Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold7214.1

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: 7751
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32


Found at i:4231 original size:89 final size:90

Alignment explanation


    Indices: 4131--4306  Score: 345
    Period size: 89  Copynumber: 2.0  Consensus size: 90

       4121 TATCTTTTGA

                                                                             
       4131 ACCCTTTTAAAAGTCTTCCGCTTAAACTGAAAACAATCTTCATCTTAAAACAATTTCGAACGAAC
          1 ACCCTTTTAAAAGTCTTCCGCTTAAACTGAAAACAATCTTCATCTTAAAACAATTTCGAACGAAC

                                     
       4196 TTCTCGTCGACGATT-GGGCAACTT
         66 TTCTCGTCGACGATTCGGGCAACTT

                                                                             
       4220 ACCCTTTTAAAAGTCTTCCGCTTAAACTGAAAACAATCTTCATCTTAAAACAATTTCGAACGAAC
          1 ACCCTTTTAAAAGTCTTCCGCTTAAACTGAAAACAATCTTCATCTTAAAACAATTTCGAACGAAC

                                  
       4285 TTCTCGTCGACGATTCGGGCAA
         66 TTCTCGTCGACGATTCGGGCAA

       4307 TCAAGTGAAT


Statistics
Matches: 86,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  89   80  0.93
  90    6  0.07

ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30


Consensus pattern (90 bp):   
ACCCTTTTAAAAGTCTTCCGCTTAAACTGAAAACAATCTTCATCTTAAAACAATTTCGAACGAAC
TTCTCGTCGACGATTCGGGCAACTT

Found at i:4662 original size:10 final size:10

Alignment explanation


    Indices: 4647--4677  Score: 53
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       4637 ATTGGAGTAA

                      
       4647 CAAAAAAAAT
          1 CAAAAAAAAT

                       
       4657 CAAAAAAAAAT
          1 C-AAAAAAAAT

                      
       4668 CAAAAAAAAT
          1 CAAAAAAAAT

       4678 TGATTGAAAA


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):   
CAAAAAAAAT

Found at i:4664 original size:11 final size:11

Alignment explanation


    Indices: 4648--4676  Score: 58
    Period size: 11  Copynumber: 2.6  Consensus size: 11

       4638 TTGGAGTAAC

                       
       4648 AAAAAAAATCA
          1 AAAAAAAATCA

                       
       4659 AAAAAAAATCA
          1 AAAAAAAATCA

                   
       4670 AAAAAAA
          1 AAAAAAA

       4677 TTGATTGAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07


Consensus pattern (11 bp):   
AAAAAAAATCA

Found at i:4698 original size:11 final size:11

Alignment explanation


    Indices: 4647--4700  Score: 56
    Period size: 11  Copynumber: 4.8  Consensus size: 11

       4637 ATTGGAGTAA

                       
       4647 CAAAAAAAA-T
          1 CAAAAAAAATT

                     * 
       4657 CAAAAAAAAAT
          1 CAAAAAAAATT

                       
       4668 CAAAAAAAATT
          1 CAAAAAAAATT

            *   *        
       4679 GATTGAAAAAATT
          1 CA--AAAAAAATT

                     
       4692 CAAAAAAAA
          1 CAAAAAAAA

       4701 AAGTGAAAAA


Statistics
Matches: 36,  Mismatches: 5, Indels: 5
        0.78            0.11        0.11

Matches are distributed among these distances:
  10    9  0.25
  11   18  0.50
  13    9  0.25

ACGTcount: A:0.74, C:0.07, G:0.04, T:0.15


Consensus pattern (11 bp):   
CAAAAAAAATT
Done.