Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g01799.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, 386

Length: 644
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30


Found at i:242 original size:15 final size:15

Alignment explanation


    Indices: 222--273  Score: 86
    Period size: 15  Copynumber: 3.5  Consensus size: 15

        212 GCCACCAATA

                           
        222 CCACCAATAACATTG
          1 CCACCAATAACATTG

                    *      
        237 CCACCAATGACATTG
          1 CCACCAATAACATTG

                           
        252 CCACCAATAACATTG
          1 CCACCAATAACATTG

            *      
        267 ACACCAA
          1 CCACCAA

        274 CAGGTACACC


Statistics
Matches: 34,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  15   34  1.00

ACGTcount: A:0.40, C:0.35, G:0.08, T:0.17


Consensus pattern (15 bp):   
CCACCAATAACATTG

Found at i:350 original size:24 final size:23

Alignment explanation


    Indices: 291--355  Score: 82
    Period size: 21  Copynumber: 2.9  Consensus size: 23

        281 ACCAATCAAG

                               *   
        291 GAACCAACAGATCCACCAATCGA
          1 GAACCAACAGATCCACCAACCGA

                                    
        314 TG--CC-ACAGATCCACCAACCGA
          1 -GAACCAACAGATCCACCAACCGA

                                 
        335 GAAACCAACAGATCCACCAAC
          1 G-AACCAACAGATCCACCAAC

        356 TGAGGTACCA


Statistics
Matches: 36,  Mismatches: 1, Indels: 8
        0.80            0.02        0.18

Matches are distributed among these distances:
  20    1  0.03
  21   16  0.44
  22    2  0.06
  23    2  0.06
  24   15  0.42

ACGTcount: A:0.42, C:0.38, G:0.12, T:0.08


Consensus pattern (23 bp):   
GAACCAACAGATCCACCAACCGA

Found at i:365 original size:24 final size:23

Alignment explanation


    Indices: 293--368  Score: 77
    Period size: 24  Copynumber: 3.3  Consensus size: 23

        283 CAATCAAGGA

                                    
        293 ACCAACAGATCCACCAA-TCGA-T
          1 ACCAACAGATCCACCAACT-GAGT

            *                 *    *
        315 GCC-ACAGATCCACCAACCGAGAA
          1 ACCAACAGATCCACCAACTGAG-T

                                    
        338 ACCAACAGATCCACCAACTGAGGT
          1 ACCAACAGATCCACCAACTGA-GT

                   
        362 ACCAACA
          1 ACCAACA

        369 TTGCCTTGAA


Statistics
Matches: 43,  Mismatches: 6, Indels: 8
        0.75            0.11        0.14

Matches are distributed among these distances:
  21   15  0.35
  22    2  0.05
  23    2  0.05
  24   23  0.53
  25    1  0.02

ACGTcount: A:0.41, C:0.37, G:0.13, T:0.09


Consensus pattern (23 bp):   
ACCAACAGATCCACCAACTGAGT
Done.