Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_547 ID=scaffold_547-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: 6357
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.29

Warning! 493 characters in sequence are not A, C, G, or T


Found at i:3173 original size:50 final size:50

Alignment explanation


    Indices: 2839--3173  Score: 424
    Period size: 50  Copynumber: 6.6  Consensus size: 50

       2829 CGATCTCGTA

                                     * *      *   *       *    
       2839 TAAGACCATGTCTGGGACATGGCATCGACATCGATATGTGA-G--CTAGTG
          1 TAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCA-TG

                                                                    
       2887 TAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATG
          1 TAAGACCATGTCTGGGACATGGCATTGGCATC---GAG---ATGAGAGGTCCCATG

                             *            *                  *
       2943 TAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAGGTCCCATA
          1 TAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCATG

                                   *      *        *          
       2993 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAAAGGTCCCATG
          1 TAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCATG

                                   *      * *                 
       3043 TAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTCCCATG
          1 TAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCATG

                       *        *  *                          
       3093 TAAGACCATGTTTGGGACATAGCGTTGGCATCGAGATGAGAGGTCCCATG
          1 TAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCATG

                                   *       
       3143 TAAGACCATGTCTGGGACATGGCTTTGGCAT
          1 TAAGACCATGTCTGGGACATGGCATTGGCAT

       3174 GTTATTATCA


Statistics
Matches: 257,  Mismatches: 21, Indels: 16
        0.87            0.07        0.05

Matches are distributed among these distances:
  48   30  0.12
  50  182  0.71
  51    2  0.01
  53    3  0.01
  54    5  0.02
  55    1  0.00
  56   32  0.12
  57    2  0.01

ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24


Consensus pattern (50 bp):   
TAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCATG

Found at i:4696 original size:23 final size:23

Alignment explanation


    Indices: 4662--4707  Score: 83
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       4652 GGGAGAGAAA

                   *               
       4662 TGTAATATCCCGAAAATTACTAC
          1 TGTAATACCCCGAAAATTACTAC

                                   
       4685 TGTAATACCCCGAAAATTACTAC
          1 TGTAATACCCCGAAAATTACTAC

       4708 AATAAGAAAG


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28


Consensus pattern (23 bp):   
TGTAATACCCCGAAAATTACTAC

Done.