Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1285

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: 3391
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37


Found at i:105 original size:15 final size:16

Alignment explanation


    Indices: 80--121  Score: 61
    Period size: 15  Copynumber: 2.8  Consensus size: 16

         70 TGTTGTTTTG

                  *         
         80 TATTAAATTTATATAA
          1 TATTAATTTTATATAA

                            
         96 -ATTAATTTTA-ATAA
          1 TATTAATTTTATATAA

                        
        110 TATTAATTTTAT
          1 TATTAATTTTAT

        122 TATATTATGT


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  14    4  0.17
  15   19  0.83

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (16 bp):   
TATTAATTTTATATAA

Found at i:126 original size:14 final size:14

Alignment explanation


    Indices: 80--128  Score: 53
    Period size: 15  Copynumber: 3.4  Consensus size: 14

         70 TGTTGTTTTG

                  *        
         80 TATTAAATTTATATA
          1 TATTAATTTTAT-TA

            *            * 
         95 AATTAATTTTAATAA
          1 TATTAATTTT-ATTA

                          
        110 TATTAATTTTATTA
          1 TATTAATTTTATTA

                 
        124 TATTA
          1 TATTA

        129 TGTGATAAAT


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

Matches are distributed among these distances:
  14    8  0.29
  15   18  0.64
  16    2  0.07

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (14 bp):   
TATTAATTTTATTA

Found at i:869 original size:2 final size:2

Alignment explanation


    Indices: 833--857  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        823 AGTGTGTGTC

                                                 
        833 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

        858 GTATGCATAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA
Done.