Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_6737

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: 5955
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:2745 original size:10 final size:10

Alignment explanation


    Indices: 2732--2769  Score: 51
    Period size: 10  Copynumber: 3.8  Consensus size: 10

       2722 TTGTAGCTAA

                      
       2732 ATTGAGCTCG
          1 ATTGAGCTCG

                      
       2742 ATTGAGCT-G
          1 ATTGAGCTCG

                       
       2751 ACTTGAGCTCG
          1 A-TTGAGCTCG

             *      
       2762 AGTGAGCT
          1 ATTGAGCT

       2770 GGAAACGAGC


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
   9    2  0.08
  10   21  0.84
  11    2  0.08

ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29


Consensus pattern (10 bp):   
ATTGAGCTCG

Found at i:2749 original size:20 final size:20

Alignment explanation


    Indices: 2709--2769  Score: 63
    Period size: 20  Copynumber: 3.0  Consensus size: 20

       2699 ACCAATAAAA

                                  
       2709 TAAA-TGAGCT-GAATTGTAGC
          1 TAAATTGAGCTCG-ATTG-AGC

                                
       2729 TAAATTGAGCTCGATTGAGC
          1 TAAATTGAGCTCGATTGAGC

             * *          *     
       2749 TGACTTGAGCTCGAGTGAGC
          1 TAAATTGAGCTCGATTGAGC

             
       2769 T
          1 T

       2770 GGAAACGAGC


Statistics
Matches: 36,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  20   25  0.69
  21   10  0.28
  22    1  0.03

ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30


Consensus pattern (20 bp):   
TAAATTGAGCTCGATTGAGC

Found at i:2770 original size:20 final size:20

Alignment explanation


    Indices: 2733--2770  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2723 TGTAGCTAAA

                      *         
       2733 TTGAGCTCGATTGAGCTGAC
          1 TTGAGCTCGAGTGAGCTGAC

                              
       2753 TTGAGCTCGAGTGAGCTG
          1 TTGAGCTCGAGTGAGCTG

       2771 GAAACGAGCT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29


Consensus pattern (20 bp):   
TTGAGCTCGAGTGAGCTGAC

Found at i:5467 original size:29 final size:27

Alignment explanation


    Indices: 5429--5499  Score: 97
    Period size: 29  Copynumber: 2.6  Consensus size: 27

       5419 CTCGCAAGAC

                               *       
       5429 TTTTCACTTTTTTTTAACTTGATTTTT
          1 TTTTCACTTTTTTTTAACTCGATTTTT

                             **          
       5456 TTTGTCACCTTTTTTTTTGCTCGATTTTT
          1 TTT-TCA-CTTTTTTTTAACTCGATTTTT

                           
       5485 TTTTCACTTTTTTTT
          1 TTTTCACTTTTTTTT

       5500 GAATTTTTTT


Statistics
Matches: 39,  Mismatches: 3, Indels: 4
        0.85            0.07        0.09

Matches are distributed among these distances:
  27   12  0.31
  28    6  0.15
  29   21  0.54

ACGTcount: A:0.10, C:0.14, G:0.06, T:0.70


Consensus pattern (27 bp):   
TTTTCACTTTTTTTTAACTCGATTTTT

Found at i:5469 original size:15 final size:15

Alignment explanation


    Indices: 5451--5499  Score: 50
    Period size: 14  Copynumber: 3.5  Consensus size: 15

       5441 TTTAACTTGA

                           
       5451 TTTTTTTTGTCACCT
          1 TTTTTTTTGTCACCT

                       * **
       5466 TTTTTTTTG-CTCGA
          1 TTTTTTTTGTCACCT

                           
       5480 TTTTTTTT-TCA-CT
          1 TTTTTTTTGTCACCT

                   
       5493 TTTTTTT
          1 TTTTTTT

       5500 GAATTTTTTT


Statistics
Matches: 27,  Mismatches: 6, Indels: 4
        0.73            0.16        0.11

Matches are distributed among these distances:
  13    7  0.26
  14   11  0.41
  15    9  0.33

ACGTcount: A:0.06, C:0.14, G:0.06, T:0.73


Consensus pattern (15 bp):   
TTTTTTTTGTCACCT

Found at i:5535 original size:15 final size:15

Alignment explanation


    Indices: 5492--5541  Score: 52
    Period size: 17  Copynumber: 3.4  Consensus size: 15

       5482 TTTTTTTCAC

                           
       5492 TTTTTTTT-G-AA-T
          1 TTTTTTTTCGAAATT

                     *       
       5504 TTTTTTTTCAATCAATT
          1 TTTTTTTTCGA--AATT

                           
       5521 TTTTTTTTCGAAATT
          1 TTTTTTTTCGAAATT

                  
       5536 TTTTTT
          1 TTTTTT

       5542 GATTTTTTTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 7
        0.77            0.05        0.17

Matches are distributed among these distances:
  12    8  0.26
  15   10  0.32
  16    2  0.06
  17   11  0.35

ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72


Consensus pattern (15 bp):   
TTTTTTTTCGAAATT
Done.