Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03165.C1

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: 1803
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36


Found at i:54 original size:1 final size:1

Alignment explanation


    Indices: 16--46  Score: 62
    Period size: 1  Copynumber: 31.0  Consensus size: 1

          6 CGCTAATAAC

                                           
         16 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

         47 CTGAAAAAGG


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   30  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:113 original size:10 final size:10

Alignment explanation


    Indices: 98--126  Score: 58
    Period size: 10  Copynumber: 2.9  Consensus size: 10

         88 AAGAAAACCC

                      
         98 TTCACTGTTA
          1 TTCACTGTTA

                      
        108 TTCACTGTTA
          1 TTCACTGTTA

                     
        118 TTCACTGTT
          1 TTCACTGTT

        127 TTCGCCAATG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   19  1.00

ACGTcount: A:0.17, C:0.21, G:0.10, T:0.52


Consensus pattern (10 bp):   
TTCACTGTTA

Found at i:596 original size:40 final size:40

Alignment explanation


    Indices: 535--611  Score: 111
    Period size: 40  Copynumber: 1.9  Consensus size: 40

        525 TCCATGGCAT

                            *          *             
        535 CTCTATACTTATGCTTGGCTAAA-AATGTATGTATGTACAC
          1 CTCTATACTTATGCTTAGCTAAAGAA-ATATGTATGTACAC

                *                                
        575 CTCTGTACTTATGCTTAGCTAAAGAAATATGTATGTA
          1 CTCTATACTTATGCTTAGCTAAAGAAATATGTATGTA

        612 TGTATGCAGC


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  40   31  0.94
  41    2  0.06

ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38


Consensus pattern (40 bp):   
CTCTATACTTATGCTTAGCTAAAGAAATATGTATGTACAC

Found at i:696 original size:28 final size:27

Alignment explanation


    Indices: 656--708  Score: 79
    Period size: 28  Copynumber: 1.9  Consensus size: 27

        646 ATAATTTATA

                          *            
        656 AAATTTTAAATTAATAATGATAAAATT
          1 AAATTTTAAATTAAAAATGATAAAATT

                     *                
        683 AAATTTTCACATTAAAAATGATAAAA
          1 AAATTTT-AAATTAAAAATGATAAAA

        709 ATATATAATT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  27    7  0.30
  28   16  0.70

ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36


Consensus pattern (27 bp):   
AAATTTTAAATTAAAAATGATAAAATT
Done.