Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_404 ID=scaffold_404-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: 7610
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.36

Warning! 197 characters in sequence are not A, C, G, or T


Found at i:3461 original size:80 final size:80

Alignment explanation


    Indices: 3328--3490  Score: 326
    Period size: 80  Copynumber: 2.0  Consensus size: 80

       3318 ATGTGATATT

                                                                             
       3328 TCTGACTTTGTTGATTATAGAAATAGAGAGTTGATGAATTTTGTATCGAGATTATCTTAACATTG
          1 TCTGACTTTGTTGATTATAGAAATAGAGAGTTGATGAATTTTGTATCGAGATTATCTTAACATTG

                           
       3393 AAAAAGATGGAGTTA
         66 AAAAAGATGGAGTTA

                                                                             
       3408 TCTGACTTTGTTGATTATAGAAATAGAGAGTTGATGAATTTTGTATCGAGATTATCTTAACATTG
          1 TCTGACTTTGTTGATTATAGAAATAGAGAGTTGATGAATTTTGTATCGAGATTATCTTAACATTG

                           
       3473 AAAAAGATGGAGTTA
         66 AAAAAGATGGAGTTA

               
       3488 TCT
          1 TCT

       3491 AAAATATGGT


Statistics
Matches: 83,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  80   83  1.00

ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38


Consensus pattern (80 bp):   
TCTGACTTTGTTGATTATAGAAATAGAGAGTTGATGAATTTTGTATCGAGATTATCTTAACATTG
AAAAAGATGGAGTTA

Found at i:5864 original size:43 final size:42

Alignment explanation


    Indices: 5804--5960  Score: 169
    Period size: 43  Copynumber: 3.7  Consensus size: 42

       5794 TATGTATTTT

                     *           *                     
       5804 CGTGTAAGAACACGTCTGGGATGTTGGCATCGAATTGTGTATA
          1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTG-ATA

                        *         *         *        *
       5847 CGTGTAAGACCATGTCTGGGACATTGGCATCGTATT-TGATT
          1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTGATA

            *                                             
       5888 TGTGTAAGACC-CTGTCTGGGACAG-TGGCATC-AATATGTGATTA
          1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAAT-TGTGA-TA

             *                            
       5931 CATGTAAGACCACGTCTGGGACGTTGGCAT
          1 CGTGTAAGACCACGTCTGGGACGTTGGCAT

       5961 TGTATGAGCC


Statistics
Matches: 94,  Mismatches: 13, Indels: 14
        0.78            0.11        0.12

Matches are distributed among these distances:
  40    2  0.02
  41   29  0.31
  42    6  0.06
  43   56  0.60
  44    1  0.01

ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30


Consensus pattern (42 bp):   
CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTGATA

Done.