Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold766

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: 4762
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:59 original size:27 final size:27

Alignment explanation


    Indices: 29--101  Score: 67
    Period size: 27  Copynumber: 2.6  Consensus size: 27

         19 TTATAGGGAA

                             *          
         29 AATATAATTAATAATT-TTAAAAAAATT
          1 AATA-AATTAATAATTAATAAAAAAATT

                   *                  *  
         56 AATAAAAATAATATATTAATAAAAAATTT
          1 AAT-AAATTAATA-ATTAATAAAAAAATT

            **               
         85 CTTAAATTAATAATTAA
          1 AATAAATTAATAATTAA

        102 AATTTAGTTT


Statistics
Matches: 37,  Mismatches: 6, Indels: 6
        0.76            0.12        0.12

Matches are distributed among these distances:
  27   15  0.41
  28   12  0.32
  29   10  0.27

ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38


Consensus pattern (27 bp):   
AATAAATTAATAATTAATAAAAAAATT

Found at i:560 original size:17 final size:18

Alignment explanation


    Indices: 540--576  Score: 58
    Period size: 17  Copynumber: 2.1  Consensus size: 18

        530 AAAATCTTAA

                              
        540 AAAACTTAATTAATT-TT
          1 AAAACTTAATTAATTATT

                   *          
        557 AAAACTTTATTAATTATT
          1 AAAACTTAATTAATTATT

              
        575 AA
          1 AA

        577 GTTTTTTCTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17   14  0.78
  18    4  0.22

ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46


Consensus pattern (18 bp):   
AAAACTTAATTAATTATT

Found at i:1240 original size:2 final size:2

Alignment explanation


    Indices: 1233--1266  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       1223 GGGGAAAGAC

                                                              
       1233 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

       1267 TATAAATCGG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
AG

Done.