Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1944

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: 7209
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33


Found at i:300 original size:1 final size:1

Alignment explanation


    Indices: 290--394  Score: 120
    Period size: 1  Copynumber: 105.0  Consensus size: 1

        280 TGGCAATTGG

                 *                 *         **     *               *    *   
        290 AAAAAGAAAAAAAAAAAAAAAAACAAAAAAAAAGGAAAAAGAAAAAAAAAAAAAAACAAAACAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

                 **     *                           
        355 AAAAAGGAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

        395 GTGAAGATTT


Statistics
Matches: 88,  Mismatches: 16, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   1   88  1.00

ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00


Consensus pattern (1 bp):   
A

Found at i:337 original size:37 final size:37

Alignment explanation


    Indices: 288--394  Score: 177
    Period size: 37  Copynumber: 3.0  Consensus size: 37

        278 CATGGCAATT

                                                 
        288 GGAAAAAG--AAAAAAAAAAAAAAAAACAAAAAAAAA
          1 GGAAAAAGAAAAAAAAAAAAAAAAAAACAAAAAAAAA

                                                  
        323 GGAAAAAGAAAAAAAAAAAAAAACAAAAC-AAAAAAAA
          1 GGAAAAAGAAAAAAAAAAAAAAA-AAAACAAAAAAAAA

                                                
        360 GGAAAAAGAAAAAAAAAAAAAAAAAAA-AAAAAAAA
          1 GGAAAAAGAAAAAAAAAAAAAAAAAAACAAAAAAAA

        395 GTGAAGATTT


Statistics
Matches: 68,  Mismatches: 0, Indels: 7
        0.91            0.00        0.09

Matches are distributed among these distances:
  35    8  0.12
  36   11  0.16
  37   44  0.65
  38    5  0.07

ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00


Consensus pattern (37 bp):   
GGAAAAAGAAAAAAAAAAAAAAAAAAACAAAAAAAAA

Done.