Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1992

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: 13950
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:4416 original size:20 final size:20

Alignment explanation


    Indices: 4391--4436  Score: 56
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       4381 AAGAATTGAA

                               *
       4391 GAGGGATACAAGAGAGGGAT
          1 GAGGGATACAAGAGAGGGAG

                   * **         
       4411 GAGGGATGCTTGAGAGGGAG
          1 GAGGGATACAAGAGAGGGAG

                  
       4431 GAGGGA
          1 GAGGGA

       4437 GCCTCTATTT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11


Consensus pattern (20 bp):   
GAGGGATACAAGAGAGGGAG

Found at i:4584 original size:24 final size:27

Alignment explanation


    Indices: 4518--4582  Score: 89
    Period size: 28  Copynumber: 2.4  Consensus size: 27

       4508 AGCCTCTATA

                     *                   
       4518 TTTGACAAATACAAAGGA-AACCACCATT
          1 TTTGACAAACACAAA--ATAACCACCATT

                                       
       4546 TTTGACAAACACAAAATAACCACCA-T
          1 TTTGACAAACACAAAATAACCACCATT

                       
       4572 TTTGACAAACA
          1 TTTGACAAACA

       4583 AATGGGTGGC


Statistics
Matches: 35,  Mismatches: 1, Indels: 4
        0.88            0.03        0.10

Matches are distributed among these distances:
  26   13  0.37
  27    8  0.23
  28   14  0.40

ACGTcount: A:0.48, C:0.23, G:0.08, T:0.22


Consensus pattern (27 bp):   
TTTGACAAACACAAAATAACCACCATT

Found at i:5522 original size:10 final size:10

Alignment explanation


    Indices: 5507--5567  Score: 52
    Period size: 10  Copynumber: 5.6  Consensus size: 10

       5497 TAGGAAAGAG

                      
       5507 GAAAAAAAAA
          1 GAAAAAAAAA

                    *  
       5517 GAAAAATAGAA
          1 GAAAAA-AAAA

                          
       5528 GAAAAGAGAAGAAA
          1 G-AAA-A-AA-AAA

                       
       5542 GAGAAAAAAAA
          1 GA-AAAAAAAA

                      
       5553 G-AAAAAAAA
          1 GAAAAAAAAA

                  
       5562 GAAAAA
          1 GAAAAA

       5568 TTTATATATT


Statistics
Matches: 42,  Mismatches: 2, Indels: 14
        0.72            0.03        0.24

Matches are distributed among these distances:
   9    9  0.21
  10   10  0.24
  11    8  0.19
  12    5  0.12
  13    4  0.10
  14    6  0.14

ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02


Consensus pattern (10 bp):   
GAAAAAAAAA

Found at i:5565 original size:9 final size:9

Alignment explanation


    Indices: 5509--5567  Score: 66
    Period size: 9  Copynumber: 6.6  Consensus size: 9

       5499 GGAAAGAGGA

                     
       5509 AAAAAAAAG
          1 AAAAAAAAG

                  *  
       5518 -AAAAATAG
          1 AAAAAAAAG

                   *  
       5526 AAGAAAAGAG
          1 AA-AAAAAAG

              *   *  
       5536 AAGAAAGAG
          1 AAAAAAAAG

                     
       5545 AAAAAAAAG
          1 AAAAAAAAG

                     
       5554 AAAAAAAAG
          1 AAAAAAAAG

                 
       5563 AAAAA
          1 AAAAA

       5568 TTTATATATT


Statistics
Matches: 43,  Mismatches: 5, Indels: 4
        0.83            0.10        0.08

Matches are distributed among these distances:
   8    7  0.16
   9   28  0.65
  10    8  0.19

ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02


Consensus pattern (9 bp):   
AAAAAAAAG

Found at i:7214 original size:25 final size:25

Alignment explanation


    Indices: 7179--7233  Score: 92
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       7169 CAAGTGCATA

                                     
       7179 TTCTAGCATAATTAAAAGAACTACT
          1 TTCTAGCATAATTAAAAGAACTACT

                  *                * 
       7204 TTCTAGTATAATTAAAAGAACTATT
          1 TTCTAGCATAATTAAAAGAACTACT

                 
       7229 TTCTA
          1 TTCTA

       7234 ATATCATAAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  25   28  1.00

ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38


Consensus pattern (25 bp):   
TTCTAGCATAATTAAAAGAACTACT

Found at i:9480 original size:20 final size:20

Alignment explanation


    Indices: 9441--9480  Score: 53
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       9431 GGTTTCTTAT

                         * *    
       9441 TTCTATGAAAATTTATTTTC
          1 TTCTATGAAAATTAAGTTTC

                   *            
       9461 TTCTATGCAAATTAAGTTTC
          1 TTCTATGAAAATTAAGTTTC

       9481 ATTCACTGAC


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.30, C:0.12, G:0.07, T:0.50


Consensus pattern (20 bp):   
TTCTATGAAAATTAAGTTTC

Found at i:11173 original size:20 final size:20

Alignment explanation


    Indices: 11150--11189  Score: 53
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      11140 ATACAAATTA

                 *              
      11150 AATTTTAAAATTAAATAAAT
          1 AATTTGAAAATTAAATAAAT

                   **           
      11170 AATTTGATCATTAAATAAAT
          1 AATTTGAAAATTAAATAAAT

      11190 CTAATTACAG


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40


Consensus pattern (20 bp):   
AATTTGAAAATTAAATAAAT
Done.