Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1617

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, 885

Length: 1475
ACGTcount: A:0.21, C:0.06, G:0.07, T:0.19

Warning! 679 characters in sequence are not A, C, G, or T


Found at i:63 original size:12 final size:12

Alignment explanation


    Indices: 46--70  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

         36 TATATGCAAG

                        
         46 TTATGTAAGTTA
          1 TTATGTAAGTTA

                        
         58 TTATGTAAGTTA
          1 TTATGTAAGTTA

             
         70 T
          1 T

         71 ACAAGATTAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52


Consensus pattern (12 bp):   
TTATGTAAGTTA

Found at i:107 original size:8 final size:7

Alignment explanation


    Indices: 89--126  Score: 53
    Period size: 7  Copynumber: 5.6  Consensus size: 7

         79 ATAATATAAG

                   
         89 TTATGTA
          1 TTATGTA

                    
         96 TTATGTTA
          1 TTATG-TA

                   
        104 TTATGTA
          1 TTATGTA

                   
        111 TTATGTA
          1 TTATGTA

                   
        118 --ATGTA
          1 TTATGTA

                
        123 TTAT
          1 TTAT

        127 CAGATTATAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 6
        0.82            0.00        0.18

Matches are distributed among these distances:
   5    5  0.18
   7   16  0.57
   8    7  0.25

ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58


Consensus pattern (7 bp):   
TTATGTA

Found at i:183 original size:21 final size:20

Alignment explanation


    Indices: 131--187  Score: 60
    Period size: 21  Copynumber: 2.8  Consensus size: 20

        121 TATTATCAGA

                          ***   
        131 TTATATATAAGTTACGGAAG
          1 TTATATATAAGTTATACAAG

                   *             
        151 TTATTATGTAAGTTATACAAG
          1 TTA-TATATAAGTTATACAAG

                            
        172 CTTATATATAAGTTAT
          1 -TTATATATAAGTTAT

        188 GTATTATGTT


Statistics
Matches: 30,  Mismatches: 5, Indels: 3
        0.79            0.13        0.08

Matches are distributed among these distances:
  20    3  0.10
  21   24  0.80
  22    3  0.10

ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42


Consensus pattern (20 bp):   
TTATATATAAGTTATACAAG

Found at i:228 original size:26 final size:26

Alignment explanation


    Indices: 152--231  Score: 69
    Period size: 24  Copynumber: 3.1  Consensus size: 26

        142 TTACGGAAGT

                           *            
        152 TATTATGTAAGTTATACAAGCTTATATA
          1 TATTATGTAAGTTATGCAAGC-T-TATA

                              **        
        180 TAAGTTATGT-A-TTATGTTA--TTATA
          1 T-A-TTATGTAAGTTATGCAAGCTTATA

                                      
        204 TATTATGTAAGTTATGCAAGCTTATA
          1 TATTATGTAAGTTATGCAAGCTTATA

              
        230 TA
          1 TA

        232 CCAATTATGT


Statistics
Matches: 41,  Mismatches: 5, Indels: 14
        0.68            0.08        0.23

Matches are distributed among these distances:
  22    6  0.15
  23    2  0.05
  24   11  0.27
  25    1  0.02
  26    7  0.17
  28    6  0.15
  29    2  0.05
  30    6  0.15

ACGTcount: A:0.36, C:0.05, G:0.12, T:0.46


Consensus pattern (26 bp):   
TATTATGTAAGTTATGCAAGCTTATA

Found at i:230 original size:52 final size:52

Alignment explanation


    Indices: 152--260  Score: 166
    Period size: 52  Copynumber: 2.1  Consensus size: 52

        142 TTACGGAAGT

                                         *                       
        152 TATTATGTAAGTTATACAAGCTTATATA-TAAGTTATGTATTATGTTATTATA
          1 TATTATGTAAGTTATACAAGCTTATATACCAA-TTATGTATTATGTTATTATA

                           *                         *         *
        204 TATTATGTAAGTTATGCAAGCTTATATACCAATTATGTATTGTGTTATTATG
          1 TATTATGTAAGTTATACAAGCTTATATACCAATTATGTATTATGTTATTATA

                 
        256 TATTA
          1 TATTA

        261 AGTTATATAC


Statistics
Matches: 52,  Mismatches: 4, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  52   50  0.96
  53    2  0.04

ACGTcount: A:0.34, C:0.06, G:0.13, T:0.48


Consensus pattern (52 bp):   
TATTATGTAAGTTATACAAGCTTATATACCAATTATGTATTATGTTATTATA
Done.