Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold793

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: 6449
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.32

Warning! 413 characters in sequence are not A, C, G, or T


Found at i:457 original size:34 final size:34

Alignment explanation


    Indices: 419--483  Score: 112
    Period size: 34  Copynumber: 1.9  Consensus size: 34

        409 ATAGATTTTA

                 *                 *          
        419 AAATTGAATTAATTAACTAGATGCAAATTAACCG
          1 AAATTAAATTAATTAACTAGATGAAAATTAACCG

                                           
        453 AAATTAAATTAATTAACTAGATGAAAATTAA
          1 AAATTAAATTAATTAACTAGATGAAAATTAA

        484 TCAGCTTTTA


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  34   29  1.00

ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31


Consensus pattern (34 bp):   
AAATTAAATTAATTAACTAGATGAAAATTAACCG

Found at i:3217 original size:122 final size:122

Alignment explanation


    Indices: 3000--3244  Score: 373
    Period size: 122  Copynumber: 2.0  Consensus size: 122

       2990 AAATATTCAC

                      *            *                                         
       3000 AATATTAACTCAAAAATCAAGGCTTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
          1 AATATTAACTAAAAAATCAAGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA

                                 *                          *        
       3065 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTTATCAACCT
         66 TTTTTAGGATGTGACAATAGGAGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT

                             * *         *                               *** 
       3122 AATATTAACTAAAAAATTAGGGCGTGACCGCTCTTGGTTCCACTAACCCAATCCTTCTAACTTGA
          1 AATATTAACTAAAAAATCAAGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA

                 *        *                            *             
       3187 TTTTTCGGATGTGATAATAGGAGTTTTAATTAGAAAGAAAGTTGAATTAATCAACCT
         66 TTTTTAGGATGTGACAATAGGAGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT

             
       3244 A
          1 A

       3245 GAGTCAGTTG


Statistics
Matches: 110,  Mismatches: 13, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
 122  110  1.00

ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32


Consensus pattern (122 bp):   
AATATTAACTAAAAAATCAAGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
TTTTTAGGATGTGACAATAGGAGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT

Found at i:4889 original size:33 final size:33

Alignment explanation


    Indices: 4846--4917  Score: 126
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       4836 TGTGCATGAC

                 *                           
       4846 ATATTCGGAGGTTATTAATTTATGCTATGTATT
          1 ATATTTGGAGGTTATTAATTTATGCTATGTATT

                                             
       4879 ATATTTGGAGGTTATTAATTTATGCTATGTATT
          1 ATATTTGGAGGTTATTAATTTATGCTATGTATT

            *     
       4912 GTATTT
          1 ATATTT

       4918 TGTTGTACTG


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  33   37  1.00

ACGTcount: A:0.26, C:0.04, G:0.18, T:0.51


Consensus pattern (33 bp):   
ATATTTGGAGGTTATTAATTTATGCTATGTATT

Found at i:6085 original size:26 final size:25

Alignment explanation


    Indices: 6055--6115  Score: 70
    Period size: 25  Copynumber: 2.4  Consensus size: 25

       6045 AATTTTTAGT

                 *                     
       6055 GTTAATTTTCAATCTCAATAT-TTTAA
          1 GTTAAATTT-AAT-TCAATATATTTAA

                         **          
       6081 GTTAAATTTAATTTTATATATTTAA
          1 GTTAAATTTAATTCAATATATTTAA

                      
       6106 GTTAAATTTA
          1 GTTAAATTTA

       6116 TTTATTTTCA


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  24    5  0.16
  25   18  0.58
  26    8  0.26

ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52


Consensus pattern (25 bp):   
GTTAAATTTAATTCAATATATTTAA
Done.