Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold7209.1

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: 7794
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31


Found at i:4286 original size:15 final size:16

Alignment explanation


    Indices: 4266--4306  Score: 57
    Period size: 17  Copynumber: 2.6  Consensus size: 16

       4256 TAGCTTCTTC

                             
       4266 TTTTTTTCACGAAAATT
          1 TTTTTTTCACGAAAA-T

                          * 
       4283 TTTTTTTCACG-AATT
          1 TTTTTTTCACGAAAAT

                     
       4298 TTTTTTTCA
          1 TTTTTTTCA

       4307 ACTTGATATC


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15   10  0.43
  16    2  0.09
  17   11  0.48

ACGTcount: A:0.22, C:0.12, G:0.05, T:0.61


Consensus pattern (16 bp):   
TTTTTTTCACGAAAAT

Found at i:4288 original size:17 final size:15

Alignment explanation


    Indices: 4266--4306  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 15

       4256 TAGCTTCTTC

                             
       4266 TTTTTTTCACGAAAATT
          1 TTTTTTTCACG--AATT

                           
       4283 TTTTTTTCACGAATT
          1 TTTTTTTCACGAATT

                     
       4298 TTTTTTTCA
          1 TTTTTTTCA

       4307 ACTTGATATC


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  15   13  0.54
  17   11  0.46

ACGTcount: A:0.22, C:0.12, G:0.05, T:0.61


Consensus pattern (15 bp):   
TTTTTTTCACGAATT

Found at i:4364 original size:12 final size:12

Alignment explanation


    Indices: 4347--4406  Score: 95
    Period size: 12  Copynumber: 5.0  Consensus size: 12

       4337 GAAACCAAAT

                        
       4347 TTTTTTTTTGAA
          1 TTTTTTTTTGAA

                        
       4359 TTTTTTTTTGAA
          1 TTTTTTTTTGAA

                       *
       4371 -TTTTTTTTGAT
          1 TTTTTTTTTGAA

                        
       4382 TTTTTTTTTGAA
          1 TTTTTTTTTGAA

                         
       4394 TTTCTTTTTTGAA
          1 TTT-TTTTTTGAA

       4407 GAAACTACTA


Statistics
Matches: 44,  Mismatches: 2, Indels: 3
        0.90            0.04        0.06

Matches are distributed among these distances:
  11   10  0.23
  12   25  0.57
  13    9  0.20

ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75


Consensus pattern (12 bp):   
TTTTTTTTTGAA

Found at i:4378 original size:23 final size:23

Alignment explanation


    Indices: 4348--4402  Score: 92
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       4338 AAACCAAATT

                                   
       4348 TTTTTTTTGAATTTTTTTTTGAA
          1 TTTTTTTTGAATTTTTTTTTGAA

                      *            
       4371 TTTTTTTTGATTTTTTTTTTGAA
          1 TTTTTTTTGAATTTTTTTTTGAA

                     
       4394 TTTCTTTTT
          1 TTT-TTTTT

       4403 TGAAGAAACT


Statistics
Matches: 30,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  23   25  0.83
  24    5  0.17

ACGTcount: A:0.13, C:0.02, G:0.07, T:0.78


Consensus pattern (23 bp):   
TTTTTTTTGAATTTTTTTTTGAA

Found at i:5441 original size:21 final size:23

Alignment explanation


    Indices: 5396--5442  Score: 62
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       5386 TCACCTGCAA

                           *  *    
       5396 TAAACACATTAAAATGAGTTTAT
          1 TAAACACATTAAAATCAGCTTAT

                                   
       5419 TAAACACATTAAAA-CA-CTTAT
          1 TAAACACATTAAAATCAGCTTAT

               
       5440 TAA
          1 TAA

       5443 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:7087 original size:20 final size:20

Alignment explanation


    Indices: 7062--7104  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       7052 AAAAGAAAAG

                                
       7062 AAAGAAGAGAGATTGAGAGA
          1 AAAGAAGAGAGATTGAGAGA

                  **       *    
       7082 AAAGAATCGAGATTGTGAGA
          1 AAAGAAGAGAGATTGAGAGA

               
       7102 AAA
          1 AAA

       7105 ACAAGAGCAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14


Consensus pattern (20 bp):   
AAAGAAGAGAGATTGAGAGA
Done.