Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1036 ID=scaffold_1036-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, 824

Length: 1374
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39


Found at i:194 original size:27 final size:27

Alignment explanation


    Indices: 163--230  Score: 127
    Period size: 27  Copynumber: 2.5  Consensus size: 27

        153 ATATTTTGTT

                                       
        163 CACCATTGGCGCCTCCCAAATAGGCAC
          1 CACCATTGGCGCCTCCCAAATAGGCAC

                               *       
        190 CACCATTGGCGCCTCCCAAGTAGGCAC
          1 CACCATTGGCGCCTCCCAAATAGGCAC

                          
        217 CACCATTGGCGCCT
          1 CACCATTGGCGCCT

        231 TCTAGATAGG


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  27   40  1.00

ACGTcount: A:0.22, C:0.41, G:0.21, T:0.16


Consensus pattern (27 bp):   
CACCATTGGCGCCTCCCAAATAGGCAC

Found at i:439 original size:27 final size:29

Alignment explanation


    Indices: 378--440  Score: 69
    Period size: 30  Copynumber: 2.2  Consensus size: 29

        368 AACCTATTTT

                                      *    
        378 GGTAAATTTTTTTTTCTGACATACTATTTCA
          1 GGTAAATTTTTTTTTCT-A-ATACTAATTCA

                                *        
        409 -GTAAATTTTTTTTTCT-ATCCTAATT-A
          1 GGTAAATTTTTTTTTCTAATACTAATTCA

                  
        435 GGTAAA
          1 GGTAAA

        441 AAACCCTGGA


Statistics
Matches: 29,  Mismatches: 2, Indels: 6
        0.78            0.05        0.16

Matches are distributed among these distances:
  26    1  0.03
  27   12  0.41
  30   16  0.55

ACGTcount: A:0.29, C:0.11, G:0.10, T:0.51


Consensus pattern (29 bp):   
GGTAAATTTTTTTTTCTAATACTAATTCA

Found at i:741 original size:15 final size:15

Alignment explanation


    Indices: 709--751  Score: 63
    Period size: 14  Copynumber: 3.0  Consensus size: 15

        699 TATAACTTTT

                          *
        709 TTTTTATTTA-CAAC
          1 TTTTTATTTACCAAA

                           
        723 TTTTTATTTACCAAA
          1 TTTTTATTTACCAAA

                           
        738 -TTTTATTTACCAAA
          1 TTTTTATTTACCAAA

        752 ATATACCAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  14   24  0.89
  15    3  0.11

ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53


Consensus pattern (15 bp):   
TTTTTATTTACCAAA

Found at i:844 original size:27 final size:27

Alignment explanation


    Indices: 814--889  Score: 127
    Period size: 27  Copynumber: 2.9  Consensus size: 27

        804 GGCCAATCAC

                                       
        814 ATTGGCGGCACCAAAGGTGCCAATGTG
          1 ATTGGCGGCACCAAAGGTGCCAATGTG

                          *            
        841 ATTGGCGGCACCAATGGTGCCAATGTG
          1 ATTGGCGGCACCAAAGGTGCCAATGTG

                           *       
        868 ATTGGCGGCACC-AATGTGCCAA
          1 ATTGGCGGCACCAAAGGTGCCAA

        890 AGGACTAAAA


Statistics
Matches: 46,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  26    8  0.17
  27   38  0.83

ACGTcount: A:0.25, C:0.24, G:0.32, T:0.20


Consensus pattern (27 bp):   
ATTGGCGGCACCAAAGGTGCCAATGTG
Done.