Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_906 ID=scaffold_906-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: 4479
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.19

Warning! 1955 characters in sequence are not A, C, G, or T


Found at i:3941 original size:20 final size:20

Alignment explanation


    Indices: 3918--3971  Score: 63
    Period size: 20  Copynumber: 2.7  Consensus size: 20

       3908 AGTTTTTCCC

                 *              
       3918 AGCTCGATTTAGCTCACATG
          1 AGCTCAATTTAGCTCACATG

                *          ***  
       3938 AGCTTAATTTAGCTCGTTTG
          1 AGCTCAATTTAGCTCACATG

                          
       3958 AGCTCAATTTAGCT
          1 AGCTCAATTTAGCT

       3972 TACTTTAGCT


Statistics
Matches: 28,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  20   28  1.00

ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37


Consensus pattern (20 bp):   
AGCTCAATTTAGCTCACATG

Found at i:3953 original size:30 final size:30

Alignment explanation


    Indices: 3918--3991  Score: 98
    Period size: 30  Copynumber: 2.5  Consensus size: 30

       3908 AGTTTTTCCC

                                            
       3918 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
          1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT

                               *      *   
       3948 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
          1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT

                          
       3978 AGCTCGTTTGAGCT
          1 AGCTCGTTTGAGCT

       3992 TGGCTTAAGT


Statistics
Matches: 40,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  29    4  0.10
  30   36  0.90

ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39


Consensus pattern (30 bp):   
AGCTCGTTTGAGCTCAATTGAGCTTAATTT

Found at i:3981 original size:20 final size:20

Alignment explanation


    Indices: 3918--3982  Score: 53
    Period size: 20  Copynumber: 3.2  Consensus size: 20

       3908 AGTTTTTCCC

                 *        *  * *
       3918 AGCTCGATTTAGCTCACATG
          1 AGCTCAATTTAGCTTACTTT

                *                
       3938 AGCTTAATTTAGC-T-CGTTT
          1 AGCTCAATTTAGCTTAC-TTT

                                 
       3957 GAGCTCAATTTAGCTTACTTT
          1 -AGCTCAATTTAGCTTACTTT

                 
       3978 AGCTC
          1 AGCTC

       3983 GTTTGAGCTT


Statistics
Matches: 35,  Mismatches: 6, Indels: 8
        0.71            0.12        0.16

Matches are distributed among these distances:
  18    1  0.03
  19    1  0.03
  20   28  0.80
  21    4  0.11
  22    1  0.03

ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38


Consensus pattern (20 bp):   
AGCTCAATTTAGCTTACTTT
Done.