Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_161 ID=scaffold_161-JGI_221_v2.0

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: 10403
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32


Found at i:3272 original size:59 final size:59

Alignment explanation


    Indices: 3151--3272  Score: 129
    Period size: 59  Copynumber: 2.1  Consensus size: 59

       3141 TTGCATCCCG

                                             *           **   *     ** 
       3151 AACAAAGTGACAATCCACCTCAATTGCAATATGTAAAGCAAATTGTTTATTGCATCTTA
          1 AACAAAGTGACAATCCACCTCAATTGCAATATGCAAAGCAAATTGACTATGGCATCGAA

                              *      *    *          *            *     
       3210 AACAAAGTGACAATCCACTTCAATTTCAATCTGCAACA-CAGATTGACTATGGCCTCGAA
          1 AACAAAGTGACAATCCACCTCAATTGCAATATGCAA-AGCAAATTGACTATGGCATCGAA

                
       3269 AACA
          1 AACA

       3273 TCGTTCTTCT


Statistics
Matches: 51,  Mismatches: 11, Indels: 2
        0.80            0.17        0.03

Matches are distributed among these distances:
  59   50  0.98
  60    1  0.02

ACGTcount: A:0.39, C:0.22, G:0.12, T:0.26


Consensus pattern (59 bp):   
AACAAAGTGACAATCCACCTCAATTGCAATATGCAAAGCAAATTGACTATGGCATCGAA

Found at i:3810 original size:21 final size:22

Alignment explanation


    Indices: 3784--3840  Score: 98
    Period size: 22  Copynumber: 2.6  Consensus size: 22

       3774 AATAGGGAAT

                       *          
       3784 ATATATAATATTTTCCT-AAAG
          1 ATATATAATATATTCCTAAAAG

                                  
       3805 ATATATAATATATTCCTAAAAG
          1 ATATATAATATATTCCTAAAAG

                          
       3827 ATATATAATATATT
          1 ATATATAATATATT

       3841 TAGATATTCC


Statistics
Matches: 34,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  21   16  0.47
  22   18  0.53

ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42


Consensus pattern (22 bp):   
ATATATAATATATTCCTAAAAG

Found at i:7382 original size:3 final size:3

Alignment explanation


    Indices: 7374--7401  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       7364 CATTATATCT

                                                 
       7374 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
          1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T

       7402 ATGTAATGCT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36


Consensus pattern (3 bp):   
TCA

Found at i:8680 original size:7 final size:7

Alignment explanation


    Indices: 8664--8693  Score: 53
    Period size: 7  Copynumber: 4.4  Consensus size: 7

       8654 TTAATAACCG

                   
       8664 AAAAAG-
          1 AAAAAGA

                   
       8670 AAAAAGA
          1 AAAAAGA

                   
       8677 AAAAAGA
          1 AAAAAGA

                   
       8684 AAAAAGA
          1 AAAAAGA

               
       8691 AAA
          1 AAA

       8694 CCAAACCCTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6    6  0.26
   7   17  0.74

ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00


Consensus pattern (7 bp):   
AAAAAGA

Done.