Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g00763.N1

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: 3058
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.32


Found at i:2268 original size:20 final size:20

Alignment explanation


    Indices: 2243--2301  Score: 100
    Period size: 20  Copynumber: 3.0  Consensus size: 20

       2233 TAAATATGGT

                                
       2243 ATGTATGATATGCACATGAC
          1 ATGTATGATATGCACATGAC

                             * *
       2263 ATGTATGATATGCACATAAT
          1 ATGTATGATATGCACATGAC

                               
       2283 ATGTATGATATGCACATGA
          1 ATGTATGATATGCACATGA

       2302 TGTAATCATA


Statistics
Matches: 36,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  20   36  1.00

ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32


Consensus pattern (20 bp):   
ATGTATGATATGCACATGAC

Found at i:2379 original size:24 final size:24

Alignment explanation


    Indices: 2352--2470  Score: 170
    Period size: 24  Copynumber: 5.0  Consensus size: 24

       2342 GAGGAAGTGA

                                   *
       2352 AAAAGGGCTTATGCCCCAGTTATC
          1 AAAAGGGCTTATGCCCCAGTTATT

                                    
       2376 AAAAGGGCTTATGCCCCAGTTA-T
          1 AAAAGGGCTTATGCCCCAGTTATT

                                    
       2399 AAAAGGGCTTATGCCCCAGTTATT
          1 AAAAGGGCTTATGCCCCAGTTATT

            *         *             
       2423 GAAAGGGCTTTTGCCCCAGTTATT
          1 AAAAGGGCTTATGCCCCAGTTATT

                        *            
       2447 AAAAGAGGC-TAGGCCTCCAGTTAT
          1 AAAAG-GGCTTATGCC-CCAGTTAT

       2471 ATGATAAATC


Statistics
Matches: 86,  Mismatches: 6, Indels: 5
        0.89            0.06        0.05

Matches are distributed among these distances:
  23   22  0.26
  24   53  0.62
  25   11  0.13

ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27


Consensus pattern (24 bp):   
AAAAGGGCTTATGCCCCAGTTATT

Found at i:2421 original size:47 final size:48

Alignment explanation


    Indices: 2352--2470  Score: 170
    Period size: 47  Copynumber: 2.5  Consensus size: 48

       2342 GAGGAAGTGA

                                                            
       2352 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
          1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT

                                   **         *             
       2399 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
          1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT

                        *            
       2447 AAAAGAGGC-TAGGCCTCCAGTTAT
          1 AAAAG-GGCTTATGCC-CCAGTTAT

       2471 ATGATAAATC


Statistics
Matches: 65,  Mismatches: 4, Indels: 4
        0.89            0.05        0.05

Matches are distributed among these distances:
  47   43  0.66
  48   11  0.17
  49   11  0.17

ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27


Consensus pattern (48 bp):   
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT

Found at i:2697 original size:31 final size:31

Alignment explanation


    Indices: 2662--2724  Score: 108
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       2652 CGTTTACAGT

                                           
       2662 AAAGGCTTCGGCCCAGTAATATGAAATATGA
          1 AAAGGCTTCGGCCCAGTAATATGAAATATGA

                             **            
       2693 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
          1 AAAGGCTTCGGCCCAGTAATATGAAATATGA

             
       2724 A
          1 A

       2725 TTATGAAAAG


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24


Consensus pattern (31 bp):   
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Done.