Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g01524.M1

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: 5588
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:2491 original size:23 final size:24

Alignment explanation


    Indices: 2446--2497  Score: 72
    Period size: 25  Copynumber: 2.2  Consensus size: 24

       2436 ATTTTGTTTC

                                     
       2446 TTTATTGTTATTATTAATGTAATTA
          1 TTTATTGTTATTATTAA-GTAATTA

                                     
       2471 TTTATTGTTTATT-TTAA-TAATTA
          1 TTTATTG-TTATTATTAAGTAATTA

                
       2494 TTTA
          1 TTTA

       2498 CATTAATCCA


Statistics
Matches: 26,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  23   10  0.38
  25   11  0.42
  26    5  0.19

ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63


Consensus pattern (24 bp):   
TTTATTGTTATTATTAAGTAATTA

Found at i:2784 original size:14 final size:14

Alignment explanation


    Indices: 2767--2801  Score: 61
    Period size: 14  Copynumber: 2.5  Consensus size: 14

       2757 TGTTCTAATC

                          
       2767 TATATTGTCTAAAT
          1 TATATTGTCTAAAT

                          
       2781 TATATTGTCTAAAT
          1 TATATTGTCTAAAT

              *    
       2795 TAGATTG
          1 TATATTG

       2802 GACTGGTCAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49


Consensus pattern (14 bp):   
TATATTGTCTAAAT

Found at i:3905 original size:17 final size:16

Alignment explanation


    Indices: 3883--3932  Score: 57
    Period size: 16  Copynumber: 3.1  Consensus size: 16

       3873 CCTGGCCTCC

                             
       3883 CACTTCAAATGTTCTTT
          1 CACTTCAAATGTT-TTT

                   *         
       3900 CACTTC-GATGTTTGTT
          1 CACTTCAAATGTTT-TT

             *              
       3916 CGCTTCAAATGTTTTT
          1 CACTTCAAATGTTTTT

             
       3932 C
          1 C

       3933 CCTGCCTTAC


Statistics
Matches: 28,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  15    1  0.04
  16   15  0.54
  17   12  0.43

ACGTcount: A:0.18, C:0.22, G:0.12, T:0.48


Consensus pattern (16 bp):   
CACTTCAAATGTTTTT

Found at i:5342 original size:27 final size:27

Alignment explanation


    Indices: 5312--5372  Score: 86
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       5302 AATGTGCAAT

                                  *    
       5312 ATGTGAAATTACAGGGTTGACGTCGTG
          1 ATGTGAAATTACAGGGTTGACGCCGTG

                      *         *      
       5339 ATGTGAAATTGCAGGGTTGATGCCGTG
          1 ATGTGAAATTACAGGGTTGACGCCGTG

             *     
       5366 ACGTGAA
          1 ATGTGAA

       5373 GTTTCGCGTA


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  27   30  1.00

ACGTcount: A:0.26, C:0.11, G:0.34, T:0.28


Consensus pattern (27 bp):   
ATGTGAAATTACAGGGTTGACGCCGTG
Done.