Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00374.F1

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: 2150
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29


Found at i:369 original size:21 final size:21

Alignment explanation


    Indices: 345--386  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        335 AAGGACTTGG

                                 
        345 GGAGAAAAAGGAAGAAGAAGA
          1 GGAGAAAAAGGAAGAAGAAGA

                *  *    *        
        366 GGAGCAAGAGGAGGAAGAAGA
          1 GGAGAAAAAGGAAGAAGAAGA

        387 TGATGATGAT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.55, C:0.02, G:0.43, T:0.00


Consensus pattern (21 bp):   
GGAGAAAAAGGAAGAAGAAGA

Found at i:409 original size:3 final size:3

Alignment explanation


    Indices: 403--450  Score: 62
    Period size: 3  Copynumber: 16.0  Consensus size: 3

        393 TGATGAGGAT

                                      *                               * 
        403 GAA GAA GAA GAA GAA GAA GAG GAA GAA GAA GAA GGAA -AA GAA GGA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA

               
        448 GAA
          1 GAA

        451 AATGGGGAAA


Statistics
Matches: 39,  Mismatches: 4, Indels: 4
        0.83            0.09        0.09

Matches are distributed among these distances:
   2    2  0.05
   3   34  0.87
   4    3  0.08

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (3 bp):   
GAA

Found at i:1798 original size:43 final size:43

Alignment explanation


    Indices: 1706--1806  Score: 134
    Period size: 43  Copynumber: 2.3  Consensus size: 43

       1696 GGTAGCCCTC

                                                       
       1706 TCTTATAACTACCATTAGTGTGCCTTAATTGGACATATAGCGT
          1 TCTTATAACTACCATTAGTGTGCCTTAATTGGACATATAGCGT

            **      *                            *       
       1749 GGTTATAATTACCATTAGTGTTG-CTTAATTGGACATTTAAG-GT
          1 TCTTATAACTACCATTAGTG-TGCCTTAATTGGACATAT-AGCGT

                           
       1792 TCTTATAACTACCAT
          1 TCTTATAACTACCAT

       1807 CAAACTTTCC


Statistics
Matches: 49,  Mismatches: 7, Indels: 4
        0.82            0.12        0.07

Matches are distributed among these distances:
  43   45  0.92
  44    4  0.08

ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40


Consensus pattern (43 bp):   
TCTTATAACTACCATTAGTGTGCCTTAATTGGACATATAGCGT
Done.