Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g01281.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: 3319
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36


Found at i:2412 original size:12 final size:12

Alignment explanation


    Indices: 2396--2442  Score: 51
    Period size: 12  Copynumber: 3.9  Consensus size: 12

       2386 GGTTATTTCT

                        
       2396 ATTTCAATTTT-
          1 ATTTCAATTTTG

                  *   *  
       2407 AGTTTCGATTCTG
          1 A-TTTCAATTTTG

                 *      
       2420 ATTTCGATTTTG
          1 ATTTCAATTTTG

                       
       2432 ATTTCAATTTT
          1 ATTTCAATTTT

       2443 AAAATACTCA


Statistics
Matches: 30,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  11    1  0.03
  12   28  0.93
  13    1  0.03

ACGTcount: A:0.21, C:0.11, G:0.11, T:0.57


Consensus pattern (12 bp):   
ATTTCAATTTTG

Found at i:2465 original size:6 final size:6

Alignment explanation


    Indices: 2454--2539  Score: 73
    Period size: 6  Copynumber: 14.3  Consensus size: 6

       2444 AAATACTCAC

                                      *  *         *  *      *     
       2454 TGATTT TGATTT TGATTT TGATTC TAATTT TGATCT CGATTT AGATTT
          1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT

            *  *                 *   *  *      *        
       2502 AGAATT TGATTT TGATTT CGATCT GGATTT CGATTT TG
          1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TG

       2540 TATTGTATGT


Statistics
Matches: 63,  Mismatches: 17, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
   6   63  1.00

ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55


Consensus pattern (6 bp):   
TGATTT

Found at i:2613 original size:48 final size:48

Alignment explanation


    Indices: 2558--2726  Score: 241
    Period size: 48  Copynumber: 3.5  Consensus size: 48

       2548 GTCATGTGCA

                         * * *                              
       2558 TGATGTTTATTGTTTGTTTCTGCCATTGTATGAATGCCATTATCAAAT
          1 TGATGTTTATTGTATATATCTGCCATTGTATGAATGCCATTATCAAAT

                         *                      *           
       2606 TGATGTTTATTGTGTATATCTGCCATTGTATGAATGTCATTATCAAAT
          1 TGATGTTTATTGTATATATCTGCCATTGTATGAATGCCATTATCAAAT

                  *     *          *                       *
       2654 TGATGTGTATTGCATATATCTGCTATTGTATGAATGCC-TTATCAAAC
          1 TGATGTTTATTGTATATATCTGCCATTGTATGAATGCCATTATCAAAT

                         *            
       2701 TGATGTTTATTGTGTATATCTGCCAT
          1 TGATGTTTATTGTATATATCTGCCAT

       2727 GATGTTTATT


Statistics
Matches: 107,  Mismatches: 14, Indels: 1
        0.88            0.11        0.01

Matches are distributed among these distances:
  47   30  0.28
  48   77  0.72

ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46


Consensus pattern (48 bp):   
TGATGTTTATTGTATATATCTGCCATTGTATGAATGCCATTATCAAAT

Found at i:3051 original size:15 final size:15

Alignment explanation


    Indices: 3031--3059  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       3021 GAAGAAAACA

                           
       3031 TGTCTGGTAGTGATG
          1 TGTCTGGTAGTGATG

                          
       3046 TGTCTGGTAGTGAT
          1 TGTCTGGTAGTGAT

       3060 AGTGATGCAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.14, C:0.07, G:0.38, T:0.41


Consensus pattern (15 bp):   
TGTCTGGTAGTGATG
Done.