Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3607

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: 18144
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:3003 original size:22 final size:22

Alignment explanation


    Indices: 2969--3012  Score: 72
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2959 AGTTTTTATG

                                  
       2969 TTATTTGATTTTTTTATTTTAA
          1 TTATTTGATTTTTTTATTTTAA

                                   
       2991 TTATTT-ATATTTTTTATTTTAA
          1 TTATTTGAT-TTTTTTATTTTAA

       3013 AAAAATTAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  21    2  0.10
  22   19  0.90

ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73


Consensus pattern (22 bp):   
TTATTTGATTTTTTTATTTTAA

Found at i:4097 original size:18 final size:15

Alignment explanation


    Indices: 4061--4089  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       4051 TATACATTAA

                           
       4061 ATAAATTTATTTTTT
          1 ATAAATTTATTTTTT

                          
       4076 ATAAATTTATTTTT
          1 ATAAATTTATTTTT

       4090 CTTTATAATC


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (15 bp):   
ATAAATTTATTTTTT

Found at i:5861 original size:17 final size:17

Alignment explanation


    Indices: 5839--5920  Score: 55
    Period size: 17  Copynumber: 4.8  Consensus size: 17

       5829 ATAAAACATG

                              
       5839 AAAATATAAATATCATA-
          1 AAAATATAAATAT-ATAT

                   *   *     
       5856 AAAATATGAATGTATAT
          1 AAAATATAAATATATAT

                    *   *     
       5873 AAAATATATATAAACTAT
          1 AAAATATAAATATA-TAT

                              
       5891 AAAA-ATAAA-ATGATAT
          1 AAAATATAAATAT-ATAT

              *            
       5907 GATAATA-AAATATA
          1 -AAAATATAAATATA

       5921 CGCGTACTAC


Statistics
Matches: 50,  Mismatches: 9, Indels: 12
        0.70            0.13        0.17

Matches are distributed among these distances:
  16    7  0.14
  17   33  0.66
  18   10  0.20

ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30


Consensus pattern (17 bp):   
AAAATATAAATATATAT

Found at i:9033 original size:29 final size:29

Alignment explanation


    Indices: 8983--9050  Score: 66
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       8973 TTTTTATATA

                 *        *  *    *       
       8983 TTTATAATTTTAAATAATTAAATTAG-AAT
          1 TTTATTATTTTAAAGAAGTAAAGT-GTAAT

                        *                
       9012 TTTATTATTTTATAGAAGTAAAGTGTAAT
          1 TTTATTATTTTAAAGAAGTAAAGTGTAAT

              *       
       9041 TTGATTATTT
          1 TTTATTATTT

       9051 ATTTATAATT


Statistics
Matches: 32,  Mismatches: 6, Indels: 2
        0.80            0.15        0.05

Matches are distributed among these distances:
  28    1  0.03
  29   31  0.97

ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51


Consensus pattern (29 bp):   
TTTATTATTTTAAAGAAGTAAAGTGTAAT

Found at i:9056 original size:40 final size:42

Alignment explanation


    Indices: 9012--9099  Score: 110
    Period size: 40  Copynumber: 2.1  Consensus size: 42

       9002 AAATTAGAAT

                          *   *      *                 
       9012 TTTATTATTTTATAGAA-GTAAA-GTGT-AATTTGATTATTTA
          1 TTTATTATTTTATAAAATATAAATGAGTCAATTTGATT-TTTA

                 *                                    
       9052 TTTATAATTTTATAAAATATAAATGAGTCAATTTGATTTTTA
          1 TTTATTATTTTATAAAATATAAATGAGTCAATTTGATTTTTA

                  
       9094 TTTATT
          1 TTTATT

       9100 TTGGGGACCT


Statistics
Matches: 40,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  40   15  0.38
  41    4  0.10
  42   12  0.30
  43    9  0.22

ACGTcount: A:0.36, C:0.01, G:0.09, T:0.53


Consensus pattern (42 bp):   
TTTATTATTTTATAAAATATAAATGAGTCAATTTGATTTTTA
Done.