Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2059

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: 8040
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31


Found at i:1398 original size:46 final size:46

Alignment explanation


    Indices: 1348--1523  Score: 209
    Period size: 46  Copynumber: 3.8  Consensus size: 46

       1338 TGGTTGAGCA

                                                          
       1348 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

                                          * *        *       
       1394 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G

                                                          * 
       1439 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
          1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

                  *                       *       
       1487 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
          1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG

       1524 GCGGTTACAT


Statistics
Matches: 111,  Mismatches: 9, Indels: 20
        0.79            0.06        0.14

Matches are distributed among these distances:
  42    2  0.02
  43    5  0.05
  45    5  0.05
  46   61  0.55
  47   29  0.26
  48    3  0.03
  50    4  0.04
  51    2  0.02

ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30


Consensus pattern (46 bp):   
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

Found at i:1504 original size:93 final size:93

Alignment explanation


    Indices: 1345--1516  Score: 310
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       1335 GGATGGTTGA

                                                           *                 
       1345 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT

                                        
       1410 TGAGTCCGAGTTCGTGAGATGTAACTAG
         66 TGAGTCCGAGTTCGTGAGATGTAACTAG

                                                                   *         
       1438 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG

                           
       1502 TTGAGTCCGAGTTCG
         65 TTGAGTCCGAGTTCG

       1517 CTTATGGGCG


Statistics
Matches: 76,  Mismatches: 2, Indels: 2
        0.95            0.03        0.03

Matches are distributed among these distances:
  92    2  0.03
  93   74  0.97

ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28


Consensus pattern (93 bp):   
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.