Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gorai.010G018000.2-JGI_221_v2.1

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, 739

Length: 1233
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:56 original size:31 final size:30

Alignment explanation


    Indices: 12--105  Score: 110
    Period size: 30  Copynumber: 3.3  Consensus size: 30

          2 GGTAAACTAA

                                          
         12 TAAAA-AAGGGACTAAATTTATAAGTTGAG
          1 TAAAATAAGGGACTAAATTTATAAGTTGAG

               *                      *     
         41 TAAGATACAGGGACT-AA-TTATAAAATT---
          1 TAAAATA-AGGGACTAAATTTAT-AAGTTGAG

                                          
         68 TAAAATAAGGGACTAAATTTATAAGTTGAG
          1 TAAAATAAGGGACTAAATTTATAAGTTGAG

                    
         98 TAAAATAA
          1 TAAAATAA

        106 AGATACTAAT


Statistics
Matches: 53,  Mismatches: 4, Indels: 15
        0.74            0.06        0.21

Matches are distributed among these distances:
  26    7  0.13
  27   12  0.23
  28    4  0.08
  29    8  0.15
  30   15  0.28
  31    7  0.13

ACGTcount: A:0.50, C:0.04, G:0.17, T:0.29


Consensus pattern (30 bp):   
TAAAATAAGGGACTAAATTTATAAGTTGAG

Found at i:114 original size:57 final size:56

Alignment explanation


    Indices: 12--121  Score: 175
    Period size: 57  Copynumber: 1.9  Consensus size: 56

          2 GGTAAACTAA

                                            *   *  *                
         12 TAAAAAAGGGACTAAATTTATAAGTTGAGTAAGATACAGGGACTAATTATAAAATT
          1 TAAAAAAGGGACTAAATTTATAAGTTGAGTAAAATAAAGAGACTAATTATAAAATT

                                                     *            
         68 TAAAATAAGGGACTAAATTTATAAGTTGAGTAAAATAAAGATACTAATTATAAA
          1 TAAAA-AAGGGACTAAATTTATAAGTTGAGTAAAATAAAGAGACTAATTATAAA

        122 GTTTGACCAG


Statistics
Matches: 49,  Mismatches: 4, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  56    5  0.10
  57   44  0.90

ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29


Consensus pattern (56 bp):   
TAAAAAAGGGACTAAATTTATAAGTTGAGTAAAATAAAGAGACTAATTATAAAATT

Found at i:528 original size:20 final size:19

Alignment explanation


    Indices: 500--560  Score: 70
    Period size: 20  Copynumber: 3.1  Consensus size: 19

        490 GAGCATATTG

                                
        500 ATGGCGAATTTTGACGGAAA
          1 ATGG-GAATTTTGACGGAAA

                          *     
        520 ATGGTGAATTTTGATGGAAA
          1 ATGG-GAATTTTGACGGAAA

               *                
        540 ATACGG-ATTTTGACGGAAA
          1 AT-GGGAATTTTGACGGAAA

              
        559 AT
          1 AT

        561 ACTTAAAAAC


Statistics
Matches: 36,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  19   14  0.39
  20   21  0.58
  21    1  0.03

ACGTcount: A:0.36, C:0.07, G:0.28, T:0.30


Consensus pattern (19 bp):   
ATGGGAATTTTGACGGAAA
Done.