Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1088

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: 19739
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:5205 original size:16 final size:17

Alignment explanation


    Indices: 5184--5225  Score: 68
    Period size: 16  Copynumber: 2.5  Consensus size: 17

       5174 TAGCTTCTTC

                             
       5184 TTTTTTTCACGAAAGTT
          1 TTTTTTTCACGAAAGTT

                          *  
       5201 TTTTTTTCACG-AATTT
          1 TTTTTTTCACGAAAGTT

                     
       5217 TTTTTTTCA
          1 TTTTTTTCA

       5226 ACTTGATATC


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  16   13  0.54
  17   11  0.46

ACGTcount: A:0.19, C:0.12, G:0.07, T:0.62


Consensus pattern (17 bp):   
TTTTTTTCACGAAAGTT

Found at i:5305 original size:16 final size:13

Alignment explanation


    Indices: 5266--5301  Score: 65
    Period size: 13  Copynumber: 2.8  Consensus size: 13

       5256 GAAACCAAAA

                         
       5266 TTTTTTTTG-AAT
          1 TTTTTTTTGAAAT

                         
       5278 TTTTTTTTGAAAT
          1 TTTTTTTTGAAAT

                       
       5291 TTTTTTTTGAA
          1 TTTTTTTTGAA

       5302 GAAACTACTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  12    9  0.39
  13   14  0.61

ACGTcount: A:0.19, C:0.00, G:0.08, T:0.72


Consensus pattern (13 bp):   
TTTTTTTTGAAAT

Found at i:6334 original size:21 final size:23

Alignment explanation


    Indices: 6289--6335  Score: 62
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       6279 TCACCTGCAA

                           *  *    
       6289 TAAACACATTAAAATGAGTTTAT
          1 TAAACACATTAAAATCAGCTTAT

                                   
       6312 TAAACACATTAAAA-CA-CTTAT
          1 TAAACACATTAAAATCAGCTTAT

               
       6333 TAA
          1 TAA

       6336 TCATAACACA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21    7  0.32
  22    1  0.05
  23   14  0.64

ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32


Consensus pattern (23 bp):   
TAAACACATTAAAATCAGCTTAT

Found at i:8141 original size:4 final size:4

Alignment explanation


    Indices: 8120--8155  Score: 56
    Period size: 4  Copynumber: 9.0  Consensus size: 4

       8110 GTTGTAAAGT

                                                         
       8120 TTTA TTT- TTTA TTTTA TTTA TTTA TTTA TTTA TTTA
          1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA

       8156 CTTAGTTTAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   3    3  0.10
   4   23  0.77
   5    4  0.13

ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78


Consensus pattern (4 bp):   
TTTA

Found at i:17468 original size:75 final size:75

Alignment explanation


    Indices: 17379--17517  Score: 278
    Period size: 75  Copynumber: 1.9  Consensus size: 75

      17369 TCTTTCTCAA

                                                                             
      17379 AGTCATAAGCTTCGATGTTCAAGACAAAGCATCTCCCCAATTGGACTTGATAGATGACATATTAT
          1 AGTCATAAGCTTCGATGTTCAAGACAAAGCATCTCCCCAATTGGACTTGATAGATGACATATTAT

                      
      17444 ATCTTCTTAG
         66 ATCTTCTTAG

                                                                            
      17454 AGTCATAAGCTTCGATGTTCAAGACAAAGCATCTCCCCAATTGGACTTGATAGATGACATATTA
          1 AGTCATAAGCTTCGATGTTCAAGACAAAGCATCTCCCCAATTGGACTTGATAGATGACATATTA

      17518 GTCTTTCAAT


Statistics
Matches: 64,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  75   64  1.00

ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Consensus pattern (75 bp):   
AGTCATAAGCTTCGATGTTCAAGACAAAGCATCTCCCCAATTGGACTTGATAGATGACATATTAT
ATCTTCTTAG
Done.