Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g00564.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: 5174
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25


Found at i:3564 original size:93 final size:93

Alignment explanation


    Indices: 3446--3647  Score: 291
    Period size: 93  Copynumber: 2.2  Consensus size: 93

       3436 AATGATTCTA

                   *     *                                                   
       3446 GTTGGGGGAAAAAGGGATCAGCAGATGCAAGTCAGGACTCTAA-CTGGGGTAAGAAAAATTGGGG
          1 GTTGGGGCAAAAAAGGATCAGCAGATGCAAGTCAGGACTC-AAGCTGGGGTAAGAAAAATTGGGG

                                      *  
       3510 CACTGGAAATGATGCTGGCCAAGACTGTG
         65 CACTGGAAATGATGCTGGCCAAGACTCTG

                                                  *                 * *      
       3539 GTTGGGGCAAAAAAGGATC-GACAGATGCAAGTCAGGATTCAAGCTGGGGTAAGAAGAGTTGGGG
          1 GTTGGGGCAAAAAAGGATCAG-CAGATGCAAGTCAGGACTCAAGCTGGGGTAAGAAAAATTGGGG

            *     *      *               
       3603 TACTGGCAATGATTCTGGCCAAGACTCTG
         65 CACTGGAAATGATGCTGGCCAAGACTCTG

                            
       3632 GTTGGGGCAAAAAAGG
          1 GTTGGGGCAAAAAAGG

       3648 TGGTTGGAAC


Statistics
Matches: 98,  Mismatches: 9, Indels: 4
        0.88            0.08        0.04

Matches are distributed among these distances:
  92    3  0.03
  93   95  0.97

ACGTcount: A:0.32, C:0.14, G:0.36, T:0.19


Consensus pattern (93 bp):   
GTTGGGGCAAAAAAGGATCAGCAGATGCAAGTCAGGACTCAAGCTGGGGTAAGAAAAATTGGGGC
ACTGGAAATGATGCTGGCCAAGACTCTG

Found at i:4001 original size:30 final size:30

Alignment explanation


    Indices: 3967--4064  Score: 124
    Period size: 30  Copynumber: 3.3  Consensus size: 30

       3957 TTTTGGTGGC

                                          
       3967 AGAGGTGGTGATGGTGGAGGCTACGGAGGT
          1 AGAGGTGGTGATGGTGGAGGCTACGGAGGT

                 *                        
       3997 AGAGGCGGTGATGGTGGAGGCTACGGAGGT
          1 AGAGGTGGTGATGGTGGAGGCTACGGAGGT

                *      ** *  *     **     
       4027 AGAGTTGGTGACAGAGGTGGCTATAGAGGT
          1 AGAGGTGGTGATGGTGGAGGCTACGGAGGT

                    
       4057 AGAGGTGG
          1 AGAGGTGG

       4065 AAGAGGGGGT


Statistics
Matches: 58,  Mismatches: 10, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  30   58  1.00

ACGTcount: A:0.22, C:0.07, G:0.51, T:0.19


Consensus pattern (30 bp):   
AGAGGTGGTGATGGTGGAGGCTACGGAGGT

Found at i:4429 original size:111 final size:111

Alignment explanation


    Indices: 4298--4513  Score: 324
    Period size: 111  Copynumber: 1.9  Consensus size: 111

       4288 AACCAGGGCT

                       *               ** *  *            **                 
       4298 GGAATGGTGGAGCAAGTGGAGGTGGAGGTAGGAGTTGGAATCAATCTGGTGCTGATCAAGGAGGC
          1 GGAATGGTGGAACAAGTGGAGGTGGAGCCAAGACTTGGAATCAATCCAGTGCTGATCAAGGAGGC

                             *                *           
       4363 CAATCCTCTAGTTGGAGTCAGGCTGGTGGCTGGAGCAAAGAGGGGG
         66 CAATCCTCTAGTTGGAGCCAGGCTGGTGGCTGGAACAAAGAGGGGG

                                                   *                         
       4409 GGAATGGTGGAACAAGTGGAGGTGGAGCCAAGACTTGGATTCAATCCAGTGCTGATCAAGGAGGC
          1 GGAATGGTGGAACAAGTGGAGGTGGAGCCAAGACTTGGAATCAATCCAGTGCTGATCAAGGAGGC

                                 *       *          
       4474 CAATCCTCTAGTTGGAGCCAGTCTGGTGGGTGGAACAAAG
         66 CAATCCTCTAGTTGGAGCCAGGCTGGTGGCTGGAACAAAG

       4514 GCTCTAGCTC


Statistics
Matches: 93,  Mismatches: 12, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
 111   93  1.00

ACGTcount: A:0.26, C:0.15, G:0.39, T:0.20


Consensus pattern (111 bp):   
GGAATGGTGGAACAAGTGGAGGTGGAGCCAAGACTTGGAATCAATCCAGTGCTGATCAAGGAGGC
CAATCCTCTAGTTGGAGCCAGGCTGGTGGCTGGAACAAAGAGGGGG
Done.