Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g00300.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, 562

Length: 938
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.18


Found at i:422 original size:45 final size:44

Alignment explanation


    Indices: 372--608  Score: 227
    Period size: 45  Copynumber: 5.4  Consensus size: 44

        362 AGGTCCGGAG

                                        *                
        372 GAAAAACGTAATGAAGAATCGAAAAGTATGACTACAGGTTTGG-A
          1 GAAAAACGTAATGAAGAA-CGAAAAGTACGACTACAGGTTTGGAA

                      *                              **   
        416 GAAAAAACGTGATGAAGAAC-AGAAAG---G-C-ACAGGTTCAGAA
          1 G-AAAAACGTAATGAAGAACGA-AAAGTACGACTACAGGTTTGGAA

                    *     *          *          *        
        456 GAAAAACGAAATGAGGAATCGAAAAATACGACTACAAGTTTGGAA
          1 GAAAAACGTAATGAAGAA-CGAAAAGTACGACTACAGGTTTGGAA

             *      *                     * *       *    
        501 GGAAAACGCAATGAAGAACGGAAAAGTACGGCCACAGGTTCGGAA
          1 GAAAAACGTAATGAAGAAC-GAAAAGTACGACTACAGGTTTGGAA

                        *                 *     *        
        546 GAAAAACGTAATCAAGAACTGAAAAGTACGCCTACAAGTTTGGAA
          1 GAAAAACGTAATGAAGAAC-GAAAAGTACGACTACAGGTTTGGAA

                              
        591 GAAAAACGTAATGAAGAA
          1 GAAAAACGTAATGAAGAA

        609 TCAAAAAGAA


Statistics
Matches: 155,  Mismatches: 27, Indels: 21
        0.76            0.13        0.10

Matches are distributed among these distances:
  39   22  0.14
  40    7  0.05
  41    2  0.01
  43    2  0.01
  44    8  0.05
  45  114  0.74

ACGTcount: A:0.48, C:0.13, G:0.25, T:0.14


Consensus pattern (44 bp):   
GAAAAACGTAATGAAGAACGAAAAGTACGACTACAGGTTTGGAA

Found at i:581 original size:90 final size:84

Alignment explanation


    Indices: 360--616  Score: 293
    Period size: 90  Copynumber: 3.0  Consensus size: 84

        350 TATGACAATA

                  *    *                            *       *                
        360 ACAGGTCCGGAGGAAAAACGTAATGAAGAATCGAAAAGTATGACTACAGGTTTGG-AGAAAAAAC
          1 ACAGGTTCGGAAGAAAAACGTAATGAAGAATCGAAAAGTACGACTACAAGTTTGGAAG-AAAAAC

              *          *      
        424 GTGATGAAGAACAGAAAGGC
         65 GTAATGAAGAACAAAAAGGC

                    *           *     *          *                    *      
        444 ACAGGTTCAGAAGAAAAACGAAATGAGGAATCGAAAAATACGACTACAAGTTTGGAAGGAAAACG
          1 ACAGGTTCGGAAGAAAAACGTAATGAAGAATCGAAAAGTACGACTACAAGTTTGGAAGAAAAACG

            *                        
        509 CAATGAAGAACGGAAAAGTACGGCC
         66 TAATGAAGAAC--AAAA--A-GG-C

                                    *                  *                     
        534 ACAGGTTCGGAAGAAAAACGTAATCAAGAA-CTGAAAAGTACGCCTACAAGTTTGGAAGAAAAAC
          1 ACAGGTTCGGAAGAAAAACGTAATGAAGAATC-GAAAAGTACGACTACAAGTTTGGAAGAAAAAC

                               
        598 GTAATGAAGAATCAAAAAG
         65 GTAATGAAGAA-CAAAAAG

        617 AACACGTCCG


Statistics
Matches: 144,  Mismatches: 20, Indels: 16
        0.80            0.11        0.09

Matches are distributed among these distances:
  84   62  0.43
  85    2  0.01
  86    4  0.03
  87    1  0.01
  88    1  0.01
  89    7  0.05
  90   66  0.46
  91    1  0.01

ACGTcount: A:0.47, C:0.13, G:0.25, T:0.14


Consensus pattern (84 bp):   
ACAGGTTCGGAAGAAAAACGTAATGAAGAATCGAAAAGTACGACTACAAGTTTGGAAGAAAAACG
TAATGAAGAACAAAAAGGC

Found at i:769 original size:45 final size:44

Alignment explanation


    Indices: 683--796  Score: 120
    Period size: 45  Copynumber: 2.5  Consensus size: 44

        673 ATCCAACGAA

                     *       *      *          **        
        683 AGATTCGAAGGAAAAACGTAATGATGAATCGAAAGTTACGACAAC
          1 AGATTC-AAAGAAAAACTTAATGAGGAATCGAAAGAAACGACAAC

                               *                      *  
        728 AGATTCAAAGAAAAAACTTCATGAGGAATCGAAAGAAACGACTAC
          1 AGATTCAAAG-AAAAACTTAATGAGGAATCGAAAGAAACGACAAC

              *  *                  
        773 AGGTTTAGAAGAAAAACTTAATGA
          1 AGATTCA-AAGAAAAACTTAATGA

        797 CGAACAAAAA


Statistics
Matches: 57,  Mismatches: 10, Indels: 4
        0.80            0.14        0.06

Matches are distributed among these distances:
  44    3  0.05
  45   51  0.89
  46    3  0.05

ACGTcount: A:0.49, C:0.12, G:0.20, T:0.18


Consensus pattern (44 bp):   
AGATTCAAAGAAAAACTTAATGAGGAATCGAAAGAAACGACAAC
Done.