Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_123 ID=scaffold_123-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: 12057
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34


Found at i:1234 original size:25 final size:25

Alignment explanation


    Indices: 1192--1245  Score: 67
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       1182 TTTTCTCAAA

                    *                 
       1192 AATTTAATTAATATAAAATATTA-AT
          1 AATTTAATAAATATAAAA-ATTAGAT

                                      
       1217 AATTTAATAAAT-TGAAAAATTAGAT
          1 AATTTAATAAATAT-AAAAATTAGAT

                
       1242 AATT
          1 AATT

       1246 AAATTAAAAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
  24    5  0.19
  25   21  0.81

ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41


Consensus pattern (25 bp):   
AATTTAATAAATATAAAAATTAGAT

Found at i:1965 original size:30 final size:30

Alignment explanation


    Indices: 1908--1969  Score: 90
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       1898 GCTTTTTGAA

                                * *       
       1908 AATATTTACAAAAAGAGGCATCTAATTTTT
          1 AATATTTACAAAAAGAGGCAACAAATTTTT

                                           
       1938 AATATTTACAAAAAGA-GCAACAAAATTTTT
          1 AATATTTACAAAAAGAGGCAAC-AAATTTTT

              
       1968 AA
          1 AA

       1970 AAATAATTTA


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  29    4  0.14
  30   25  0.86

ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32


Consensus pattern (30 bp):   
AATATTTACAAAAAGAGGCAACAAATTTTT

Found at i:8033 original size:37 final size:37

Alignment explanation


    Indices: 7983--8059  Score: 154
    Period size: 37  Copynumber: 2.1  Consensus size: 37

       7973 AATTTCCTAA

                                                 
       7983 CTTATGAACATACTTACCTACCAAAATCCATTTATCT
          1 CTTATGAACATACTTACCTACCAAAATCCATTTATCT

                                                 
       8020 CTTATGAACATACTTACCTACCAAAATCCATTTATCT
          1 CTTATGAACATACTTACCTACCAAAATCCATTTATCT

               
       8057 CTT
          1 CTT

       8060 GACTATATCC


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  37   40  1.00

ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36


Consensus pattern (37 bp):   
CTTATGAACATACTTACCTACCAAAATCCATTTATCT
Done.