Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00740.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, 1000

Length: 4770
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32


Found at i:622 original size:30 final size:32

Alignment explanation


    Indices: 588--650  Score: 94
    Period size: 33  Copynumber: 2.0  Consensus size: 32

        578 AGGAAGAGAA

                                            
        588 AGGATA-GG-GAAGAAGGGGAAGGAGGAGGAG
          1 AGGATAGGGAGAAGAAGGGGAAGGAGGAGGAG

                                 *           
        618 AGGATAGGGAAGAAGAAGGGGGAGGAGGAGGAG
          1 AGGATAGGG-AGAAGAAGGGGAAGGAGGAGGAG

        651 GAGAGTTGAG


Statistics
Matches: 29,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  30    6  0.21
  31    2  0.07
  33   21  0.72

ACGTcount: A:0.40, C:0.00, G:0.57, T:0.03


Consensus pattern (32 bp):   
AGGATAGGGAGAAGAAGGGGAAGGAGGAGGAG

Found at i:1714 original size:20 final size:20

Alignment explanation


    Indices: 1675--1715  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1665 AAAAAAAACT

                         *      
       1675 ATTTTTAGAAAATTCATTTA
          1 ATTTTTAGAAAATACATTTA

                           *    
       1695 ATTTTTAGAAAATACTTTTA
          1 ATTTTTAGAAAATACATTTA

             
       1715 A
          1 A

       1716 GTGAAGAATA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49


Consensus pattern (20 bp):   
ATTTTTAGAAAATACATTTA

Found at i:1894 original size:23 final size:23

Alignment explanation


    Indices: 1856--1899  Score: 63
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       1846 TTTAAATATG

                            *      
       1856 TTTTTAAAAAATATTGCTTTTAT
          1 TTTTTAAAAAATATTGATTTTAT

                                  
       1879 TTTTTAATAAAA-ATTGATTTT
          1 TTTTTAA-AAAATATTGATTTT

       1900 TCAAAAAGGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  23   15  0.79
  24    4  0.21

ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57


Consensus pattern (23 bp):   
TTTTTAAAAAATATTGATTTTAT

Found at i:2086 original size:17 final size:17

Alignment explanation


    Indices: 2064--2098  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       2054 TAAGTAGTTC

                             
       2064 CTAATGTTTTATTCCGT
          1 CTAATGTTTTATTCCGT

                             
       2081 CTAATGTTTTATTCCGT
          1 CTAATGTTTTATTCCGT

             
       2098 C
          1 C

       2099 CCATATTTTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.17, C:0.20, G:0.11, T:0.51


Consensus pattern (17 bp):   
CTAATGTTTTATTCCGT

Found at i:2455 original size:33 final size:33

Alignment explanation


    Indices: 2413--2476  Score: 128
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       2403 TATCTTTCCA

                                             
       2413 CTGTTTAATATATCCTCCTTTGACTTTTTTTCT
          1 CTGTTTAATATATCCTCCTTTGACTTTTTTTCT

                                           
       2446 CTGTTTAATATATCCTCCTTTGACTTTTTTT
          1 CTGTTTAATATATCCTCCTTTGACTTTTTTT

       2477 TTTACTTCTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   31  1.00

ACGTcount: A:0.16, C:0.20, G:0.06, T:0.58


Consensus pattern (33 bp):   
CTGTTTAATATATCCTCCTTTGACTTTTTTTCT

Found at i:3243 original size:13 final size:13

Alignment explanation


    Indices: 3225--3250  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       3215 CTGTTCGTAC

                         
       3225 TGCAGTTTACTTG
          1 TGCAGTTTACTTG

                         
       3238 TGCAGTTTACTTG
          1 TGCAGTTTACTTG

       3251 CTGAATATTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46


Consensus pattern (13 bp):   
TGCAGTTTACTTG
Done.