Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g00002.C1

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: 4872
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38


Found at i:2028 original size:116 final size:117

Alignment explanation


    Indices: 1871--2084  Score: 367
    Period size: 116  Copynumber: 1.8  Consensus size: 117

       1861 CTGTAATGTG

                                     *                               *       
       1871 TTTTATTTTATTTTTTCTGATTGTTTGTTTCCCTTTGTATTTAACGACATTTTCTTGTAAATATT
          1 TTTTATTTTATTTTTTCTGATTGTTAGTTTCCCTTTGTATTTAACGACATTTTCTTGCAAATATT

                                  *                             
       1936 TGAATAATTGAATCCCATTAATTAGATTTTATATTGCCTGTTATGTGTTTTA
         66 TGAATAATTGAATCCCATTAATGAGATTTTATATTGCCTGTTATGTGTTTTA

                                                                          *  
       1988 TTTTATTTTATTTTTT-TGATTGTTAGTTTCCCTTTGTATTTAACGACATTTTCTTGCAAATCTT
          1 TTTTATTTTATTTTTTCTGATTGTTAGTTTCCCTTTGTATTTAACGACATTTTCTTGCAAATATT

                 *                   *       
       2052 TGAATGATTGAATCCCATTAATGAGGTTTTATA
         66 TGAATAATTGAATCCCATTAATGAGATTTTATA

       2085 GCGAAGATAT


Statistics
Matches: 91,  Mismatches: 6, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
 116   75  0.82
 117   16  0.18

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


Consensus pattern (117 bp):   
TTTTATTTTATTTTTTCTGATTGTTAGTTTCCCTTTGTATTTAACGACATTTTCTTGCAAATATT
TGAATAATTGAATCCCATTAATGAGATTTTATATTGCCTGTTATGTGTTTTA

Found at i:2228 original size:42 final size:42

Alignment explanation


    Indices: 2182--2275  Score: 120
    Period size: 42  Copynumber: 2.3  Consensus size: 42

       2172 GTAAATACCG

                            *        *         *       
       2182 CTCATATCCCAC-CTTGGAATAATCTATTCCAGGGTTATCCCT
          1 CTCATATCCCACTCTTAGAATAATCAATTCC-GGGATATCCCT

                 *                                    
       2224 CTCATTTCCC-CTCTTAGAATAATCAATTCCGGGATATCCCT
          1 CTCATATCCCACTCTTAGAATAATCAATTCCGGGATATCCCT

              *        
       2265 CTGATATCCCA
          1 CTCATATCCCA

       2276 TCCCGGTTCG


Statistics
Matches: 44,  Mismatches: 6, Indels: 4
        0.81            0.11        0.07

Matches are distributed among these distances:
  41   19  0.43
  42   25  0.57

ACGTcount: A:0.24, C:0.32, G:0.11, T:0.33


Consensus pattern (42 bp):   
CTCATATCCCACTCTTAGAATAATCAATTCCGGGATATCCCT

Found at i:2415 original size:16 final size:16

Alignment explanation


    Indices: 2396--2449  Score: 74
    Period size: 16  Copynumber: 3.4  Consensus size: 16

       2386 CATTCCGAGG

                            
       2396 ATATCCCGGCTTAGGT
          1 ATATCCCGGCTTAGGT

                    **      
       2412 ATATCCCGAATTAGG-
          1 ATATCCCGGCTTAGGT

               *            
       2427 ATAGCCCGGCTTAGGT
          1 ATATCCCGGCTTAGGT

                   
       2443 ATATCCC
          1 ATATCCC

       2450 ACTTGCGGAT


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

Found at i:2460 original size:31 final size:31

Alignment explanation


    Indices: 2393--2475  Score: 105
    Period size: 31  Copynumber: 2.7  Consensus size: 31

       2383 TCCCATTCCG

                                           
       2393 AGGATATCCCGGCTTAGGTATATCCCGAATT
          1 AGGATATCCCGGCTTAGGTATATCCCGAATT

                  *                     *  
       2424 AGGATAGCCCGGCTTAGGTATATCCC-ACTT
          1 AGGATATCCCGGCTTAGGTATATCCCGAATT

             *           *  *     
       2454 GCGGATATCCCGGTTTCGGTAT
          1 -AGGATATCCCGGCTTAGGTAT

       2476 TAATTACCAT


Statistics
Matches: 45,  Mismatches: 6, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  30    3  0.07
  31   42  0.93

ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29


Consensus pattern (31 bp):   
AGGATATCCCGGCTTAGGTATATCCCGAATT
Done.