Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1614

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: 24092
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:592 original size:18 final size:18

Alignment explanation


    Indices: 566--617  Score: 77
    Period size: 18  Copynumber: 2.8  Consensus size: 18

        556 CCGTTTACGT

                               
        566 ACTATTTCACGTATACGGA
          1 ACTA-TTCACGTATACGGA

                             *
        585 ACTATTCACGTATACGGT
          1 ACTATTCACGTATACGGA

               *           
        603 ACTGTTCACGTATAC
          1 ACTATTCACGTATAC

        618 AGTAATTGGG


Statistics
Matches: 31,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  18   27  0.87
  19    4  0.13

ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33


Consensus pattern (18 bp):   
ACTATTCACGTATACGGA

Found at i:4650 original size:11 final size:11

Alignment explanation


    Indices: 4634--4664  Score: 53
    Period size: 11  Copynumber: 2.8  Consensus size: 11

       4624 TAGAATATAC

                       
       4634 CCCATACCTTG
          1 CCCATACCTTG

                      *
       4645 CCCATACCTTT
          1 CCCATACCTTG

                     
       4656 CCCATACCT
          1 CCCATACCT

       4665 ACCCATACTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29


Consensus pattern (11 bp):   
CCCATACCTTG

Found at i:10194 original size:6 final size:6

Alignment explanation


    Indices: 10171--10205  Score: 52
    Period size: 6  Copynumber: 5.8  Consensus size: 6

      10161 AAGAGGAGGC

                     *  *                           
      10171 GGTGGA GGGGGG GGTGGA GGTGGA GGTGGA GGTGG
          1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGG

      10206 TGATGATGGC


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.11, C:0.00, G:0.74, T:0.14


Consensus pattern (6 bp):   
GGTGGA

Found at i:20665 original size:3 final size:3

Alignment explanation


    Indices: 20652--20684  Score: 57
    Period size: 3  Copynumber: 11.0  Consensus size: 3

      20642 ATTAACTTAT

                 *                                     
      20652 TAA TCA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

      20685 AAGAACACAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   28  1.00

ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33


Consensus pattern (3 bp):   
TAA

Found at i:22162 original size:13 final size:13

Alignment explanation


    Indices: 22146--22170  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      22136 TGGATTTGGA

                         
      22146 TTTTAAAATTTAG
          1 TTTTAAAATTTAG

                        
      22159 TTTTAAAATTTA
          1 TTTTAAAATTTA

      22171 TGATTTATGA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56


Consensus pattern (13 bp):   
TTTTAAAATTTAG

Found at i:22989 original size:5 final size:5

Alignment explanation


    Indices: 22972--23003  Score: 57
    Period size: 5  Copynumber: 6.6  Consensus size: 5

      22962 ATTGAAATAT

                                                   
      22972 TTATA TT-TA TTATA TTATA TTATA TTATA TTA
          1 TTATA TTATA TTATA TTATA TTATA TTATA TTA

      23004 AATGCATGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   4    4  0.15
   5   22  0.85

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (5 bp):   
TTATA

Done.