Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2344

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: 384062
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 3 of 3

Found at i:375147 original size:1 final size:1

Alignment explanation


    Indices: 375143--375256  Score: 66
    Period size: 1  Copynumber: 114.0  Consensus size: 1

     375133 CCGGACCCCC

                 *     *   *       *  *     *         *    *       *      * *
     375143 TTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTCTTTTGTTTTTTTGTTTTTTATC
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

            * **         *      **        *                  
     375208 ATCATTTTTTTTTGTTTTTTCATTTTTTTTGTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

     375257 GGAGGACGCC


Statistics
Matches: 80,  Mismatches: 33, Indels: 0
        0.71            0.29        0.00

Matches are distributed among these distances:
   1   80  1.00

ACGTcount: A:0.04, C:0.04, G:0.08, T:0.84


Consensus pattern (1 bp):   
T

Found at i:375171 original size:21 final size:21

Alignment explanation


    Indices: 375146--375257  Score: 99
    Period size: 21  Copynumber: 5.4  Consensus size: 21

     375136 GACCCCCTTT

                                 
     375146 TTGTTTTTGTTTGTTTTTTTA
          1 TTGTTTTTGTTTGTTTTTTTA

                                 *
     375167 TTGTTTTTGTTT-TTTTTTCTT
          1 TTGTTTTTGTTTGTTTTTT-TA

                                   
     375188 TTG-TTTT-TTTGTTTTTTATCA
          1 TTGTTTTTGTTTGTTTTTT-T-A

             **     *          * 
     375209 TCATTTTTTTTTGTTTTTTCA
          1 TTGTTTTTGTTTGTTTTTTTA

              *                  
     375230 TTTTTTTTGTTT-TTTTTTT-
          1 TTGTTTTTGTTTGTTTTTTTA

              *      
     375249 TTTTTTTTG
          1 TTGTTTTTG

     375258 GAGGACGCCG


Statistics
Matches: 76,  Mismatches: 10, Indels: 12
        0.78            0.10        0.12

Matches are distributed among these distances:
  19   12  0.16
  20   23  0.30
  21   27  0.36
  22    4  0.05
  23   10  0.13

ACGTcount: A:0.04, C:0.04, G:0.09, T:0.83


Consensus pattern (21 bp):   
TTGTTTTTGTTTGTTTTTTTA

Done.