Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_681 ID=scaffold_681-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: 4666
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40


Found at i:613 original size:23 final size:24

Alignment explanation


    Indices: 587--632  Score: 67
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        577 TATCCACAAT

                      *             
        587 AAAA-TTATATTTTAATTTTCCCA
          1 AAAATTTATAATTTAATTTTCCCA

                           *       
        610 AAAATTTATAATTTACTTTTCCC
          1 AAAATTTATAATTTAATTTTCCC

        633 TTCAATTAAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  23    4  0.20
  24   16  0.80

ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48


Consensus pattern (24 bp):   
AAAATTTATAATTTAATTTTCCCA

Found at i:1278 original size:16 final size:18

Alignment explanation


    Indices: 1246--1290  Score: 60
    Period size: 16  Copynumber: 2.7  Consensus size: 18

       1236 CTATAACATT

                              
       1246 GTTTCATTTT-TTATTA-
          1 GTTTCATTTTATTATTAG

                              
       1262 GTTTCATTTTATT-TTAG
          1 GTTTCATTTTATTATTAG

                *       
       1279 GTTTTATTTTAT
          1 GTTTCATTTTAT

       1291 GTATCTTTAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  16   13  0.50
  17   13  0.50

ACGTcount: A:0.18, C:0.04, G:0.09, T:0.69


Consensus pattern (18 bp):   
GTTTCATTTTATTATTAG
Done.