Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g00856.C4

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: 4945
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41


Found at i:502 original size:16 final size:16

Alignment explanation


    Indices: 481--512  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

        471 GCGTGGAAGA

                            
        481 AAGAGAATAGTTTCAG
          1 AAGAGAATAGTTTCAG

                            
        497 AAGAGAATAGTTTCAG
          1 AAGAGAATAGTTTCAG

        513 TTGAATATTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25


Consensus pattern (16 bp):   
AAGAGAATAGTTTCAG

Found at i:1438 original size:39 final size:39

Alignment explanation


    Indices: 1384--1466  Score: 130
    Period size: 39  Copynumber: 2.1  Consensus size: 39

       1374 CCACTGGCCA

                    *                              
       1384 CCACCATCGTCGTTCACCAGTCAGGCAGTCACCACCGGT
          1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT

                                     *        **   
       1423 CCACCATCATCGTTCACCAGTCAGGTAGTCACCATTGGT
          1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT

                 
       1462 CCACC
          1 CCACC

       1467 CGTCACCACC


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  39   40  1.00

ACGTcount: A:0.22, C:0.40, G:0.18, T:0.20


Consensus pattern (39 bp):   
CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT

Found at i:3793 original size:31 final size:31

Alignment explanation


    Indices: 3757--3819  Score: 126
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       3747 TTCCTTATTT

                                           
       3757 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
          1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

                                           
       3788 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
          1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

             
       3819 C
          1 C

       3820 TTCTCGTACT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.06, C:0.33, G:0.03, T:0.57


Consensus pattern (31 bp):   
CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
Done.