Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold4016

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, 363

Length: 605
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.43


Found at i:549 original size:10 final size:9

Alignment explanation


    Indices: 531--599  Score: 50
    Period size: 9  Copynumber: 7.6  Consensus size: 9

        521 AGCGGGGTTC

                     
        531 TTTTTCTTT
          1 TTTTTCTTT

                      
        540 TTTTTAC-TT
          1 TTTTT-CTTT

               **    
        549 TTTCCCTTT
          1 TTTTTCTTT

                  *   
        558 TTTTGTTTTT
          1 TTTT-TCTTT

                 *   
        568 TTTTTGTTT
          1 TTTTTCTTT

                 *   
        577 TTTTTGTTT
          1 TTTTTCTTT

             * *     
        586 TCTCTCTTT
          1 TTTTTCTTT

                 
        595 TTTTT
          1 TTTTT

        600 TTGGAT


Statistics
Matches: 46,  Mismatches: 11, Indels: 6
        0.73            0.17        0.10

Matches are distributed among these distances:
   8    1  0.02
   9   37  0.80
  10    8  0.17

ACGTcount: A:0.01, C:0.12, G:0.04, T:0.83


Consensus pattern (9 bp):   
TTTTTCTTT

Found at i:569 original size:11 final size:11

Alignment explanation


    Indices: 555--581  Score: 54
    Period size: 11  Copynumber: 2.5  Consensus size: 11

        545 ACTTTTTCCC

                       
        555 TTTTTTTGTTT
          1 TTTTTTTGTTT

                       
        566 TTTTTTTGTTT
          1 TTTTTTTGTTT

                 
        577 TTTTT
          1 TTTTT

        582 GTTTTCTCTC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   16  1.00

ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93


Consensus pattern (11 bp):   
TTTTTTTGTTT

Found at i:570 original size:20 final size:20

Alignment explanation


    Indices: 547--586  Score: 53
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        537 TTTTTTTTAC

                                
        547 TTTTTCCCTTTTTTTGTTTT
          1 TTTTTCCCTTTTTTTGTTTT

                 ***            
        567 TTTTTTGTTTTTTTTGTTTT
          1 TTTTTCCCTTTTTTTGTTTT

        587 CTCTCTTTTT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85


Consensus pattern (20 bp):   
TTTTTCCCTTTTTTTGTTTT

Found at i:597 original size:20 final size:20

Alignment explanation


    Indices: 555--602  Score: 62
    Period size: 20  Copynumber: 2.4  Consensus size: 20

        545 ACTTTTTCCC

                         * *    
        555 TTTTTTTGTTTTTTTTTTGT
          1 TTTTTTTGTTTTTCTCTTGT

                                 
        575 TTTTTTTGTTTTCTCTCTT-T
          1 TTTTTTTGTTTT-TCTCTTGT

                    
        595 TTTTTTTG
          1 TTTTTTTG

        603 GAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  20   21  0.84
  21    4  0.16

ACGTcount: A:0.00, C:0.06, G:0.08, T:0.85


Consensus pattern (20 bp):   
TTTTTTTGTTTTTCTCTTGT
Done.