Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_612 ID=scaffold_612-JGI_221_v2.0

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: 5249
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32


Found at i:856 original size:180 final size:180

Alignment explanation


    Indices: 554--906  Score: 652
    Period size: 180  Copynumber: 2.0  Consensus size: 180

        544 TGCATGTTCC

                                 *                                           
        554 CTTCAGGCCACAATCTCCATTGTCCCCTCATGAAGTAAGATTTCATTCCTCTTCTACCATCCTCA
          1 CTTCAGGCCACAATCTCCATTATCCCCTCATGAAGTAAGATTTCATTCCTCTTCTACCATCCTCA

                    *                                                        
        619 ACAAGTCTGAAAATAGGCTACAATCTATGTCATCTTTAAAGTCATGAGATCCCTCTAAACACAGA
         66 ACAAGTCTAAAAATAGGCTACAATCTATGTCATCTTTAAAGTCATGAGATCCCTCTAAACACAGA

                                     *      *                 
        684 TCCCACTCAAAAGGAACTTCTGAGTTCGTAACTGCATCACTCAAAAGGAA
        131 TCCCACTCAAAAGGAACTTCTGAGTCCGTAACAGCATCACTCAAAAGGAA

                                                              *              
        734 CTTCAGGCCACAATCTCCATTATCCCCTCATGAAGTAAGATTTCATTCCTGTTCTACCATCCTCA
          1 CTTCAGGCCACAATCTCCATTATCCCCTCATGAAGTAAGATTTCATTCCTCTTCTACCATCCTCA

                                                                             
        799 ACAAGTCTAAAAATAGGCTACAATCTATGTCATCTTTAAAGTCATGAGATCCCTCTAAACACAGA
         66 ACAAGTCTAAAAATAGGCTACAATCTATGTCATCTTTAAAGTCATGAGATCCCTCTAAACACAGA

                                                 *     
        864 TCCCACTCAAAAGGAACTTCTGAGTCCGTAACAGCATTACTCA
        131 TCCCACTCAAAAGGAACTTCTGAGTCCGTAACAGCATCACTCA

        907 TGTCATTGAT


Statistics
Matches: 167,  Mismatches: 6, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 180  167  1.00

ACGTcount: A:0.32, C:0.28, G:0.12, T:0.27


Consensus pattern (180 bp):   
CTTCAGGCCACAATCTCCATTATCCCCTCATGAAGTAAGATTTCATTCCTCTTCTACCATCCTCA
ACAAGTCTAAAAATAGGCTACAATCTATGTCATCTTTAAAGTCATGAGATCCCTCTAAACACAGA
TCCCACTCAAAAGGAACTTCTGAGTCCGTAACAGCATCACTCAAAAGGAA

Found at i:5011 original size:98 final size:98

Alignment explanation


    Indices: 4837--5033  Score: 340
    Period size: 98  Copynumber: 2.0  Consensus size: 98

       4827 GTACAATAAA

                                                                         *   
       4837 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
          1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT

                  *           *              
       4902 CCTCTAGAATCCCAAACTTGGAATATTTCCTTT
         66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT

                             *  *                                            
       4935 ACTTTAAAAGAACATCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
          1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT

               *                             
       5000 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
         66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT

             
       5033 A
          1 A

       5034 TTATTTTTAA


Statistics
Matches: 93,  Mismatches: 6, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  98   93  1.00

ACGTcount: A:0.37, C:0.25, G:0.11, T:0.28


Consensus pattern (98 bp):   
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Done.