Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_531 ID=scaffold_531-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: 6005
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36


Found at i:2081 original size:23 final size:25

Alignment explanation


    Indices: 2048--2111  Score: 78
    Period size: 25  Copynumber: 2.6  Consensus size: 25

       2038 TCATAATTTA

                                  *  
       2048 TTTTTTAAAATTATAAA-A-ACTAT
          1 TTTTTTAAAATTATAAATATACGAT

                  *                  
       2071 TTTTTTGAAATTATAAATATACGAT
          1 TTTTTTAAAATTATAAATATACGAT

                  *    *    
       2096 TTTTTTTAAATCATAA
          1 TTTTTTAAAATTATAA

       2112 TTTTTTTAAG


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  23   16  0.46
  24    1  0.03
  25   18  0.51

ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50


Consensus pattern (25 bp):   
TTTTTTAAAATTATAAATATACGAT

Found at i:2668 original size:18 final size:19

Alignment explanation


    Indices: 2645--2680  Score: 56
    Period size: 18  Copynumber: 1.9  Consensus size: 19

       2635 GGTCGTCCCA

                               
       2645 ATTCATTTAT-ATCTAGAC
          1 ATTCATTTATGATCTAGAC

                    *         
       2663 ATTCATTTGTGATCTAGA
          1 ATTCATTTATGATCTAGA

       2681 TTCATTACTC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    9  0.56
  19    7  0.44

ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44


Consensus pattern (19 bp):   
ATTCATTTATGATCTAGAC

Found at i:4722 original size:31 final size:32

Alignment explanation


    Indices: 4687--4755  Score: 97
    Period size: 31  Copynumber: 2.2  Consensus size: 32

       4677 GTGGGTGACC

                          *             *   
       4687 AAAATGAAAA-TGATTTTTAATGGCAATGCCT
          1 AAAATGAAAAGTGAGTTTTAATGGCAATACCT

                         *                  
       4718 AAAAT-AAAAGTGGGTTTTAATGGCAATACCT
          1 AAAATGAAAAGTGAGTTTTAATGGCAATACCT

                   
       4749 AAAATGA
          1 AAAATGA

       4756 TTTTTTCTTT


Statistics
Matches: 33,  Mismatches: 3, Indels: 3
        0.85            0.08        0.08

Matches are distributed among these distances:
  30    4  0.12
  31   28  0.85
  32    1  0.03

ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29


Consensus pattern (32 bp):   
AAAATGAAAAGTGAGTTTTAATGGCAATACCT
Done.