Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1358

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: 1933
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38


Found at i:289 original size:17 final size:19

Alignment explanation


    Indices: 269--311  Score: 63
    Period size: 17  Copynumber: 2.4  Consensus size: 19

        259 CTGTCATCTC

                               
        269 CCCCAAATCCCTAA-A-TT
          1 CCCCAAATCCCTAACAGTT

                *              
        286 CCCCTAATCCCTAACAGTT
          1 CCCCAAATCCCTAACAGTT

                   
        305 CCCCAAA
          1 CCCCAAA

        312 CCCGACGTAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  17   13  0.59
  18    1  0.05
  19    8  0.36

ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21


Consensus pattern (19 bp):   
CCCCAAATCCCTAACAGTT

Found at i:769 original size:17 final size:19

Alignment explanation


    Indices: 749--791  Score: 63
    Period size: 17  Copynumber: 2.4  Consensus size: 19

        739 CTGTCATCTC

                               
        749 CCCCAAATCCCTAA-A-TT
          1 CCCCAAATCCCTAACAGTT

                *              
        766 CCCCTAATCCCTAACAGTT
          1 CCCCAAATCCCTAACAGTT

                   
        785 CCCCAAA
          1 CCCCAAA

        792 CCCGACGTAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  17   13  0.59
  18    1  0.05
  19    8  0.36

ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21


Consensus pattern (19 bp):   
CCCCAAATCCCTAACAGTT

Found at i:1148 original size:6 final size:6

Alignment explanation


    Indices: 1134--1177  Score: 70
    Period size: 6  Copynumber: 7.3  Consensus size: 6

       1124 TCCCGTTGAA

                *                                 *            
       1134 ATATAT ATATGT ATATGT ATATGT ATATGT ATACGT ATATGT AT
          1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT AT

       1178 TAAAACTAAA


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   35  1.00

ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48


Consensus pattern (6 bp):   
ATATGT

Done.