Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00392.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: 4044
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29


Found at i:1000 original size:72 final size:75

Alignment explanation


    Indices: 914--1225  Score: 270
    Period size: 75  Copynumber: 4.3  Consensus size: 75

        904 ACTGAATTGC

                                       * *                *      *           
        914 CTACAAGTGCTAAAGAGATGGATAAGACTTTGGA-GA-T-GAACATTGAATTGTTACCAAAGCCT
          1 CTACAAGTGCTAAAGAGATGGATAAGAATATGGAGGAGTGGAACATCGAATTGATACCAAAGCCT

                      
        976 ATAGAAGATT
         66 ATAGAAGATT

                    *            * * *                *             *      * 
        986 CTACAAGTCCTAAAGAGATGGGTCATAATATGGAGGAGTGGAGCATCGAATTGATATCAAAGCTT
          1 CTACAAGTGCTAAAGAGATGGATAAGAATATGGAGGAGTGGAACATCGAATTGATACCAAAGCCT

              *       
       1051 ATGGAAGATT
         66 ATAGAAGATT

              *                    *                        *  * *          *
       1061 CTCCAAGTGCT-AA-AGA--GATCAG--TATGGAGGAG-GAGAACATCAAACTCATACCAAAGCT
          1 CTACAAGTGCTAAAGAGATGGATAAGAATATGGAGGAGTG-GAACATCGAATTGATACCAAAGCC

                       
       1119 TATAGAAGATT
         65 TATAGAAGATT

                               *    *       *             *          **      
       1130 CTACAAGTGCTAAAGAGATAGATATGAATATGAAGGAG-GAGAACGTTC-AATTGATGTCAAAGC
          1 CTACAAGTGCTAAAGAGATGGATAAGAATATGGAGGAGTG-GAAC-ATCGAATTGATACCAAAGC

            *           
       1193 TTATAGAAGATT
         64 CTATAGAAGATT

              *   *              
       1205 CTTCAAATGCTAAAGAGATGG
          1 CTACAAGTGCTAAAGAGATGG

       1226 GTAAAGATGT


Statistics
Matches: 195,  Mismatches: 34, Indels: 19
        0.79            0.14        0.08

Matches are distributed among these distances:
  68    1  0.01
  69   49  0.25
  70    2  0.01
  71    7  0.04
  72   28  0.14
  73    9  0.05
  74    3  0.02
  75   94  0.48
  76    2  0.01

ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24


Consensus pattern (75 bp):   
CTACAAGTGCTAAAGAGATGGATAAGAATATGGAGGAGTGGAACATCGAATTGATACCAAAGCCT
ATAGAAGATT

Found at i:1068 original size:75 final size:75

Alignment explanation


    Indices: 951--1227  Score: 284
    Period size: 75  Copynumber: 3.8  Consensus size: 75

        941 CTTTGGAGAT

                  *      *         *                   *                     
        951 GAACATTGAATTGTTACCAAAGCCTATAGAAGATTCTACAAGTCCTAAAGAGATGGGTCATAATA
          1 GAACATCGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTCATAATA

                       
       1016 TGGAGGAGTG-
         66 TGGAGGAG-GA

              *             *          *         *                        *  
       1026 GAGCATCGAATTGATATCAAAGCTTATGGAAGATTCTCCAAGTGCTAAAGAGA----TC--AGTA
          1 GAACATCGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTCATAATA

                      
       1085 TGGAGGAGGA
         66 TGGAGGAGGA

                   *  * *                                         * *        
       1095 GAACATCAAACTCATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATAGAT-ATGAAT
          1 GAACATCGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTCAT-AAT

               *       
       1159 ATGAAGGAGGA
         65 ATGGAGGAGGA

                 *          **                    *   *                
       1170 GAACGTTC-AATTGATGTCAAAGCTTATAGAAGATTCTTCAAATGCTAAAGAGATGGGT
          1 GAAC-ATCGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGT

       1228 AAAGATGTGG


Statistics
Matches: 166,  Mismatches: 27, Indels: 18
        0.79            0.13        0.09

Matches are distributed among these distances:
  68    1  0.01
  69   57  0.34
  71    2  0.01
  73    1  0.01
  75  103  0.62
  76    2  0.01

ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25


Consensus pattern (75 bp):   
GAACATCGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTCATAATA
TGGAGGAGGA

Done.