Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1498

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: 33458
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:22140 original size:21 final size:23

Alignment explanation


    Indices: 22095--22141  Score: 62
    Period size: 23  Copynumber: 2.1  Consensus size: 23

      22085 TCACCTGCAA

                           *  *    
      22095 TAAACACATTAAAATGAGTTTAT
          1 TAAACACATTAAAATCAGCTTAT

                                   
      22118 TAAACACATTAAAA-CA-CTTAT
          1 TAAACACATTAAAATCAGCTTAT

               
      22139 TAA
          1 TAA

      22142 TCATAACACA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21    7  0.32
  22    1  0.05
  23   14  0.64

ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32


Consensus pattern (23 bp):   
TAAACACATTAAAATCAGCTTAT

Found at i:27498 original size:14 final size:14

Alignment explanation


    Indices: 27479--27531  Score: 88
    Period size: 14  Copynumber: 3.6  Consensus size: 14

      27469 TAGCTTCTTC

                            
      27479 TTTTTTTCACGAATTT
          1 TTTTTTTCACGAA--T

                          
      27495 TTTTTTTCACGAAT
          1 TTTTTTTCACGAAT

                          
      27509 TTTTTTTCACGAAT
          1 TTTTTTTCACGAAT

                     
      27523 TTTTTTTCA
          1 TTTTTTTCA

      27532 ACTTGATATC


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  14   24  0.65
  16   13  0.35

ACGTcount: A:0.19, C:0.13, G:0.06, T:0.62


Consensus pattern (14 bp):   
TTTTTTTCACGAAT

Found at i:27500 original size:16 final size:16

Alignment explanation


    Indices: 27479--27529  Score: 88
    Period size: 16  Copynumber: 3.3  Consensus size: 16

      27469 TAGCTTCTTC

                            
      27479 TTTTTTTCACGAATTT
          1 TTTTTTTCACGAATTT

                            
      27495 TTTTTTTCACGAA--T
          1 TTTTTTTCACGAATTT

                            
      27509 TTTTTTTCACGAATTT
          1 TTTTTTTCACGAATTT

                 
      27525 TTTTT
          1 TTTTT

      27530 CAACTTGATA


Statistics
Matches: 33,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
  14   14  0.42
  16   19  0.58

ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65


Consensus pattern (16 bp):   
TTTTTTTCACGAATTT

Found at i:27603 original size:10 final size:11

Alignment explanation


    Indices: 27575--27606  Score: 57
    Period size: 10  Copynumber: 3.0  Consensus size: 11

      27565 ACCAAATTTT

                       
      27575 TTTTTTTTGAA
          1 TTTTTTTTGAA

                       
      27586 TTTTTTTT-AA
          1 TTTTTTTTGAA

                       
      27596 TTTTTTTTGAA
          1 TTTTTTTTGAA

      27607 GAAACTACTA


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

Matches are distributed among these distances:
  10   10  0.50
  11   10  0.50

ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75


Consensus pattern (11 bp):   
TTTTTTTTGAA

Found at i:28609 original size:21 final size:23

Alignment explanation


    Indices: 28564--28610  Score: 62
    Period size: 23  Copynumber: 2.1  Consensus size: 23

      28554 TCACCTGCAA

                           *  *    
      28564 TAAACACATTAAAATGAGTTTAT
          1 TAAACACATTAAAATCAGCTTAT

                                   
      28587 TAAACACATTAAAA-CA-CTTAT
          1 TAAACACATTAAAATCAGCTTAT

               
      28608 TAA
          1 TAA

      28611 TCATAACACA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21    7  0.32
  22    1  0.05
  23   14  0.64

ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32


Consensus pattern (23 bp):   
TAAACACATTAAAATCAGCTTAT

Found at i:29918 original size:31 final size:30

Alignment explanation


    Indices: 29877--29935  Score: 75
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      29867 TTCCTACTCA

                                   *        
      29877 TTTCTCTTCTTTCTTCAAC-TTCTTTTTCAAT
          1 TTTCTCTTC-TT-TTCAACATTCCTTTTCAAT

                 *                      
      29908 TTTCTTTTCTTTTCAACATTCCTTTTCA
          1 TTTCTCTTCTTTTCAACATTCCTTTTCA

      29936 CTCTCAATCT


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

Matches are distributed among these distances:
  29    6  0.24
  30   11  0.44
  31    8  0.32

ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61


Consensus pattern (30 bp):   
TTTCTCTTCTTTTCAACATTCCTTTTCAAT
Done.