size: 16  Copynumber: 2.4  Consensus size: 16

        462 ACACGCACGC

                  *         
        472 ATATATTATAATATAA
          1 ATATATAATAATATAA

                        *  *
        488 ATATATAATAATCTAT
          1 ATATATAATAATATAA

                   
        504 ATATATA
          1 ATATATA

        511 TTAAAATAAT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  16   20  1.00

ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44


Consensus pattern (16 bp):   
ATATATAATAATATAA

Found at i:3134 original size:16 final size:16

Alignment explanation


    Indices: 3079--3134  Score: 78
    Period size: 16  Copynumber: 3.5  Consensus size: 16

       3069 GTTGGATAAG

                             
       3079 TTAA-TTAAGATTTAAA
          1 TTAATTTAA-ATTTAAA

                  *         
       3095 TTAATTAAAATTTAAA
          1 TTAATTTAAATTTAAA

               *            
       3111 TTATTTTAAATTTAAA
          1 TTAATTTAAATTTAAA

                    
       3127 TTAATTTA
          1 TTAATTTA

       3135 TGTTCGATTT


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  16   32  0.91
  17    3  0.09

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


Consensus pattern (16 bp):   
TTAATTTAAATTTAAA

Found at i:3668 original size:3 final size:3

Alignment explanation


    Indices: 3655--3693  Score: 69
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       3645 ATTTGGGGTT

                                                               
       3655 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

       3694 TAGTTTAGGT


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   3   32  0.91
   4    3  0.09

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTA

Found at i:5454 original size:16 final size:18

Alignment explanation


    Indices: 5420--5456  Score: 51
    Period size: 16  Copynumber: 2.2  Consensus size: 18

       5410 ATTTTAAGGC

                              
       5420 TTTCTATAGACATAAAAA
          1 TTTCTATAGACATAAAAA

                          *   
       5438 TTTCT-TAG-CATATAAA
          1 TTTCTATAGACATAAAAA

               
       5454 TTT
          1 TTT

       5457 AACATCAGTG


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  16   10  0.56
  17    3  0.17
  18    5  0.28

ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43


Consensus pattern (18 bp):   
TTTCTATAGACATAAAAA
Done.