Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3505

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: 35829
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:6462 original size:4 final size:4

Alignment explanation


    Indices: 6453--6480  Score: 56
    Period size: 4  Copynumber: 7.0  Consensus size: 4

       6443 TTAAACTAAG

                                              
       6453 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
          1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA

       6481 AATAAAACTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   24  1.00

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (4 bp):   
TAAA

Found at i:7035 original size:4 final size:4

Alignment explanation


    Indices: 7026--7056  Score: 53
    Period size: 4  Copynumber: 7.8  Consensus size: 4

       7016 TATTTTTATT

                                          *       
       7026 TTTA TTTA TTTA TTTA TTTA TTTA CTTA TTT
          1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT

       7057 TAAATTTTTA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   4   25  1.00

ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74


Consensus pattern (4 bp):   
TTTA

Found at i:10376 original size:10 final size:10

Alignment explanation


    Indices: 10361--10391  Score: 53
    Period size: 10  Copynumber: 3.0  Consensus size: 10

      10351 AATTGTAGAT

                      
      10361 TCAAAAAAAA
          1 TCAAAAAAAA

                       
      10371 TCAAAAAAAAA
          1 TC-AAAAAAAA

                      
      10382 TCAAAAAAAA
          1 TCAAAAAAAA

      10392 ATATTTTGAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  10   10  0.50
  11   10  0.50

ACGTcount: A:0.81, C:0.10, G:0.00, T:0.10


Consensus pattern (10 bp):   
TCAAAAAAAA

Found at i:10380 original size:12 final size:11

Alignment explanation


    Indices: 10363--10393  Score: 62
    Period size: 11  Copynumber: 2.8  Consensus size: 11

      10353 TTGTAGATTC

                       
      10363 AAAAAAAATCA
          1 AAAAAAAATCA

                       
      10374 AAAAAAAATCA
          1 AAAAAAAATCA

                     
      10385 AAAAAAAAT
          1 AAAAAAAAT

      10394 ATTTTGAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.84, C:0.06, G:0.00, T:0.10


Consensus pattern (11 bp):   
AAAAAAAATCA

Found at i:12686 original size:17 final size:18

Alignment explanation


    Indices: 12647--12688  Score: 52
    Period size: 17  Copynumber: 2.4  Consensus size: 18

      12637 AAGAAGAAAA

                              
      12647 ACAAAA-AGATGAGTGAT
          1 ACAAAAGAGATGAGTGAT

             *                
      12664 AAAAAAGAGA-GAGTGAT
          1 ACAAAAGAGATGAGTGAT

            *       
      12681 TCAAAAGA
          1 ACAAAAGA

      12689 AAAAGAAATG


Statistics
Matches: 21,  Mismatches: 3, Indels: 2
        0.81            0.12        0.08

Matches are distributed among these distances:
  17   18  0.86
  18    3  0.14

ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14


Consensus pattern (18 bp):   
ACAAAAGAGATGAGTGAT
Done.