Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1413

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: 38659
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31


Found at i:1178 original size:8 final size:8

Alignment explanation


    Indices: 1165--1193  Score: 58
    Period size: 8  Copynumber: 3.6  Consensus size: 8

       1155 AAAAAGCACA

                    
       1165 AAGCAACT
          1 AAGCAACT

                    
       1173 AAGCAACT
          1 AAGCAACT

                    
       1181 AAGCAACT
          1 AAGCAACT

                 
       1189 AAGCA
          1 AAGCA

       1194 GGTTGATTTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   21  1.00

ACGTcount: A:0.52, C:0.24, G:0.14, T:0.10


Consensus pattern (8 bp):   
AAGCAACT

Found at i:5541 original size:16 final size:16

Alignment explanation


    Indices: 5499--5543  Score: 56
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       5489 AATTATAATT

                             
       5499 TTTTAAATAAAA-ATTA
          1 TTTT-AATAAAATATTA

                  *          
       5515 TTTTACTTAAAATATTA
          1 TTTTA-ATAAAATATTA

                        
       5532 TTTTAATAAAAT
          1 TTTTAATAAAAT

       5544 GTTTAAATTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  15    1  0.04
  16   15  0.60
  17    9  0.36

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (16 bp):   
TTTTAATAAAATATTA

Found at i:31356 original size:40 final size:40

Alignment explanation


    Indices: 31289--31458  Score: 184
    Period size: 40  Copynumber: 4.3  Consensus size: 40

      31279 CCATTACAAA

                             *           * *        
      31289 ATGTGCATTCAA-GGTATCGAAGTACAAATATGGGCACAT
          1 ATGTGCATTCAAGGGTACCGAAGTACAAACAGGGGCACAT

                     *         *           *      * 
      31328 ATGTGCATTTAAGGGTACCAAAGTACAAACAAGGGCACGT
          1 ATGTGCATTCAAGGGTACCGAAGTACAAACAGGGGCACAT

                               *         *         * 
      31368 ATGTGCAATT--AGGGTACTGAAGTACAAGCAGGGGCACGT
          1 ATGTGC-ATTCAAGGGTACCGAAGTACAAACAGGGGCACAT

                       *     **                     
      31407 ATGTGCATTCAGGGGTATTGAAGTACAAACAGGGGCACAT
          1 ATGTGCATTCAAGGGTACCGAAGTACAAACAGGGGCACAT

                   *    
      31447 ATGTGCAATCAA
          1 ATGTGCATTCAA

      31459 ACAATAATTT


Statistics
Matches: 111,  Mismatches: 16, Indels: 7
        0.83            0.12        0.05

Matches are distributed among these distances:
  38    3  0.03
  39   42  0.38
  40   63  0.57
  41    3  0.03

ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22


Consensus pattern (40 bp):   
ATGTGCATTCAAGGGTACCGAAGTACAAACAGGGGCACAT

Done.