Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g01745.N3

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: 8924
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33


Found at i:874 original size:14 final size:14

Alignment explanation


    Indices: 852--885  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

        842 AATAGAAAAC

                *         
        852 TTTTCATCACTTTT
          1 TTTTTATCACTTTT

                          
        866 TTTTTATCACTTTT
          1 TTTTTATCACTTTT

             *    
        880 TCTTTA
          1 TTTTTA

        886 GCCTCCGGGC


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68


Consensus pattern (14 bp):   
TTTTTATCACTTTT

Found at i:2404 original size:16 final size:17

Alignment explanation


    Indices: 2383--2416  Score: 61
    Period size: 16  Copynumber: 2.1  Consensus size: 17

       2373 AATTAGAGAA

                             
       2383 TTCTATTTAA-TTCTAT
          1 TTCTATTTAATTTCTAT

                             
       2399 TTCTATTTAATTTCTAT
          1 TTCTATTTAATTTCTAT

             
       2416 T
          1 T

       2417 AAATCCATTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   10  0.59
  17    7  0.41

ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65


Consensus pattern (17 bp):   
TTCTATTTAATTTCTAT

Found at i:3108 original size:15 final size:15

Alignment explanation


    Indices: 3090--3120  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3080 ATAACTAAAG

                           
       3090 AAAAAATAGATAGAT
          1 AAAAAATAGATAGAT

                           
       3105 AAAAAATAGATAGAT
          1 AAAAAATAGATAGAT

             
       3120 A
          1 A

       3121 GATGAGAGAT


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:0.68, C:0.00, G:0.13, T:0.19


Consensus pattern (15 bp):   
AAAAAATAGATAGAT

Found at i:8789 original size:26 final size:26

Alignment explanation


    Indices: 8760--8848  Score: 82
    Period size: 23  Copynumber: 3.7  Consensus size: 26

       8750 AAATTACAAG

                   *                  
       8760 TTATTAGCAATTAATATTAATTTATA
          1 TTATTAGTAATTAATATTAATTTATA

                 *  *            **   
       8786 TTATTTGTTATTAATATTAA-GAATA
          1 TTATTAGTAATTAATATTAATTTATA

                            *         
       8811 TTA--AGTAATTAATAAT-ATTTATA
          1 TTATTAGTAATTAATATTAATTTATA

                             
       8834 TTATTA-T-ATTAATAT
          1 TTATTAGTAATTAATAT

       8849 ATTTCGATTT


Statistics
Matches: 49,  Mismatches: 11, Indels: 9
        0.71            0.16        0.13

Matches are distributed among these distances:
  22    1  0.02
  23   23  0.47
  24    1  0.02
  25    7  0.14
  26   17  0.35

ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52


Consensus pattern (26 bp):   
TTATTAGTAATTAATATTAATTTATA

Found at i:8905 original size:15 final size:14

Alignment explanation


    Indices: 8872--8918  Score: 55
    Period size: 15  Copynumber: 3.4  Consensus size: 14

       8862 AATCTATATT

                          
       8872 TCTA-TATTATTTA
          1 TCTATTATTATTTA

                           
       8885 T-T-TTATTATTCTA
          1 TCTATTATTATT-TA

                           
       8898 TCTATTATTATATTA
          1 TCTATTATTAT-TTA

                  
       8913 TCTATT
          1 TCTATT

       8919 TATAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 8
        0.78            0.00        0.22

Matches are distributed among these distances:
  12    8  0.28
  13    4  0.14
  14    1  0.03
  15   15  0.52
  16    1  0.03

ACGTcount: A:0.28, C:0.09, G:0.00, T:0.64


Consensus pattern (14 bp):   
TCTATTATTATTTA
Done.