Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1231

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: 2314
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39


Found at i:944 original size:42 final size:44

Alignment explanation


    Indices: 879--963  Score: 122
    Period size: 43  Copynumber: 2.0  Consensus size: 44

        869 GCAGGCCACC

                                                         
        879 TAAAATATACTATCTAAAGAAGTAA-TTTATT-ATTTAATTTAAT
          1 TAAAATATACTATCTAAAGAAGTAATTTTATTAATTT-ATTTAAT

                     *        *                        
        922 TAAAATATAGT-TCTAAATAAGTAATTTTATTAATTTATTTAA
          1 TAAAATATACTATCTAAAGAAGTAATTTTATTAATTTATTTAA

        964 ACATAAATTA


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
  42   12  0.32
  43   22  0.58
  44    4  0.11

ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46


Consensus pattern (44 bp):   
TAAAATATACTATCTAAAGAAGTAATTTTATTAATTTATTTAAT

Found at i:1586 original size:8 final size:8

Alignment explanation


    Indices: 1575--1618  Score: 52
    Period size: 8  Copynumber: 5.1  Consensus size: 8

       1565 TATATTTAAA

                    
       1575 TATATTTT
          1 TATATTTT

                 *  
       1583 TATATATT
          1 TATATTTT

                     
       1591 TATATTTTT
          1 TATA-TTTT

                      
       1600 TATAAATTTT
          1 TAT--ATTTT

                    
       1610 TATATTTT
          1 TATATTTT

             
       1618 T
          1 T

       1619 TTTTCAAAAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
   8   17  0.55
   9    6  0.19
  10    7  0.23
  11    1  0.03

ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70


Consensus pattern (8 bp):   
TATATTTT

Found at i:1620 original size:10 final size:9

Alignment explanation


    Indices: 1560--1619  Score: 50
    Period size: 10  Copynumber: 6.4  Consensus size: 9

       1550 GTTTTAGTGA

                      
       1560 TTTTATATAT
          1 TTTTATAT-T

              **      
       1570 TTAAATATAT
          1 TTTTATAT-T

                     
       1580 TTTTATA-T
          1 TTTTATATT

            *        
       1588 ATTTATATT
          1 TTTTATATT

                    * 
       1597 TTTTATAAAT
          1 TTTTAT-ATT

                     
       1607 TTTTATATT
          1 TTTTATATT

                
       1616 TTTT
          1 TTTT

       1620 TTTCAAAATA


Statistics
Matches: 40,  Mismatches: 8, Indels: 5
        0.75            0.15        0.09

Matches are distributed among these distances:
   8    7  0.17
   9   12  0.30
  10   21  0.52

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (9 bp):   
TTTTATATT

Found at i:1691 original size:25 final size:26

Alignment explanation


    Indices: 1637--1694  Score: 66
    Period size: 25  Copynumber: 2.3  Consensus size: 26

       1627 ATACTATAAG

                                    * 
       1637 ATTTTTATATATTTGTAATTGTATGC
          1 ATTTTTATATATTTGTAATTGTATAC

                                 *    *
       1663 ATTTTTATA-ATTT-TATATTTTATAT
          1 ATTTTTATATATTTGTA-ATTGTATAC

                   
       1688 ATTTTTA
          1 ATTTTTA

       1695 AAAAAATTAA


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  24    2  0.07
  25   17  0.61
  26    9  0.32

ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64


Consensus pattern (26 bp):   
ATTTTTATATATTTGTAATTGTATAC
Done.