Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold384

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: 365111
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.31

Warning! 24399 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:362837 original size:17 final size:17

Alignment explanation


    Indices: 362804--362837  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

     362794 ATATGGATTA

                       *     
     362804 CTTTTTCTATGTAATTC
          1 CTTTTTCTATGCAATTC

                        *    
     362821 CTTTTTCTATGCCATTC
          1 CTTTTTCTATGCAATTC

     362838 AGAACTTGAG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.15, C:0.24, G:0.06, T:0.56


Consensus pattern (17 bp):   
CTTTTTCTATGCAATTC

Found at i:363629 original size:21 final size:21

Alignment explanation


    Indices: 363588--363630  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 21

     363578 AATAAAGTAG

                        *        
     363588 ATTATATATTATTTTTATAGT
          1 ATTATATATTATATTTATAGT

                                  
     363609 ATTATATATTATGATTT-TAGT
          1 ATTATATATTAT-ATTTATAGT

             
     363630 A
          1 A

     363631 AATTCATGTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  21   17  0.85
  22    3  0.15

ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58


Consensus pattern (21 bp):   
ATTATATATTATATTTATAGT

Found at i:363859 original size:18 final size:18

Alignment explanation


    Indices: 363836--363875  Score: 66
    Period size: 16  Copynumber: 2.3  Consensus size: 18

     363826 CTCTTAAACA

                              
     363836 AATATTTTTTTTATTTTT
          1 AATATTTTTTTTATTTTT

                              
     363854 AATA--TTTTTTATTTTT
          1 AATATTTTTTTTATTTTT

                  
     363870 AATATT
          1 AATATT

     363876 CCAATGTATT


Statistics
Matches: 20,  Mismatches: 0, Indels: 4
        0.83            0.00        0.17

Matches are distributed among these distances:
  16   16  0.80
  18    4  0.20

ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72


Consensus pattern (18 bp):   
AATATTTTTTTTATTTTT

Found at i:363863 original size:16 final size:16

Alignment explanation


    Indices: 363842--363875  Score: 68
    Period size: 16  Copynumber: 2.1  Consensus size: 16

     363832 AACAAATATT

                            
     363842 TTTTTTATTTTTAATA
          1 TTTTTTATTTTTAATA

                            
     363858 TTTTTTATTTTTAATA
          1 TTTTTTATTTTTAATA

              
     363874 TT
          1 TT

     363876 CCAATGTATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (16 bp):   
TTTTTTATTTTTAATA

Found at i:364041 original size:30 final size:30

Alignment explanation


    Indices: 364005--364073  Score: 79
    Period size: 30  Copynumber: 2.3  Consensus size: 30

     363995 GGTGCAATTG

                                    *     
     364005 TATAAATATAAAT-TTAATTTTAATTCAAT
          1 TATAAATATAAATCTTAATTTTAACTCAAT

                     *              *      
     364034 ATATAAAT-GAAATCTTAATTTTAGCTCAAT
          1 -TATAAATATAAATCTTAATTTTAACTCAAT

                *     
     364064 TATACATATA
          1 TATAAATATA

     364074 CCTACAAAGC


Statistics
Matches: 32,  Mismatches: 5, Indels: 4
        0.78            0.12        0.10

Matches are distributed among these distances:
  29   10  0.31
  30   22  0.69

ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43


Consensus pattern (30 bp):   
TATAAATATAAATCTTAATTTTAACTCAAT

Found at i:364905 original size:23 final size:23

Alignment explanation


    Indices: 364861--364905  Score: 63
    Period size: 23  Copynumber: 2.0  Consensus size: 23

     364851 TCTTATTTTG

                     *       *     
     364861 TTGATTTGTGTATAATTTATTTA
          1 TTGATTTGTATATAATTGATTTA

                         *        
     364884 TTGATTTGTATATTATTGATTT
          1 TTGATTTGTATATAATTGATTT

     364906 CAAATATCTT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.24, C:0.00, G:0.13, T:0.62


Consensus pattern (23 bp):   
TTGATTTGTATATAATTGATTTA

Done.