Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1715

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: 45851
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33


Found at i:1606 original size:18 final size:17

Alignment explanation


    Indices: 1584--1631  Score: 60
    Period size: 18  Copynumber: 2.8  Consensus size: 17

       1574 GCACTCTTTC

                             
       1584 TTTTTTTTCTTTTCCAA
          1 TTTTTTTTCTTTTCCAA

                   *      *   
       1601 TCTTTTTCTCTTTTTCAA
          1 T-TTTTTTTCTTTTCCAA

                 *       
       1619 TTTTTGTTCTTTT
          1 TTTTTTTTCTTTT

       1632 TCGGTTTCTT


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  17   11  0.42
  18   15  0.58

ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73


Consensus pattern (17 bp):   
TTTTTTTTCTTTTCCAA

Found at i:1632 original size:17 final size:16

Alignment explanation


    Indices: 1585--1633  Score: 62
    Period size: 17  Copynumber: 2.9  Consensus size: 16

       1575 CACTCTTTCT

                        *   
       1585 TTTTTTTCTTTTCCAA
          1 TTTTTTTCTTTTTCAA

                              
       1601 TCTTTTTCTCTTTTTCAA
          1 T-TTTTT-TCTTTTTCAA

                           
       1619 TTTTTGTTCTTTTTC
          1 TTTTT-TTCTTTTTC

       1634 GGTTTCTTTT


Statistics
Matches: 29,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  16    1  0.03
  17   17  0.59
  18   11  0.38

ACGTcount: A:0.08, C:0.18, G:0.02, T:0.71


Consensus pattern (16 bp):   
TTTTTTTCTTTTTCAA

Found at i:2560 original size:19 final size:19

Alignment explanation


    Indices: 2536--2575  Score: 71
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       2526 AACTGCTCTC

                     *         
       2536 TTTTTTTTCTCAATTTTTT
          1 TTTTTTTTCACAATTTTTT

                               
       2555 TTTTTTTTCACAATTTTTT
          1 TTTTTTTTCACAATTTTTT

              
       2574 TT
          1 TT

       2576 CAAATTTTTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78


Consensus pattern (19 bp):   
TTTTTTTTCACAATTTTTT

Found at i:2571 original size:13 final size:12

Alignment explanation


    Indices: 2555--2585  Score: 53
    Period size: 13  Copynumber: 2.5  Consensus size: 12

       2545 TCAATTTTTT

                         
       2555 TTTTTTTTCACAA
          1 TTTTTTTTCA-AA

                        
       2568 TTTTTTTTCAAA
          1 TTTTTTTTCAAA

                  
       2580 TTTTTT
          1 TTTTTT

       2586 ACAACTTGTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12    8  0.44
  13   10  0.56

ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71


Consensus pattern (12 bp):   
TTTTTTTTCAAA

Found at i:16872 original size:24 final size:24

Alignment explanation


    Indices: 16848--16894  Score: 67
    Period size: 25  Copynumber: 1.9  Consensus size: 24

      16838 AAACTACTTC

                                     
      16848 TAAAGAAAACTCAAGAGAGAATTCT
          1 TAAAGAAAACTCAA-AGAGAATTCT

             **                   
      16873 TGGAGAAAACTCAAAGAGAATT
          1 TAAAGAAAACTCAAAGAGAATT

      16895 TTTCACTTAA


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

Matches are distributed among these distances:
  24    8  0.40
  25   12  0.60

ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19


Consensus pattern (24 bp):   
TAAAGAAAACTCAAAGAGAATTCT

Found at i:26859 original size:4 final size:4

Alignment explanation


    Indices: 26850--26879  Score: 60
    Period size: 4  Copynumber: 7.5  Consensus size: 4

      26840 AAGTTTTATT

                                                 
      26850 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
          1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT

      26880 ACTTAATTTA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   26  1.00

ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77


Consensus pattern (4 bp):   
TTTA

Found at i:29395 original size:20 final size:21

Alignment explanation


    Indices: 29360--29398  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 21

      29350 CAGCTCGTTG

                                 
      29360 AGCTCAATTCAGCTCATTTCC
          1 AGCTCAATTCAGCTCATTTCC

                     *         
      29381 AGCTC-ATTGAGCTCATTT
          1 AGCTCAATTCAGCTCATTT

      29399 GCTGTTTGAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36


Consensus pattern (21 bp):   
AGCTCAATTCAGCTCATTTCC

Found at i:29805 original size:13 final size:13

Alignment explanation


    Indices: 29787--29812  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      29777 TGTGTCCTAA

                         
      29787 TATGAATTAAATT
          1 TATGAATTAAATT

                         
      29800 TATGAATTAAATT
          1 TATGAATTAAATT

      29813 GCTTTCAGGC


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:0.46, C:0.00, G:0.08, T:0.46


Consensus pattern (13 bp):   
TATGAATTAAATT
Done.