Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold589

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: 25575
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.17

Warning! 12681 characters in sequence are not A, C, G, or T


Found at i:14536 original size:15 final size:15

Alignment explanation


    Indices: 14516--14548  Score: 50
    Period size: 15  Copynumber: 2.2  Consensus size: 15

      14506 TACCTATAGA

                            
      14516 AATTCTCA-AAGGCAG
          1 AATTCTCACAA-GCAG

                           
      14531 AATTCTCACAAGCAG
          1 AATTCTCACAAGCAG

               
      14546 AAT
          1 AAT

      14549 AAATCTCACC


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15   15  0.88
  16    2  0.12

ACGTcount: A:0.42, C:0.21, G:0.15, T:0.21


Consensus pattern (15 bp):   
AATTCTCACAAGCAG

Found at i:15955 original size:19 final size:19

Alignment explanation


    Indices: 15933--15984  Score: 54
    Period size: 19  Copynumber: 2.7  Consensus size: 19

      15923 TATTTTCTTG

                                
      15933 TTTTTCTTTTCTTGTTTT-C
          1 TTTTTCTTTTCTT-TTTTAC

                                
      15952 TTTTTAC-TTTCTTTTTTAC
          1 TTTTT-CTTTTCTTTTTTAC

            *      *      
      15971 ATTTTCTCTTCTTT
          1 TTTTTCTTTTCTTT

      15985 CTTTTTCATT


Statistics
Matches: 28,  Mismatches: 2, Indels: 6
        0.78            0.06        0.17

Matches are distributed among these distances:
  18    5  0.18
  19   22  0.79
  20    1  0.04

ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75


Consensus pattern (19 bp):   
TTTTTCTTTTCTTTTTTAC

Found at i:15956 original size:14 final size:14

Alignment explanation


    Indices: 15925--15955  Score: 55
    Period size: 13  Copynumber: 2.3  Consensus size: 14

      15915 TTTTTTCATA

                          
      15925 TTTTCTTGTTTTTC
          1 TTTTCTTGTTTTTC

                          
      15939 TTTTCTTG-TTTTC
          1 TTTTCTTGTTTTTC

                
      15952 TTTT
          1 TTTT

      15956 TACTTTCTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    9  0.53
  14    8  0.47

ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81


Consensus pattern (14 bp):   
TTTTCTTGTTTTTC

Found at i:17529 original size:41 final size:41

Alignment explanation


    Indices: 17484--17566  Score: 166
    Period size: 41  Copynumber: 2.0  Consensus size: 41

      17474 AAATTAAAAT

                                                     
      17484 GTCCTTAAAAACATTGGCCCAATAATCAATTAGGCCTATGA
          1 GTCCTTAAAAACATTGGCCCAATAATCAATTAGGCCTATGA

                                                     
      17525 GTCCTTAAAAACATTGGCCCAATAATCAATTAGGCCTATGA
          1 GTCCTTAAAAACATTGGCCCAATAATCAATTAGGCCTATGA

             
      17566 G
          1 G

      17567 ATGTTTCATC


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  41   42  1.00

ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27


Consensus pattern (41 bp):   
GTCCTTAAAAACATTGGCCCAATAATCAATTAGGCCTATGA
Done.