Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold660

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: 86107
ACGTcount: A:0.09, C:0.04, G:0.05, T:0.08

Warning! 63724 characters in sequence are not A, C, G, or T


Found at i:75022 original size:20 final size:20

Alignment explanation


    Indices: 74999--75045  Score: 60
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      74989 TGGGTAAAAT

                         *       
      74999 TGAGCTGAATTGATCTCGAA-
          1 TGAGCTGAATTGAGCTC-AAC

                    *           
      75019 TGAGCTGACTTGAGCTCAAC
          1 TGAGCTGAATTGAGCTCAAC

                   
      75039 TGAGCTG
          1 TGAGCTG

      75046 GAAACGAGCT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  19    2  0.08
  20   22  0.92

ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28


Consensus pattern (20 bp):   
TGAGCTGAATTGAGCTCAAC

Found at i:79318 original size:36 final size:38

Alignment explanation


    Indices: 79278--79351  Score: 98
    Period size: 41  Copynumber: 1.9  Consensus size: 38

      79268 ACATCTATTT

                                                  
      79278 AATATG-T-CGAATTTAATGCTGCCACTACATGTTATA
          1 AATATGCTGCGAATTTAATGCTGCCACTACATGTTATA

                                       *          
      79314 AATATGCCTGGACGAATTTAATGCTGCTACTACATGTT
          1 AATATG-CT-G-CGAATTTAATGCTGCCACTACATGTT

      79352 TGGCCGAATT


Statistics
Matches: 32,  Mismatches: 1, Indels: 5
        0.84            0.03        0.13

Matches are distributed among these distances:
  36    6  0.19
  38    1  0.03
  41   25  0.78

ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35


Consensus pattern (38 bp):   
AATATGCTGCGAATTTAATGCTGCCACTACATGTTATA

Found at i:80404 original size:41 final size:41

Alignment explanation


    Indices: 80359--80466  Score: 189
    Period size: 41  Copynumber: 2.6  Consensus size: 41

      80349 AATTCGGCCA

                      *                    *         
      80359 AACATGTAGTAGCAGCATTAAATTCGTCCAGGCATATTTAT
          1 AACATGTAGTGGCAGCATTAAATTCGTCCAGACATATTTAT

                                     *               
      80400 AACATGTAGTGGCAGCATTAAATTCATCCAGACATATTTAT
          1 AACATGTAGTGGCAGCATTAAATTCGTCCAGACATATTTAT

                                      
      80441 AACATGTAGTGGCAGCATTAAATTCG
          1 AACATGTAGTGGCAGCATTAAATTCG

      80467 ACATATTAAA


Statistics
Matches: 63,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  41   63  1.00

ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31


Consensus pattern (41 bp):   
AACATGTAGTGGCAGCATTAAATTCGTCCAGACATATTTAT

Found at i:81282 original size:18 final size:18

Alignment explanation


    Indices: 81259--81300  Score: 66
    Period size: 18  Copynumber: 2.3  Consensus size: 18

      81249 TTTTCAATCC

                     *  *     
      81259 TGTTTTTAATGATTTTTA
          1 TGTTTTTAACGAATTTTA

                              
      81277 TGTTTTTAACGAATTTTA
          1 TGTTTTTAACGAATTTTA

                  
      81295 TGTTTT
          1 TGTTTT

      81301 CAAGTTCTTA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  18   22  1.00

ACGTcount: A:0.21, C:0.02, G:0.12, T:0.64


Consensus pattern (18 bp):   
TGTTTTTAACGAATTTTA
Done.