Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold966

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: 3778
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32


Found at i:130 original size:28 final size:27

Alignment explanation


    Indices: 85--188  Score: 72
    Period size: 27  Copynumber: 3.6  Consensus size: 27

         75 TTTAGATAAT

                          *             
         85 ATATATTAT-TATATTTAAAATTTTAAA
          1 ATAT-TTATGTATAATTAAAATTTTAAA

                                         
        112 ATATTTCATGTATAATT-AAA-TTTACAA
          1 ATATTT-ATGTATAATTAAAATTTTA-AA

                          *                 
        139 ATAATTTAT-TAATTATTAAAAGTATTTAAAA
          1 AT-ATTTATGT-ATAATTAAAA-T-TTT-AAA

                               
        170 TATATATTATGTATAATTA
          1 -ATAT-TTATGTATAATTA

        189 TATTAAATCA


Statistics
Matches: 61,  Mismatches: 3, Indels: 21
        0.72            0.04        0.25

Matches are distributed among these distances:
  26    7  0.11
  27   20  0.33
  28   13  0.21
  31    7  0.11
  32   13  0.21
  33    1  0.02

ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48


Consensus pattern (27 bp):   
ATATTTATGTATAATTAAAATTTTAAA

Found at i:473 original size:23 final size:23

Alignment explanation


    Indices: 442--486  Score: 65
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        432 CCCTTTCATG

                                    
        442 AATTGAATTATT-TCAATTTATTT
          1 AATTGAATT-TTATCAATTTATTT

                *                 
        465 AATTTAATTTTATCAATTTATT
          1 AATTGAATTTTATCAATTTATT

        487 CGATCTAGGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  22    2  0.10
  23   18  0.90

ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58


Consensus pattern (23 bp):   
AATTGAATTTTATCAATTTATTT

Found at i:702 original size:19 final size:20

Alignment explanation


    Indices: 678--719  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

        668 TAACTTACCC

                  *             
        678 AATTAATTA-TCAAATATAA
          1 AATTAAGTACTCAAATATAA

                            *   
        697 AATTAAGTACTCAAATGTAA
          1 AATTAAGTACTCAAATATAA

               
        717 AAT
          1 AAT

        720 AATCCAACGC


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  19    8  0.40
  20   12  0.60

ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33


Consensus pattern (20 bp):   
AATTAAGTACTCAAATATAA

Done.