Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g02444.R1

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: 4390
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26


Found at i:2462 original size:135 final size:135

Alignment explanation


    Indices: 2220--2482  Score: 391
    Period size: 135  Copynumber: 1.9  Consensus size: 135

       2210 GCTACTAGAA

                                *    *               * *    *                
       2220 AGGGGAAGAGTTTCAACTTTGCTTGGCAGTGATTTCCGAGATACAATGGACCGATTAATGACTTC
          1 AGGGGAAGAGTTTCAACTTTACTTGACAGTGATTTCCGAGAGAAAATGAACCGATTAATGACTTC

                     *                                      *                
       2285 TCGTGTACAGATCCAAGCGGATGGGGCAGAAAGTCAACAAGAAGTGGATGATAAGGAAGGAATTA
         66 TCGTGTACAAATCCAAGCGGATGGGGCAGAAAGTCAACAAGAAGTGGAGGATAAGGAAGGAATTA

                 
       2350 TATGC
        131 TATGC

                                 *               *                           
       2355 AGGGGAAGAGTTTCAACTTTATTTGACAGTGATTTCCTAGAGAAAATGAACCGATTAATGACTTC
          1 AGGGGAAGAGTTTCAACTTTACTTGACAGTGATTTCCGAGAGAAAATGAACCGATTAATGACTTC

                        *     *    **  *                 *                 
       2420 TCGTGTACAAATGCAAGCTGATGTTGCTGAAAGTCAACAAGAAGTTGAGGATAAGGAAGGAAT
         66 TCGTGTACAAATCCAAGCGGATGGGGCAGAAAGTCAACAAGAAGTGGAGGATAAGGAAGGAAT

       2483 GGTCCAACGA


Statistics
Matches: 113,  Mismatches: 15, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
 135  113  1.00

ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25


Consensus pattern (135 bp):   
AGGGGAAGAGTTTCAACTTTACTTGACAGTGATTTCCGAGAGAAAATGAACCGATTAATGACTTC
TCGTGTACAAATCCAAGCGGATGGGGCAGAAAGTCAACAAGAAGTGGAGGATAAGGAAGGAATTA
TATGC

Found at i:2546 original size:3 final size:3

Alignment explanation


    Indices: 2502--2528  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

       2492 AGTGTCTTAC

                                               
       2502 GAA GAA GAA GAA GAA GAA GAA GAA GAA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA

       2529 TACGACGATG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (3 bp):   
GAA

Found at i:3525 original size:6 final size:6

Alignment explanation


    Indices: 3514--3542  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

       3504 GTTTTAATTA

                                             
       3514 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
          1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA

       3543 AGATTCAATC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83


Consensus pattern (6 bp):   
TTTTAT

Done.