Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_703 ID=scaffold_703-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: 4576
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.35

Warning! 100 characters in sequence are not A, C, G, or T


Found at i:220 original size:24 final size:23

Alignment explanation


    Indices: 174--226  Score: 97
    Period size: 23  Copynumber: 2.3  Consensus size: 23

        164 AAAGAATTTC

                                   
        174 TTTTTTAAATTGTACTGGGAATT
          1 TTTTTTAAATTGTACTGGGAATT

                                 * 
        197 TTTTTTAAATTGTACTGGGAAAT
          1 TTTTTTAAATTGTACTGGGAATT

                   
        220 TTTTTTA
          1 TTTTTTA

        227 TTTTTTTCGT


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  23   29  1.00

ACGTcount: A:0.26, C:0.04, G:0.15, T:0.55


Consensus pattern (23 bp):   
TTTTTTAAATTGTACTGGGAATT

Found at i:425 original size:112 final size:112

Alignment explanation


    Indices: 220--430  Score: 309
    Period size: 112  Copynumber: 1.8  Consensus size: 112

        210 ACTGGGAAAT

                                *                                            
        220 TTTTTTATTTTTTTCGTATATTGATATCTGATTCTGACACGGAAAAAAAAAAAGAAATTTTTTTT
          1 TTTTTTATTTTTTTCGTATACTGATATCTGATTCTGACAC----AAAAAAAAAGAAATTTTTTTT

                            *                                  
        285 AAAATTGTACTGGGTGTCGGCCATTGACAGGCCAATACCTAAAAAAAATTG
         62 AAAATTGTACTGGGTGCCGGCCATTGACAGGCCAATACCTAAAAAAAATTG

                                       *                         *           
        336 TTTTTTATTTTTTTCGTATACTGATATTTGACTT-TGACAC-AAAAAAAAGAATTTGTTTTTTAA
          1 TTTTTTATTTTTTTCGTATACTGATATCTGA-TTCTGACACAAAAAAAAAGAAATT-TTTTTTAA

                              *             
        399 AATTGTACTGGGTGCCGGTCATTGACAGGCCA
         64 AATTGTACTGGGTGCCGGCCATTGACAGGCCA

        431 GCACCAAAAT


Statistics
Matches: 88,  Mismatches: 5, Indels: 8
        0.87            0.05        0.08

Matches are distributed among these distances:
 111   13  0.15
 112   38  0.43
 116   35  0.40
 117    2  0.02

ACGTcount: A:0.32, C:0.12, G:0.16, T:0.39


Consensus pattern (112 bp):   
TTTTTTATTTTTTTCGTATACTGATATCTGATTCTGACACAAAAAAAAAGAAATTTTTTTTAAAA
TTGTACTGGGTGCCGGCCATTGACAGGCCAATACCTAAAAAAAATTG

Found at i:1424 original size:24 final size:24

Alignment explanation


    Indices: 1397--1452  Score: 103
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       1387 TATTAAATAT

                                    
       1397 ATATATTTGATTAAAAATAAAAAA
          1 ATATATTTGATTAAAAATAAAAAA

                                   *
       1421 ATATATTTGATTAAAAATAAAAAT
          1 ATATATTTGATTAAAAATAAAAAA

                    
       1445 ATATATTT
          1 ATATATTT

       1453 AATATATAAT


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  24   31  1.00

ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39


Consensus pattern (24 bp):   
ATATATTTGATTAAAAATAAAAAA

Found at i:2643 original size:22 final size:24

Alignment explanation


    Indices: 2618--2662  Score: 67
    Period size: 22  Copynumber: 2.0  Consensus size: 24

       2608 TTTATACAAC

                                    
       2618 ATTATCAAT-AATAATA-TAATAT
          1 ATTATCAATAAATAATAGTAATAT

                   *               
       2640 ATTATCATTAAATAATAGTAATA
          1 ATTATCAATAAATAATAGTAATA

       2663 ATTTTATTTA


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

Matches are distributed among these distances:
  22    8  0.40
  23    7  0.35
  24    5  0.25

ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40


Consensus pattern (24 bp):   
ATTATCAATAAATAATAGTAATAT
Done.