Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_122 ID=scaffold_122-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: 12384
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33

Warning! 200 characters in sequence are not A, C, G, or T


Found at i:1472 original size:11 final size:11

Alignment explanation


    Indices: 1456--1480  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       1446 ATAATAATCA

                       
       1456 TTTATTTTTAT
          1 TTTATTTTTAT

                       
       1467 TTTATTTTTAT
          1 TTTATTTTTAT

               
       1478 TTT
          1 TTT

       1481 TGGTGATATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84


Consensus pattern (11 bp):   
TTTATTTTTAT

Found at i:2005 original size:18 final size:18

Alignment explanation


    Indices: 1961--2010  Score: 57
    Period size: 18  Copynumber: 2.8  Consensus size: 18

       1951 TCACCCATCC

                              *
       1961 AATATTAAATAATTAAAAT
          1 AATATTAAA-AATTAAAAA

            **                
       1980 TTTA-TAAAAATTAAAAA
          1 AATATTAAAAATTAAAAA

                          
       1997 AATATTAAAAATTA
          1 AATATTAAAAATTA

       2011 TAAACCAGTT


Statistics
Matches: 25,  Mismatches: 5, Indels: 3
        0.76            0.15        0.09

Matches are distributed among these distances:
  17   10  0.40
  18   13  0.52
  19    2  0.08

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (18 bp):   
AATATTAAAAATTAAAAA

Found at i:3290 original size:19 final size:20

Alignment explanation


    Indices: 3263--3310  Score: 55
    Period size: 19  Copynumber: 2.5  Consensus size: 20

       3253 GTTGGTAAAT

                *               
       3263 ACATGTGTA-ATAATAATAA
          1 ACATATGTATATAATAATAA

                      *        *
       3282 ACATATGTATTTAATAATAT
          1 ACATATGTATATAATAATAA

                      
       3302 A-ATATGTAT
          1 ACATATGTAT

       3311 TTCTTATTAA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  19   16  0.64
  20    9  0.36

ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40


Consensus pattern (20 bp):   
ACATATGTATATAATAATAA

Found at i:3311 original size:19 final size:20

Alignment explanation


    Indices: 3273--3312  Score: 64
    Period size: 19  Copynumber: 2.0  Consensus size: 20

       3263 ACATGTGTAA

                                
       3273 TAATAATAAACATATGTATT
          1 TAATAATAAACATATGTATT

                    *           
       3293 TAATAATATA-ATATGTATT
          1 TAATAATAAACATATGTATT

             
       3312 T
          1 T

       3313 CTTATTAATT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  19   10  0.53
  20    9  0.47

ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45


Consensus pattern (20 bp):   
TAATAATAAACATATGTATT
Done.