Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1190

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: 29030
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:11765 original size:5 final size:5

Alignment explanation


    Indices: 11755--11786  Score: 64
    Period size: 5  Copynumber: 6.4  Consensus size: 5

      11745 TTTAAAGTTG

                                                  
      11755 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA AT
          1 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA AT

      11787 ATATGTGTTA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   27  1.00

ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41


Consensus pattern (5 bp):   
ATTGA

Found at i:22800 original size:77 final size:78

Alignment explanation


    Indices: 22707--22863  Score: 298
    Period size: 77  Copynumber: 2.0  Consensus size: 78

      22697 GTATTGGAAG

                                                                             
      22707 AAAGTATTAACAGAATTGTTATTTCTAAGATTTCCTATCA-TTGAAATGTCAGTACTTTGTTTTC
          1 AAAGTATTAACAGAATTGTTATTTCTAAGATTTCCTATCATTTGAAATGTCAGTACTTTGTTTTC

                         
      22771 AAAATTTGCTAAT
         66 AAAATTTGCTAAT

                                                         *                   
      22784 AAAGTATTAACAGAATTGTTATTTCTAAGATTTCCTATCATTTGAGATGTCAGTACTTTGTTTTC
          1 AAAGTATTAACAGAATTGTTATTTCTAAGATTTCCTATCATTTGAAATGTCAGTACTTTGTTTTC

                         
      22849 AAAATTTGCTAAT
         66 AAAATTTGCTAAT

              
      22862 AA
          1 AA

      22864 CTAAGACTGA


Statistics
Matches: 78,  Mismatches: 1, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
  77   40  0.51
  78   38  0.49

ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43


Consensus pattern (78 bp):   
AAAGTATTAACAGAATTGTTATTTCTAAGATTTCCTATCATTTGAAATGTCAGTACTTTGTTTTC
AAAATTTGCTAAT

Found at i:25451 original size:20 final size:21

Alignment explanation


    Indices: 25426--25470  Score: 58
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      25416 GTGAGAACTT

                                  
      25426 TAAAAT-AAAATAATG-AAAAA
          1 TAAAATGAAAATAA-GAAAAAA

                        *        
      25446 TAAAATGAAAATTAGAAAAAA
          1 TAAAATGAAAATAAGAAAAAA

                
      25467 TAAA
          1 TAAA

      25471 TTGGTTTCAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  20    7  0.32
  21   15  0.68

ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20


Consensus pattern (21 bp):   
TAAAATGAAAATAAGAAAAAA
Done.