Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3201

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: 18765
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:458 original size:30 final size:30

Alignment explanation


    Indices: 422--494  Score: 146
    Period size: 30  Copynumber: 2.4  Consensus size: 30

        412 CTACCACGTT

                                          
        422 GATTTGAGACTACTGGTAGTCCTCCGTGTC
          1 GATTTGAGACTACTGGTAGTCCTCCGTGTC

                                          
        452 GATTTGAGACTACTGGTAGTCCTCCGTGTC
          1 GATTTGAGACTACTGGTAGTCCTCCGTGTC

                         
        482 GATTTGAGACTAC
          1 GATTTGAGACTAC

        495 CACGTTGCCG


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   43  1.00

ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33


Consensus pattern (30 bp):   
GATTTGAGACTACTGGTAGTCCTCCGTGTC

Found at i:8329 original size:20 final size:20

Alignment explanation


    Indices: 8306--8359  Score: 63
    Period size: 20  Copynumber: 2.7  Consensus size: 20

       8296 AGTTTTTCCC

                 *              
       8306 AGCTCGATTTAGCTCACATG
          1 AGCTCAATTTAGCTCACATG

                *          ***  
       8326 AGCTTAATTTAGCTCGTTTG
          1 AGCTCAATTTAGCTCACATG

                          
       8346 AGCTCAATTTAGCT
          1 AGCTCAATTTAGCT

       8360 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:8341 original size:30 final size:30

Alignment explanation


    Indices: 8306--8379  Score: 98
    Period size: 30  Copynumber: 2.5  Consensus size: 30

       8296 AGTTTTTCCC

                                            
       8306 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
          1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT

                               *      *   
       8336 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
          1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT

                          
       8366 AGCTCGTTTGAGCT
          1 AGCTCGTTTGAGCT

       8380 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:8369 original size:20 final size:20

Alignment explanation


    Indices: 8306--8370  Score: 53
    Period size: 20  Copynumber: 3.2  Consensus size: 20

       8296 AGTTTTTCCC

                 *        *  * *
       8306 AGCTCGATTTAGCTCACATG
          1 AGCTCAATTTAGCTTACTTT

                *                
       8326 AGCTTAATTTAGC-T-CGTTT
          1 AGCTCAATTTAGCTTAC-TTT

                                 
       8345 GAGCTCAATTTAGCTTACTTT
          1 -AGCTCAATTTAGCTTACTTT

                 
       8366 AGCTC
          1 AGCTC

       8371 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.