Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00001.N2

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: 9959
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.41


Found at i:1754 original size:31 final size:31

Alignment explanation


    Indices: 1718--1780  Score: 126
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       1708 TTCCTTATTT

                                           
       1718 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
          1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

                                           
       1749 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
          1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

             
       1780 C
          1 C

       1781 TTCTCGTACT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.06, C:0.33, G:0.03, T:0.57


Consensus pattern (31 bp):   
CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

Found at i:5309 original size:116 final size:116

Alignment explanation


    Indices: 5099--5311  Score: 356
    Period size: 116  Copynumber: 1.8  Consensus size: 116

       5089 CTGTAATGTG

                                     *                              *        
       5099 TTTTATTTTATTTTTTCTGATTGTTTGTTTCCCTTTGTATTTAACGACATTTTCTGTAAATATTT
          1 TTTTATTTTATTTTTTCTGATTGTTAGTTTCCCTTTGTATTTAACGACATTTTCTGCAAATATTT

                                 *                             
       5164 GAATAATTGAATCCCATTAATTAGATTTTATATTGCCTGTTATGTGTTTTA
         66 GAATAATTGAATCCCATTAATGAGATTTTATATTGCCTGTTATGTGTTTTA

                                                                          *  
       5215 TTTTATTTTATTTTTT-TGATTGTTAGTTTCCCTTTGTATTTAACGACATTTTCTTGCAAATCTT
          1 TTTTATTTTATTTTTTCTGATTGTTAGTTTCCCTTTGTATTTAACGACATTTTC-TGCAAATATT

                 *                   *       
       5279 TGAATGATTGAATCCCATTAATGAGGTTTTATA
         65 TGAATAATTGAATCCCATTAATGAGATTTTATA

       5312 GCGAAGATAT


Statistics
Matches: 90,  Mismatches: 6, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
 115   36  0.40
 116   54  0.60

ACGTcount: A:0.23, C:0.11, G:0.12, T:0.54


Consensus pattern (116 bp):   
TTTTATTTTATTTTTTCTGATTGTTAGTTTCCCTTTGTATTTAACGACATTTTCTGCAAATATTT
GAATAATTGAATCCCATTAATGAGATTTTATATTGCCTGTTATGTGTTTTA

Found at i:5454 original size:41 final size:40

Alignment explanation


    Indices: 5409--5501  Score: 114
    Period size: 41  Copynumber: 2.3  Consensus size: 40

       5399 GTAAATACCG

                          *        *         *       
       5409 CTCATATCCCACTTGGAATAATCTATTCCAGGGTTATCCCT
          1 CTCATATCCCACTTAGAATAATCAATTCC-GGGATATCCCT

                 *     *                             
       5450 CTCATTTCCCCTCTTAGAATAATCAATTCCGGGATATCCCT
          1 CTCATAT-CCCACTTAGAATAATCAATTCCGGGATATCCCT

              *        
       5491 CTGATATCCCA
          1 CTCATATCCCA

       5502 TCCCGGTTCG


Statistics
Matches: 43,  Mismatches: 8, Indels: 3
        0.80            0.15        0.06

Matches are distributed among these distances:
  40    3  0.07
  41   21  0.49
  42   19  0.44

ACGTcount: A:0.25, C:0.31, G:0.11, T:0.33


Consensus pattern (40 bp):   
CTCATATCCCACTTAGAATAATCAATTCCGGGATATCCCT

Found at i:5641 original size:16 final size:16

Alignment explanation


    Indices: 5622--5675  Score: 74
    Period size: 16  Copynumber: 3.4  Consensus size: 16

       5612 CATTCCGAGG

                            
       5622 ATATCCCGGCTTAGGT
          1 ATATCCCGGCTTAGGT

                    **      
       5638 ATATCCCGAATTAGG-
          1 ATATCCCGGCTTAGGT

               *            
       5653 ATAGCCCGGCTTAGGT
          1 ATATCCCGGCTTAGGT

                   
       5669 ATATCCC
          1 ATATCCC

       5676 ACTCTGCGGA


Statistics
Matches: 31,  Mismatches: 6, Indels: 2
        0.79            0.15        0.05

Matches are distributed among these distances:
  15   12  0.39
  16   19  0.61

ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28


Consensus pattern (16 bp):   
ATATCCCGGCTTAGGT

Done.