Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold5910.1

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: 16127
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.30

Warning! 474 characters in sequence are not A, C, G, or T


Found at i:4402 original size:17 final size:18

Alignment explanation


    Indices: 4370--4406  Score: 58
    Period size: 17  Copynumber: 2.1  Consensus size: 18

       4360 TGTTGAGCTG

                              
       4370 AACTTAATTAAATTAACT
          1 AACTTAATTAAATTAACT

                     *        
       4388 AACTT-ATTTAATTAACT
          1 AACTTAATTAAATTAACT

              
       4405 AA
          1 AA

       4407 GTTTATTCCA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17   13  0.72
  18    5  0.28

ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41


Consensus pattern (18 bp):   
AACTTAATTAAATTAACT

Found at i:5591 original size:20 final size:20

Alignment explanation


    Indices: 5545--5591  Score: 67
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       5535 AGCTCGTTTC

                      *         
       5545 CAGCTCACTCGAGCTCAAGT
          1 CAGCTCACTCAAGCTCAAGT

              *               * 
       5565 CAACTCACTCAAGCTCAATT
          1 CAGCTCACTCAAGCTCAAGT

                   
       5585 CAGCTCA
          1 CAGCTCA

       5592 TTAGCCCAAT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21


Consensus pattern (20 bp):   
CAGCTCACTCAAGCTCAAGT

Found at i:7543 original size:30 final size:30

Alignment explanation


    Indices: 7509--7605  Score: 106
    Period size: 30  Copynumber: 3.2  Consensus size: 30

       7499 AGCTCACTCC

                                           
       7509 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
          1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT

                       *    * *   * * *   
       7539 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
          1 TAGCTCAACTTTAGCTCACGAGCTAAACCT

            *                          *  
       7569 CAGCTCAACTTTAGCTCACGAGCTAAAACT
          1 TAGCTCAACTTTAGCTCACGAGCTAAACCT

                   
       7599 TAGCTCA
          1 TAGCTCA

       7606 TTTTAGTTTA


Statistics
Matches: 51,  Mismatches: 15, Indels: 2
        0.75            0.22        0.03

Matches are distributed among these distances:
  29    1  0.02
  30   50  0.98

ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29


Consensus pattern (30 bp):   
TAGCTCAACTTTAGCTCACGAGCTAAACCT

Found at i:11865 original size:21 final size:22

Alignment explanation


    Indices: 11826--11869  Score: 63
    Period size: 21  Copynumber: 2.0  Consensus size: 22

      11816 ATGCATACTC

                                  
      11826 CTTCAAGCTCAAATCAGCTCAA
          1 CTTCAAGCTCAAATCAGCTCAA

                        * *       
      11848 CTTCAA-CTCAACTTAGCTCAA
          1 CTTCAAGCTCAAATCAGCTCAA

             
      11869 C
          1 C

      11870 GAGCTCGTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  21   14  0.70
  22    6  0.30

ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25


Consensus pattern (22 bp):   
CTTCAAGCTCAAATCAGCTCAA

Found at i:15375 original size:11 final size:11

Alignment explanation


    Indices: 15359--15389  Score: 55
    Period size: 10  Copynumber: 2.9  Consensus size: 11

      15349 ACTACGCAGC

                       
      15359 CGAAAAAAAAT
          1 CGAAAAAAAAT

                       
      15370 CG-AAAAAAAT
          1 CGAAAAAAAAT

                      
      15380 CGAAAAAAAA
          1 CGAAAAAAAA

      15390 AGTGATTTAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  10   10  0.53
  11    9  0.47

ACGTcount: A:0.74, C:0.10, G:0.10, T:0.06


Consensus pattern (11 bp):   
CGAAAAAAAAT

Done.