Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1160

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: 11310
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30


Found at i:233 original size:28 final size:28

Alignment explanation


    Indices: 172--249  Score: 131
    Period size: 28  Copynumber: 2.8  Consensus size: 28

        162 TCTCACAATC

                                       *
        172 GGGGATACTCCAACCCCGTTA-TTTCGT
          1 GGGGATACTCCAACCCCGTTATTTTCGA

                      *                 
        199 GGGGATACTCTAACCCCGTTATTTTCGA
          1 GGGGATACTCCAACCCCGTTATTTTCGA

                                   
        227 GGGGATACTCCAACCCCGTTATT
          1 GGGGATACTCCAACCCCGTTATT

        250 ATCTCCAAAA


Statistics
Matches: 47,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  27   20  0.43
  28   27  0.57

ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29


Consensus pattern (28 bp):   
GGGGATACTCCAACCCCGTTATTTTCGA

Found at i:233 original size:97 final size:98

Alignment explanation


    Indices: 67--243  Score: 243
    Period size: 97  Copynumber: 1.8  Consensus size: 98

         57 AACCAATTTT

                   *                                                         
         67 TCACAATTGAGGACACTCCAACCCCGTTAATCATCGGGGATACTTCAACACCATTATTTACGAGG
          1 TCACAATCGAGGACACTCCAACCCCGTTAATCATCGGGGATACTTCAACACCATTATTTACGAGG

                                             
        132 GGATACT-CAACCCCTGCTCTAAATATTGATTC
         66 GGATACTCCAACCCCTGCTCTAAATATTGATTC

                     *   *                *  *                 *  *      *   
        164 TCACAATCGGGGATACTCCAACCCCGTTATTTCGT-GGGGATAC-TCTAACCCCGTTATTTTCGA
          1 TCACAATCGAGGACACTCCAACCCCGTTA-ATCATCGGGGATACTTC-AACACCATTATTTACGA

                             
        227 GGGGATACTCCAACCCC
         64 GGGGATACTCCAACCCC

        244 GTTATTATCT


Statistics
Matches: 69,  Mismatches: 8, Indels: 5
        0.84            0.10        0.06

Matches are distributed among these distances:
  96    2  0.03
  97   57  0.83
  98   10  0.14

ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27


Consensus pattern (98 bp):   
TCACAATCGAGGACACTCCAACCCCGTTAATCATCGGGGATACTTCAACACCATTATTTACGAGG
GGATACTCCAACCCCTGCTCTAAATATTGATTC

Found at i:8110 original size:13 final size:13

Alignment explanation


    Indices: 8092--8116  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       8082 ATTACTCAAA

                         
       8092 TGTATCGATACAT
          1 TGTATCGATACAT

                        
       8105 TGTATCGATACA
          1 TGTATCGATACA

       8117 CTGATCTTTG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (13 bp):   
TGTATCGATACAT
Done.