Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3889

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, 379

Length: 632
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31


Found at i:131 original size:17 final size:18

Alignment explanation


    Indices: 99--151  Score: 63
    Period size: 17  Copynumber: 3.0  Consensus size: 18

         89 TCAAATTAGG

                  *  *        
         99 TTCGTGAATTAAAAAAAA
          1 TTCGTGCATAAAAAAAAA

                            **
        117 TTCGTGCA-AAAAAAATT
          1 TTCGTGCATAAAAAAAAA

                              
        134 TTCGTGCATAAAAAAAAA
          1 TTCGTGCATAAAAAAAAA

        152 AGGTTGTATT


Statistics
Matches: 28,  Mismatches: 6, Indels: 2
        0.78            0.17        0.06

Matches are distributed among these distances:
  17   14  0.50
  18   14  0.50

ACGTcount: A:0.53, C:0.09, G:0.11, T:0.26


Consensus pattern (18 bp):   
TTCGTGCATAAAAAAAAA

Found at i:458 original size:12 final size:12

Alignment explanation


    Indices: 443--487  Score: 65
    Period size: 11  Copynumber: 3.8  Consensus size: 12

        433 TAAAAAAAAG

                        
        443 GAAAAAAAATTC
          1 GAAAAAAAATTC

                         
        455 GAAAAAAAAATT-
          1 G-AAAAAAAATTC

            *           
        467 TAAAAAAAATTC
          1 GAAAAAAAATTC

                     
        479 GAAAAAAAA
          1 GAAAAAAAA

        488 ATTTTGTATT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  11   10  0.34
  12    9  0.31
  13   10  0.34

ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16


Consensus pattern (12 bp):   
GAAAAAAAATTC

Found at i:460 original size:13 final size:13

Alignment explanation


    Indices: 444--490  Score: 71
    Period size: 13  Copynumber: 3.8  Consensus size: 13

        434 AAAAAAAAGG

                         
        444 AAAAAAAATTCGA
          1 AAAAAAAATTCGA

                        *
        457 AAAAAAAATT--T
          1 AAAAAAAATTCGA

                         
        468 AAAAAAAATTCGA
          1 AAAAAAAATTCGA

                      
        481 AAAAAAAATT
          1 AAAAAAAATT

        491 TTGTATTCAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  11   10  0.33
  13   20  0.67

ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19


Consensus pattern (13 bp):   
AAAAAAAATTCGA

Found at i:471 original size:24 final size:24

Alignment explanation


    Indices: 444--491  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        434 AAAAAAAAGG

                                    
        444 AAAAAAAATTCGAAAAAAAAATTT
          1 AAAAAAAATTCGAAAAAAAAATTT

                                    
        468 AAAAAAAATTCGAAAAAAAAATTT
          1 AAAAAAAATTCGAAAAAAAAATTT

        492 TGTATTCAAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21


Consensus pattern (24 bp):   
AAAAAAAATTCGAAAAAAAAATTT
Done.