Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00871.N3

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: 2152
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30


Found at i:1883 original size:20 final size:21

Alignment explanation


    Indices: 1845--1884  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       1835 ATGTCATATC

                                 
       1845 AGTATTCTTATTCTGAATTTT
          1 AGTATTCTTATTCTGAATTTT

                                 
       1866 AGTATT-TTAATT-TGAATTT
          1 AGTATTCTT-ATTCTGAATTT

       1885 AATTTTTTTC


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  20    9  0.50
  21    9  0.50

ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57


Consensus pattern (21 bp):   
AGTATTCTTATTCTGAATTTT

Found at i:1988 original size:269 final size:269

Alignment explanation


    Indices: 1509--1994  Score: 753
    Period size: 269  Copynumber: 1.8  Consensus size: 269

       1499 ATTAAGAGGG

                                                          *                  
       1509 GAAAGGATTGTATGAAACAGTGACGCCACGTCATCTGTATCCCTTTTCAATAGTTTTATGTCATA
          1 GAAAGGATTGTATGAAACAGTGACGCCACGTCATCTGTATCCCTTTCCAATAGTTTTATGTCATA

                                                                             
       1574 TCAATATTCTTATCCAGAATTTCAAGATTTTATCCTGAAAAAAATCAAATTCAAATTAAAATCCT
         66 TCAATATTCTTATCCAGAATTTCAAGATTTTATCCTGAAAAAAATCAAATTCAAATTAAAATCCT

                                        *                                    
       1639 GAAATTCAGGATAAGAATACTGATGTGGTATAAAACTATTGGAAAGGGATACAGATGACGTGGCG
        131 GAAATTCAGGATAAGAATACTGATGTGGCATAAAACTATTGGAAAGGGATACAGATGACGTGGCG

                                                                             
       1704 TCACTGTTTCATACAATCCTTTTTCCAATTAAGAGATTGTTGAGGCGTGAATAAACTATATATAT
        196 TCACTGTTTCATACAATCCTTTTTCCAATTAAGAGATTGTTGAGGCGTGAATAAACTATATATAT

                     
       1769 ATCAGGGGA
        261 ATCAGGGGA

                       *     *                                               
       1778 GAAAGGATTGTGTGAAATAGTGACGCCACGTCATCTGTATCCCTTTCCAATAGTTTTATGTCATA
          1 GAAAGGATTGTATGAAACAGTGACGCCACGTCATCTGTATCCCTTTCCAATAGTTTTATGTCATA

               *         * *       *            *    ***   ****     *        
       1843 TCAGTATTCTTATTCTGAATTT-TAGTATTTTAAT-TTGAATTTAATTTTTTTCAGGA-TAAAAT
         66 TCAATATTCTTATCCAGAATTTCAAG-ATTTT-ATCCTGAAAAAAATCAAATTCA-AATTAAAAT

            *                                                                
       1905 TCTGAAATTCAGGATAAGAATACTGATGTGGCATAAAACTATTGGAAAGGGATACAGATGACGTG
        128 CCTGAAATTCAGGATAAGAATACTGATGTGGCATAAAACTATTGGAAAGGGATACAGATGACGTG

             *                       
       1970 GTGTCACTGTTTCATACAATCCTTT
        193 GCGTCACTGTTTCATACAATCCTTT

       1995 CCTTATATCA


Statistics
Matches: 195,  Mismatches: 19, Indels: 6
        0.89            0.09        0.03

Matches are distributed among these distances:
 268    2  0.01
 269  190  0.97
 270    3  0.02

ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35


Consensus pattern (269 bp):   
GAAAGGATTGTATGAAACAGTGACGCCACGTCATCTGTATCCCTTTCCAATAGTTTTATGTCATA
TCAATATTCTTATCCAGAATTTCAAGATTTTATCCTGAAAAAAATCAAATTCAAATTAAAATCCT
GAAATTCAGGATAAGAATACTGATGTGGCATAAAACTATTGGAAAGGGATACAGATGACGTGGCG
TCACTGTTTCATACAATCCTTTTTCCAATTAAGAGATTGTTGAGGCGTGAATAAACTATATATAT
ATCAGGGGA
Done.