Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g00284.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: 3442
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:2647 original size:42 final size:42

Alignment explanation


    Indices: 2588--2676  Score: 151
    Period size: 42  Copynumber: 2.1  Consensus size: 42

       2578 TCCTAATTGG

                        *                      *      
       2588 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAA
          1 GAAAATAGTTCCATTATTCTAATAAACTACTAAAAGATAAAA

                                                      
       2630 GAAAATAGTTCCATTATTCTAATAAACTACTAAAAGATAAAA
          1 GAAAATAGTTCCATTATTCTAATAAACTACTAAAAGATAAAA

            *    
       2672 TAAAA
          1 GAAAA

       2677 ATATTCCTAG


Statistics
Matches: 44,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  42   44  1.00

ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29


Consensus pattern (42 bp):   
GAAAATAGTTCCATTATTCTAATAAACTACTAAAAGATAAAA

Found at i:2697 original size:43 final size:42

Alignment explanation


    Indices: 2589--2698  Score: 98
    Period size: 42  Copynumber: 2.6  Consensus size: 42

       2579 CCTAATTGGG

                       ***    *               *      *
       2589 AAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAAG
          1 AAAATAGTTCCAGAATTCGAATAAACTACTAAAAGATAAAAA

                        **    *                        
       2631 AAAATAGTTCCATTATTCTAATAAACTACTAAAAGATAAAATA
          1 AAAATAGTTCCAGAATTCGAATAAACTACTAAAAGATAAAA-A

                                       
       2674 AAAATA-TTCCTAGAATAT-GAATAAA
          1 AAAATAGTTCC-AGAAT-TCGAATAAA

       2699 ACTTATCTAC


Statistics
Matches: 59,  Mismatches: 6, Indels: 5
        0.84            0.09        0.07

Matches are distributed among these distances:
  42   43  0.73
  43   15  0.25
  44    1  0.02

ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30


Consensus pattern (42 bp):   
AAAATAGTTCCAGAATTCGAATAAACTACTAAAAGATAAAAA

Found at i:2723 original size:19 final size:18

Alignment explanation


    Indices: 2701--2740  Score: 71
    Period size: 19  Copynumber: 2.2  Consensus size: 18

       2691 TGAATAAAAC

                               
       2701 TTATCTACCTAAATAAGAT
          1 TTATCTACCTAAATAA-AT

                              
       2720 TTATCTACCTAAATAAAT
          1 TTATCTACCTAAATAAAT

               
       2738 TTA
          1 TTA

       2741 AAATATATAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    5  0.24
  19   16  0.76

ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40


Consensus pattern (18 bp):   
TTATCTACCTAAATAAAT
Done.