Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1720

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: 6908
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31


Found at i:5353 original size:39 final size:40

Alignment explanation


    Indices: 5310--5404  Score: 97
    Period size: 39  Copynumber: 2.5  Consensus size: 40

       5300 ACCAGCTCGA

                           *            *         * 
       5310 AGCCTGCGGGA-CTTTAGCCCGGACATATTTCCAACACGT
          1 AGCCTGCGGGACCTTAAGCCCGGACATAATTCCAACACAT

                   *          *     *         *     
       5349 AGCCTG-AGGACCTTAAGTCCGGATATAATTCCAGCACAT
          1 AGCCTGCGGGACCTTAAGCCCGGACATAATTCCAACACAT

                         *    
       5388 AGCCTGC-GGACCCTAAG
          1 AGCCTGCGGGACCTTAAG

       5405 TCCAGATATA


Statistics
Matches: 46,  Mismatches: 8, Indels: 4
        0.79            0.14        0.07

Matches are distributed among these distances:
  38    3  0.07
  39   43  0.93

ACGTcount: A:0.26, C:0.29, G:0.23, T:0.21


Consensus pattern (40 bp):   
AGCCTGCGGGACCTTAAGCCCGGACATAATTCCAACACAT

Found at i:5405 original size:39 final size:39

Alignment explanation


    Indices: 5328--5414  Score: 111
    Period size: 39  Copynumber: 2.2  Consensus size: 39

       5318 GGACTTTAGC

                 *   *         *             *     
       5328 CCGGACATATTTCCAACACGTAGCCTGAGGACCTTAAGT
          1 CCGGATATAATTCCAACACATAGCCTGAGGACCCTAAGT

                           *           *           
       5367 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
          1 CCGGATATAATTCCAACACATAGCCTGAGGACCCTAAGT

              *      
       5406 CCAGATATA
          1 CCGGATATA

       5415 CATCACTGAA


Statistics
Matches: 41,  Mismatches: 7, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  39   41  1.00

ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22


Consensus pattern (39 bp):   
CCGGATATAATTCCAACACATAGCCTGAGGACCCTAAGT

Found at i:6633 original size:18 final size:18

Alignment explanation


    Indices: 6604--6642  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       6594 ATGAAATTTT

                               
       6604 AATTAGTATTATGAGATAA
          1 AATTAGTATTATGAGA-AA

                        *     
       6623 AATTA-TATTATTAGAAA
          1 AATTAGTATTATGAGAAA

               
       6640 AAT
          1 AAT

       6643 ATTACTGTAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  17    5  0.26
  18    9  0.47
  19    5  0.26

ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38


Consensus pattern (18 bp):   
AATTAGTATTATGAGAAA

Found at i:6729 original size:10 final size:11

Alignment explanation


    Indices: 6714--6742  Score: 51
    Period size: 10  Copynumber: 2.7  Consensus size: 11

       6704 TTGATATTTG

                       
       6714 AAATTTTTAT-
          1 AAATTTTTATA

                       
       6724 AAATTTTTATA
          1 AAATTTTTATA

                    
       6735 AAATTTTT
          1 AAATTTTT

       6743 TAATATTATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  10   10  0.56
  11    8  0.44

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (11 bp):   
AAATTTTTATA

Found at i:6754 original size:21 final size:21

Alignment explanation


    Indices: 6714--6754  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6704 TTGATATTTG

                           *     
       6714 AAATTTTTATAAATTTTTATA
          1 AAATTTTTATAAATTATTATA

                                 
       6735 AAATTTTT-TAATATTATTAT
          1 AAATTTTTATAA-ATTATTAT

       6755 TATATGGAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    3  0.17
  21   15  0.83

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (21 bp):   
AAATTTTTATAAATTATTATA
Done.