Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g00535.P4

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: 4385
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36


Found at i:613 original size:35 final size:35

Alignment explanation


    Indices: 568--637  Score: 140
    Period size: 35  Copynumber: 2.0  Consensus size: 35

        558 ATCCATTGGG

                                               
        568 TTTTTGCAGATTCAGTCAAAGATGCTTAGTAAACT
          1 TTTTTGCAGATTCAGTCAAAGATGCTTAGTAAACT

                                               
        603 TTTTTGCAGATTCAGTCAAAGATGCTTAGTAAACT
          1 TTTTTGCAGATTCAGTCAAAGATGCTTAGTAAACT

        638 GAGTTAAATT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   35  1.00

ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37


Consensus pattern (35 bp):   
TTTTTGCAGATTCAGTCAAAGATGCTTAGTAAACT

Found at i:2352 original size:26 final size:27

Alignment explanation


    Indices: 2310--2374  Score: 71
    Period size: 26  Copynumber: 2.4  Consensus size: 27

       2300 TTTAATTAGT

                                       
       2310 TTTTTAAATTTTAAATAATATTAA-AA
          1 TTTTTAAATTTTAAATAATATTAATAA

                    *           *     * 
       2336 TTTTTATAGTTTT-AATAATTTTAATGA
          1 TTTTTA-AATTTTAAATAATATTAATAA

                   *    
       2363 TTTTTAATTTTT
          1 TTTTTAAATTTT

       2375 TAATTTTTTA


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  26   21  0.64
  27   12  0.36

ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60


Consensus pattern (27 bp):   
TTTTTAAATTTTAAATAATATTAATAA

Found at i:2357 original size:9 final size:9

Alignment explanation


    Indices: 2316--2366  Score: 50
    Period size: 9  Copynumber: 5.7  Consensus size: 9

       2306 TAGTTTTTTA

                      
       2316 AATTTTAAAT
          1 AATTTT-AAT

               *     
       2326 AATATTAA-
          1 AATTTTAAT

                  *  
       2334 AATTTTTAT
          1 AATTTTAAT

             *       
       2343 AGTTTTAAT
          1 AATTTTAAT

                     
       2352 AATTTTAAT
          1 AATTTTAAT

            *     
       2361 GATTTT
          1 AATTTT

       2367 TAATTTTTTA


Statistics
Matches: 33,  Mismatches: 7, Indels: 3
        0.77            0.16        0.07

Matches are distributed among these distances:
   8    6  0.18
   9   22  0.67
  10    5  0.15

ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55


Consensus pattern (9 bp):   
AATTTTAAT

Found at i:2834 original size:6 final size:6

Alignment explanation


    Indices: 2823--2849  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       2813 ACAGCTGTCA

                                           
       2823 GTGGCG GTGGCG GTGGCG GTGGCG GTG
          1 GTGGCG GTGGCG GTGGCG GTGGCG GTG

       2850 CTGTTGCTGT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.00, C:0.15, G:0.67, T:0.19


Consensus pattern (6 bp):   
GTGGCG

Done.