Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1493

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: 34520
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:5409 original size:29 final size:29

Alignment explanation


    Indices: 5370--5432  Score: 117
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       5360 CTTACGAAAA

                        *                
       5370 TTTTTCATAAGATCTTCATAATAATTTTT
          1 TTTTTCATAAGAGCTTCATAATAATTTTT

                                         
       5399 TTTTTCATAAGAGCTTCATAATAATTTTT
          1 TTTTTCATAAGAGCTTCATAATAATTTTT

                 
       5428 TTTTT
          1 TTTTT

       5433 AAAAAAAGCC


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   33  1.00

ACGTcount: A:0.29, C:0.10, G:0.05, T:0.57


Consensus pattern (29 bp):   
TTTTTCATAAGAGCTTCATAATAATTTTT

Found at i:6560 original size:30 final size:30

Alignment explanation


    Indices: 6526--6582  Score: 105
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       6516 TTTTTTAAAG

                            *             
       6526 AAAAATTATTATGAAGCTCTTATGAAATAA
          1 AAAAATTATTATGAAGATCTTATGAAATAA

                                       
       6556 AAAAATTATTATGAAGATCTTATGAAA
          1 AAAAATTATTATGAAGATCTTATGAAA

       6583 AATTTTCGTA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33


Consensus pattern (30 bp):   
AAAAATTATTATGAAGATCTTATGAAATAA

Found at i:12401 original size:6 final size:6

Alignment explanation


    Indices: 12390--12428  Score: 78
    Period size: 6  Copynumber: 6.5  Consensus size: 6

      12380 TTTCTTCTCT

                                                         
      12390 CTCCAA CTCCAA CTCCAA CTCCAA CTCCAA CTCCAA CTC
          1 CTCCAA CTCCAA CTCCAA CTCCAA CTCCAA CTCCAA CTC

      12429 ACTCACTCTT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   33  1.00

ACGTcount: A:0.31, C:0.51, G:0.00, T:0.18


Consensus pattern (6 bp):   
CTCCAA

Found at i:15226 original size:17 final size:15

Alignment explanation


    Indices: 15203--15245  Score: 54
    Period size: 15  Copynumber: 2.9  Consensus size: 15

      15193 AATAAAAAAA

                            
      15203 TATTTATTTAATTATT
          1 TATTTA-TTAATTATT

                            
      15219 TAATTTATT-ATTATT
          1 T-ATTTATTAATTATT

                         
      15234 T-TTTATTAATTA
          1 TATTTATTAATTA

      15246 AATTAATAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  13    6  0.24
  14    4  0.16
  15    7  0.28
  16    3  0.12
  17    5  0.20

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (15 bp):   
TATTTATTAATTATT

Found at i:17194 original size:2 final size:2

Alignment explanation


    Indices: 17187--17214  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      17177 TTTCTGTTTC

                                                     
      17187 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      17215 TCGTGTTAAA


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

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:29268 original size:2 final size:2

Alignment explanation


    Indices: 29263--29293  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      29253 AGAGAGAGAG

                                                          
      29263 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A

      29294 GAGGAAGAGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Done.