Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold726

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: 8402
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34


Found at i:8 original size:3 final size:3

Alignment explanation


    Indices: 1--40  Score: 80
    Period size: 3  Copynumber: 13.3  Consensus size: 3

                                                                 
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A

         41 CCTTTGAACT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   37  1.00

ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:5604 original size:56 final size:58

Alignment explanation


    Indices: 5509--5632  Score: 153
    Period size: 56  Copynumber: 2.1  Consensus size: 58

       5499 TTGTAATAAG

                          * *                            * *         *  
       5509 ATTATTATTAAATATATTTTAATAACAAATAATAAATAATTTAATCATATT-TTAACGTA
          1 ATTATTATTAAATACAATTTAAT-A-AAATAATAAATAATTTAATAAAATTCTTAACATA

                                            *                     *   
       5568 ATTATTATTAAATACAATTTAAT-AAATAATATATAATTTAATAAAATTCTTAATATA
          1 ATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAAAATTCTTAACATA

                    
       5625 ATTATTAT
          1 ATTATTAT

       5633 ATGAATTAAA


Statistics
Matches: 57,  Mismatches: 7, Indels: 4
        0.84            0.10        0.06

Matches are distributed among these distances:
  56   22  0.39
  57   14  0.25
  59   21  0.37

ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45


Consensus pattern (58 bp):   
ATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAAAATTCTTAACATA

Found at i:5647 original size:33 final size:33

Alignment explanation


    Indices: 5592--5666  Score: 82
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       5582 CAATTTAATA

                *                 *  *        
       5592 AATAATATATAATTTAATAAAATTCTTAATATA-
          1 AATATTATATAATTTAA-AAAAATCATAATATAT

             *                                
       5625 ATTATTATATGAA-TTAAAAAAATCATAATATAT
          1 AATATTATAT-AATTTAAAAAAATCATAATATAT

                     
       5658 AATATTATA
          1 AATATTATA

       5667 AAAATAATAT


Statistics
Matches: 35,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  32   13  0.37
  33   20  0.57
  34    2  0.06

ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41


Consensus pattern (33 bp):   
AATATTATATAATTTAAAAAAATCATAATATAT

Found at i:7605 original size:23 final size:24

Alignment explanation


    Indices: 7565--7616  Score: 74
    Period size: 23  Copynumber: 2.3  Consensus size: 24

       7555 ATAGAAAAAG

                      *             
       7565 ATATA-TATGCAACGATATATATT
          1 ATATATTATGAAACGATATATATT

                                    
       7588 ATATATTATGAAAC-ATATATATT
          1 ATATATTATGAAACGATATATATT

                   
       7611 A-ATATT
          1 ATATATT

       7617 GTGTTAGTTA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  22    5  0.19
  23   15  0.56
  24    7  0.26

ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42


Consensus pattern (24 bp):   
ATATATTATGAAACGATATATATT
Done.