Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_527 ID=scaffold_527-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: 6019
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:190 original size:20 final size:20

Alignment explanation


    Indices: 167--230  Score: 69
    Period size: 20  Copynumber: 3.2  Consensus size: 20

        157 CAGCTCCTTT

                 *               
        167 AGCTCGTTTCAGCTCCAA-TC
          1 AGCTCATTTCAGCT-CAATTC

                     *          
        187 AGCTCATTTGAGCTCAATTC
          1 AGCTCATTTCAGCTCAATTC

                                *
        207 AGCTCA-TTCGAGCTCAATTT
          1 AGCTCATTTC-AGCTCAATTC

                
        227 AGCT
          1 AGCT

        231 TTCTTTCAGC


Statistics
Matches: 38,  Mismatches: 4, Indels: 4
        0.83            0.09        0.09

Matches are distributed among these distances:
  19    5  0.13
  20   33  0.87

ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33


Consensus pattern (20 bp):   
AGCTCATTTCAGCTCAATTC

Found at i:2638 original size:24 final size:24

Alignment explanation


    Indices: 2581--2661  Score: 81
    Period size: 24  Copynumber: 3.4  Consensus size: 24

       2571 CTTTTGTAAT

                           * *      
       2581 GAAATCGAAACAGCATGTGAAAAA
          1 GAAATCGAAACAGCAAGAGAAAAA

                **     *    *       
       2605 GAAAAAGAAACTGCAAAAGAAAAA
          1 GAAATCGAAACAGCAAGAGAAAAA

                      *  **         
       2629 GAAATCGAAAAAGTGAGAGAAAAA
          1 GAAATCGAAACAGCAAGAGAAAAA

                     
       2653 GAAATCGAA
          1 GAAATCGAA

       2662 GAAAATAAAA


Statistics
Matches: 44,  Mismatches: 13, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  24   44  1.00

ACGTcount: A:0.62, C:0.09, G:0.21, T:0.09


Consensus pattern (24 bp):   
GAAATCGAAACAGCAAGAGAAAAA

Found at i:2640 original size:18 final size:18

Alignment explanation


    Indices: 2598--2641  Score: 63
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       2588 AAACAGCATG

                              
       2598 TGAAAAAGAAAAAGAAAC
          1 TGAAAAAGAAAAAGAAAC

              *               
       2616 TGCAAAAGAAAAAGAAA-
          1 TGAAAAAGAAAAAGAAAC

                     
       2633 TCGAAAAAG
          1 T-GAAAAAG

       2642 TGAGAGAAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  17    1  0.04
  18   22  0.96

ACGTcount: A:0.68, C:0.07, G:0.18, T:0.07


Consensus pattern (18 bp):   
TGAAAAAGAAAAAGAAAC

Found at i:4858 original size:20 final size:21

Alignment explanation


    Indices: 4835--4898  Score: 71
    Period size: 20  Copynumber: 3.2  Consensus size: 21

       4825 CAGCTCCTTT

                 *   *           
       4835 AGCTCGTTTCAGCTCCAA-TC
          1 AGCTCATTTAAGCTCCAATTC

                                 
       4855 AGCTCATTTAAGCT-CAATTC
          1 AGCTCATTTAAGCTCCAATTC

                     *          *
       4875 AGCTCATTTGAGCT-CAATTT
          1 AGCTCATTTAAGCTCCAATTC

                
       4895 AGCT
          1 AGCT

       4899 TTCTTTCAGC


Statistics
Matches: 39,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  19    3  0.08
  20   36  0.92

ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34


Consensus pattern (21 bp):   
AGCTCATTTAAGCTCCAATTC
Done.