Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_14635

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, 831

Length: 1385
ACGTcount: A:0.31, C:0.12, G:0.34, T:0.23


Found at i:522 original size:12 final size:12

Alignment explanation


    Indices: 505--545  Score: 55
    Period size: 12  Copynumber: 3.4  Consensus size: 12

        495 TGATGAGGAG

                    *   
        505 GAAGAGGAAGAT
          1 GAAGAGGATGAT

                       *
        517 GAAGAGGATGAG
          1 GAAGAGGATGAT

              *         
        529 GATGAGGATGAT
          1 GAAGAGGATGAT

                 
        541 GAAGA
          1 GAAGA

        546 TGATCCTGGG


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  12   24  1.00

ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12


Consensus pattern (12 bp):   
GAAGAGGATGAT

Found at i:523 original size:18 final size:18

Alignment explanation


    Indices: 496--530  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        486 AGAATCGGAT

                 *            
        496 GATGAGGAGGAAGAGGAA
          1 GATGAAGAGGAAGAGGAA

                       *     
        514 GATGAAGAGGATGAGGA
          1 GATGAAGAGGAAGAGGA

        531 TGAGGATGAT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.43, C:0.00, G:0.49, T:0.09


Consensus pattern (18 bp):   
GATGAAGAGGAAGAGGAA

Found at i:895 original size:18 final size:18

Alignment explanation


    Indices: 874--919  Score: 65
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        864 AGATGGGGTA

                    *     *   
        874 GAGGATGATGATGAGGAG
          1 GAGGATGAGGATGAAGAG

                              
        892 GAGGATGAGGATGAAGAG
          1 GAGGATGAGGATGAAGAG

                 *    
        910 GAGGAAGAGG
          1 GAGGATGAGG

        920 TAGATAATGA


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   25  1.00

ACGTcount: A:0.37, C:0.00, G:0.52, T:0.11


Consensus pattern (18 bp):   
GAGGATGAGGATGAAGAG

Found at i:1204 original size:3 final size:3

Alignment explanation


    Indices: 1196--1255  Score: 120
    Period size: 3  Copynumber: 20.0  Consensus size: 3

       1186 GACCCAGGGA

                                                                           
       1196 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
          1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG

                           
       1244 ATG ATG ATG ATG
          1 ATG ATG ATG ATG

       1256 TAGAAGAGGA


Statistics
Matches: 57,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   57  1.00

ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33


Consensus pattern (3 bp):   
ATG

Done.