Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03604.N1

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: 5412
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:265 original size:13 final size:14

Alignment explanation


    Indices: 247--275  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

        237 ACTTTTGCTC

                          
        247 AAAAAAAAAA-CAA
          1 AAAAAAAAAACCAA

                          
        260 AAAAAAAAAACCAA
          1 AAAAAAAAAACCAA

              
        274 AA
          1 AA

        276 CCTTCAAATC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   10  0.67
  14    5  0.33

ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00


Consensus pattern (14 bp):   
AAAAAAAAAACCAA

Found at i:4108 original size:162 final size:162

Alignment explanation


    Indices: 3832--4178  Score: 577
    Period size: 162  Copynumber: 2.1  Consensus size: 162

       3822 TGTGCCCAAT

                       *         * *                       *                *
       3832 TTGCAAACTCTAAAGATAGAGTGTTGCTTTGGAATGGAAGAAATAATTCAAGACTCACAAGTATT
          1 TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC

                                        *                                    
       3897 AACCATAAGCTTCCAATGCCTAAGGGAATTACAAGTCACAAAATGCAATAAATTGAAATTTCTCT
         66 AACCATAAGCTTCCAATGCCTAAGGGAAGTACAAGTCACAAAATGCAATAAATTGAAATTTCTCT

                                      *     
       3962 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
        131 TCCCAATGTGTGTTGCTAATAGTCTTCGGAAA

                           *                      *                          
       3994 TTGCAAACTCTGAAGGTAGAGAGGTGCTTTGGAATGGATGAAATAATCCAAGACTCACAAGTATC
          1 TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC

                                                    * *        *             
       4059 AACCATAAGCTTCCAATGCCTAAGGGAAGTACAAGTCACACACTGCAATAATTTGAAATTTCTCT
         66 AACCATAAGCTTCCAATGCCTAAGGGAAGTACAAGTCACAAAATGCAATAAATTGAAATTTCTCT

                                         *  
       4124 TCCCAATGTGTGTTGCTAATAGTCTTCGGCAA
        131 TCCCAATGTGTGTTGCTAATAGTCTTCGGAAA

                                   
       4156 TTGCAAACTCTGAAGATAGAGAG
          1 TTGCAAACTCTGAAGATAGAGAG

       4179 CTGTTCCCAA


Statistics
Matches: 171,  Mismatches: 14, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
 162  171  1.00

ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28


Consensus pattern (162 bp):   
TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC
AACCATAAGCTTCCAATGCCTAAGGGAAGTACAAGTCACAAAATGCAATAAATTGAAATTTCTCT
TCCCAATGTGTGTTGCTAATAGTCTTCGGAAA

Found at i:5343 original size:24 final size:23

Alignment explanation


    Indices: 5274--5344  Score: 63
    Period size: 24  Copynumber: 3.0  Consensus size: 23

       5264 TAATTCTAAT

                            *       
       5274 ATTACAGAAGATAAATTTAAAAAC
          1 ATTACAGAAG-TAAATATAAAAAC

              *   *     *            
       5298 ATCA-ATAATGTTAATATGAAAAAC
          1 ATTACAGAA-GTAAATAT-AAAAAC

                                   
       5322 ATTACAGAACGTAAATATAAAAA
          1 ATTACAGAA-GTAAATATAAAAA

       5345 TTTTGTTTCT


Statistics
Matches: 36,  Mismatches: 8, Indels: 6
        0.72            0.16        0.12

Matches are distributed among these distances:
  23    8  0.22
  24   18  0.50
  25   10  0.28

ACGTcount: A:0.58, C:0.08, G:0.08, T:0.25


Consensus pattern (23 bp):   
ATTACAGAAGTAAATATAAAAAC
Done.