Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00860.F4

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: 4666
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29


Found at i:756 original size:3 final size:3

Alignment explanation


    Indices: 748--781  Score: 50
    Period size: 3  Copynumber: 11.3  Consensus size: 3

        738 GATTCCAATA

                              *                  *       
        748 ATG ATG ATG ATG ATA ATG ATG ATG ATG AAG ATG A
          1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A

        782 CTTGTATGAT


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29


Consensus pattern (3 bp):   
ATG

Found at i:763 original size:15 final size:15

Alignment explanation


    Indices: 745--775  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        735 GATGATTCCA

                           
        745 ATAATGATGATGATG
          1 ATAATGATGATGATG

                           
        760 ATAATGATGATGATG
          1 ATAATGATGATGATG

             
        775 A
          1 A

        776 AGATGACTTG


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

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32


Consensus pattern (15 bp):   
ATAATGATGATGATG

Found at i:3460 original size:150 final size:149

Alignment explanation


    Indices: 3189--3777  Score: 837
    Period size: 150  Copynumber: 3.9  Consensus size: 149

       3179 AGAAGAGAAA

                            **                      *                       *
       3189 GCACAGTGAAGAAAATGATGGAAGGAAAACTGATAAAAAGCGTGGAGGACA-GACTCCTAGAAGC
          1 GCACAGTGAAGAAAATCTTGGAAGGAAAACTGAT-AAAAGAGTGGAGGA-AGGACTCCTAGAAGT

                                               *                           * 
       3253 GAGACACAT-GATGGAATTCCTCACTCTTCTCCATTCAATGTGATGGGTAGTAGTAGATCCTCGG
         64 GAGACACATAG-TGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAG

                                  
       3317 TGGAAGGTGCCTCCTCCAAATT
        128 TGGAAGGTGCCTCCTCCAAATT

                                *                   *                        
       3339 GCACAGTGAAGAAAATCTTGTAAGGAAAACTGATATAAAGGGTGGAGGAAGGACTCCTAGAAGTG
          1 GCACAGTGAAGAAAATCTTGGAAGGAAAACTGATA-AAAGAGTGGAGGAAGGACTCCTAGAAGTG

               **                          *                                 
       3404 AGATGCATAGTGGAATTCCTCACTCTTCTCCGTCCAATGTGATGGGTAGTAGTAGATCCTCAGTG
         65 AGACACATAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAGTG

            *           *       
       3469 AAAGGTGCCTCCCCCAAATT
        130 GAAGGTGCCTCCTCCAAATT

                                                                             
       3489 GCACAGTGAAGAAAATCTTGGAAGGAAAACTGATAAAATGAGTGGAGGAAGGACTCCTAGAAGTG
          1 GCACAGTGAAGAAAATCTTGGAAGGAAAACTGATAAAA-GAGTGGAGGAAGGACTCCTAGAAGTG

                   **          *           * *   *                           
       3554 AGACACACGGTGGAATTCCCCACTCTTCTCCGTACAACGTGATGGGTAGTAGTAGATCCTCAGTG
         65 AGACACATAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAGTG

                       *        
       3619 GAAGGTGCCTCTTCCAAATT
        130 GAAGGTGCCTCCTCCAAATT

                **                         *                                 
       3639 GCACTCTGAAGAAAATCTTGGAAGGAAAACTAATAAGAAGAGT---GGAAGGACTCCTAGAAGTG
          1 GCACAGTGAAGAAAATCTTGGAAGGAAAACTGATAA-AAGAGTGGAGGAAGGACTCCTAGAAGTG

                 * *           *                               *             
       3701 AGACATACAGTGGAATTCCGCACTCTTCTCCATCCAATGTGATGGGTAGTATTAGATCCTCAGTG
         65 AGACACATAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAGTG

               *        
       3766 GAATGTGCCTCC
        130 GAAGGTGCCTCC

       3778 AGATCGCCTA


Statistics
Matches: 398,  Mismatches: 36, Indels: 13
        0.89            0.08        0.03

Matches are distributed among these distances:
 147   87  0.22
 149    5  0.01
 150  303  0.76
 151    3  0.01

ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23


Consensus pattern (149 bp):   
GCACAGTGAAGAAAATCTTGGAAGGAAAACTGATAAAAGAGTGGAGGAAGGACTCCTAGAAGTGA
GACACATAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAGTGG
AAGGTGCCTCCTCCAAATT

Done.