Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1972

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: 16032
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36


Found at i:4161 original size:13 final size:13

Alignment explanation


    Indices: 4143--4168  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       4133 CAATTTTTTG

                         
       4143 TGTATCGATACAT
          1 TGTATCGATACAT

                         
       4156 TGTATCGATACAT
          1 TGTATCGATACAT

       4169 ACTTGCTGTA


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

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38


Consensus pattern (13 bp):   
TGTATCGATACAT

Found at i:6719 original size:13 final size:13

Alignment explanation


    Indices: 6701--6739  Score: 69
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       6691 ATAATCACCC

                        *
       6701 TGTATCGATACAG
          1 TGTATCGATACAA

                         
       6714 TGTATCGATACAA
          1 TGTATCGATACAA

                         
       6727 TGTATCGATACAA
          1 TGTATCGATACAA

       6740 AGAAAAATGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  13   25  1.00

ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31


Consensus pattern (13 bp):   
TGTATCGATACAA

Found at i:6750 original size:20 final size:20

Alignment explanation


    Indices: 6725--6803  Score: 77
    Period size: 20  Copynumber: 3.7  Consensus size: 20

       6715 GTATCGATAC

                                
       6725 AATGTATCGATACAAAGAAA
          1 AATGTATCGATACAAAGAAA

                          *          
       6745 AATGTATCGATACATAGAATTTCCA
          1 AATGTATCGATACAAAGAA-----A

            *             *     
       6770 GATGTATCGATACACAGAAA
          1 AATGTATCGATACAAAGAAA

            *             
       6790 CATGTATCGATACA
          1 AATGTATCGATACA

       6804 TTTTGGACAT


Statistics
Matches: 50,  Mismatches: 4, Indels: 10
        0.78            0.06        0.16

Matches are distributed among these distances:
  20   32  0.64
  25   18  0.36

ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25


Consensus pattern (20 bp):   
AATGTATCGATACAAAGAAA

Found at i:8832 original size:15 final size:15

Alignment explanation


    Indices: 8812--8842  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       8802 ATTTCGTTTG

                   *       
       8812 GAGCTTCTTCATTTT
          1 GAGCTTCCTCATTTT

                           
       8827 GAGCTTCCTCATTTT
          1 GAGCTTCCTCATTTT

             
       8842 G
          1 G

       8843 GACATTTTTA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48


Consensus pattern (15 bp):   
GAGCTTCCTCATTTT

Found at i:10671 original size:21 final size:21

Alignment explanation


    Indices: 10642--10686  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      10632 AAGTTTTCAT

                      *          
      10642 TTTTCTTAGCTAAC-TCATTA
          1 TTTTCTTAGCCAACTTCATTA

                              *   
      10662 TTTTCATTAGCCAACTTCTTTA
          1 TTTTC-TTAGCCAACTTCATTA

               
      10684 TTT
          1 TTT

      10687 CAACTTGCAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  20    5  0.24
  21    8  0.38
  22    8  0.38

ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53


Consensus pattern (21 bp):   
TTTTCTTAGCCAACTTCATTA
Done.