Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_440 ID=scaffold_440-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: 7683
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.29

Warning! 712 characters in sequence are not A, C, G, or T


Found at i:4059 original size:19 final size:20

Alignment explanation


    Indices: 4035--4074  Score: 73
    Period size: 19  Copynumber: 2.0  Consensus size: 20

       4025 CCTCTTCTTA

                                
       4035 AATTAGGTTTAA-TTTTATT
          1 AATTAGGTTTAATTTTTATT

                                
       4054 AATTAGGTTTAATTTTTATT
          1 AATTAGGTTTAATTTTTATT

             
       4074 A
          1 A

       4075 GTTACTTGTG


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

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

ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57


Consensus pattern (20 bp):   
AATTAGGTTTAATTTTTATT

Found at i:5878 original size:70 final size:70

Alignment explanation


    Indices: 5760--5896  Score: 238
    Period size: 70  Copynumber: 2.0  Consensus size: 70

       5750 TTGCATGCCC

                                                                             
       5760 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGACCAACACCTCCTTTATTGCTGC
          1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGACCAACACCTCCTTTATTGCTGC

                 
       5825 TGTTG
         66 TGTTG

                *          *                          *       *              
       5830 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACGTCCTTTATTGCTGC
          1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGACCAACACCTCCTTTATTGCTGC

              
       5895 TG
         66 TG

       5897 ATTTAATTCA


Statistics
Matches: 63,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  70   63  1.00

ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34


Consensus pattern (70 bp):   
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGACCAACACCTCCTTTATTGCTGC
TGTTG

Found at i:6676 original size:17 final size:17

Alignment explanation


    Indices: 6654--6686  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       6644 AAAGAAAGAA

                             
       6654 AAAAATTGAAAAAAAAT
          1 AAAAATTGAAAAAAAAT

                            
       6671 AAAAATTGAAAAAAAA
          1 AAAAATTGAAAAAAAA

       6687 GGATTTCGTG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15


Consensus pattern (17 bp):   
AAAAATTGAAAAAAAAT
Done.