Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_456 ID=scaffold_456-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: 7036
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.28

Warning! 262 characters in sequence are not A, C, G, or T


Found at i:558 original size:14 final size:14

Alignment explanation


    Indices: 541--581  Score: 57
    Period size: 14  Copynumber: 2.9  Consensus size: 14

        531 ATTCATTCTT

                          
        541 TTTTATTTTTAAAA
          1 TTTTATTTTTAAAA

                 *        
        555 TTTTAATTTTAAAA
          1 TTTTATTTTTAAAA

                          
        569 -TTTATTTATTAAA
          1 TTTTATTT-TTAAA

        582 TTTATTGATG


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  13    6  0.25
  14   18  0.75

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (14 bp):   
TTTTATTTTTAAAA

Found at i:1268 original size:16 final size:16

Alignment explanation


    Indices: 1247--1283  Score: 58
    Period size: 16  Copynumber: 2.3  Consensus size: 16

       1237 TGGAAAGATG

                             
       1247 GAAAACT-GAAGGAGTA
          1 GAAAACTAGAAGGA-TA

                            
       1263 GAAAACTAGAAGGATA
          1 GAAAACTAGAAGGATA

                 
       1279 GAAAA
          1 GAAAA

       1284 TATAATTTTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  16   14  0.70
  17    6  0.30

ACGTcount: A:0.57, C:0.05, G:0.27, T:0.11


Consensus pattern (16 bp):   
GAAAACTAGAAGGATA

Found at i:5159 original size:3 final size:3

Alignment explanation


    Indices: 5151--5178  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       5141 TTATATTGAT

                                                 
       5151 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
          1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A

       5179 GTTATGAAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32


Consensus pattern (3 bp):   
ATC

Done.