Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008434.1 Kokia drynarioides strain JFW-HI SEQ_123105, whole genome shotgun sequence

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: 32693
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:5895 original size:32 final size:33

Alignment explanation


    Indices: 5859--5926  Score: 111
    Period size: 35  Copynumber: 2.0  Consensus size: 33

       5849 TCTTAGAAGA

                                             
       5859 TAAGGGAGAATCATA-TAAGATTAGATTGATAT
          1 TAAGGGAGAATCATATTAAGATTAGATTGATAT

                                               
       5891 TAAGGGAGAATCATATCTTAAGATTAGATTGATAT
          1 TAAGGGAGAATCATA--TTAAGATTAGATTGATAT

             
       5926 T
          1 T

       5927 GTAATCTTGT


Statistics
Matches: 33,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  32   15  0.45
  35   18  0.55

ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34


Consensus pattern (33 bp):   
TAAGGGAGAATCATATTAAGATTAGATTGATAT

Found at i:11509 original size:63 final size:63

Alignment explanation


    Indices: 11410--11537  Score: 220
    Period size: 63  Copynumber: 2.0  Consensus size: 63

      11400 GGTCTGTCTG

                                *                                 *        
      11410 CTGGCACTGATATTGAGCTAGAAGAAAAAATGGATAATTTGTCTCTTGAAGAGCGTAGCAAAA
          1 CTGGCACTGATATTGAGCTACAAGAAAAAATGGATAATTTGTCTCTTGAAGAGCATAGCAAAA

                           * *                                             
      11473 CTGGCACTGATATTGTGGTACAAGAAAAAATGGATAATTTGTCTCTTGAAGAGCATAGCAAAA
          1 CTGGCACTGATATTGAGCTACAAGAAAAAATGGATAATTTGTCTCTTGAAGAGCATAGCAAAA

              
      11536 CT
          1 CT

      11538 ATGGTAGAAA


Statistics
Matches: 61,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  63   61  1.00

ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27


Consensus pattern (63 bp):   
CTGGCACTGATATTGAGCTACAAGAAAAAATGGATAATTTGTCTCTTGAAGAGCATAGCAAAA

Found at i:14202 original size:16 final size:17

Alignment explanation


    Indices: 14181--14213  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      14171 TGATATATGT

                             
      14181 TTAAA-TAAAAAATTTA
          1 TTAAATTAAAAAATTTA

                   *         
      14197 TTAAATTGAAAAATTTA
          1 TTAAATTAAAAAATTTA

      14214 AATATAATAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16    5  0.33
  17   10  0.67

ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39


Consensus pattern (17 bp):   
TTAAATTAAAAAATTTA

Found at i:25558 original size:32 final size:33

Alignment explanation


    Indices: 25522--25589  Score: 111
    Period size: 35  Copynumber: 2.0  Consensus size: 33

      25512 TCTTAGAAGA

                                             
      25522 TAAGGGAGAATCATA-TAAGATTAGATTGATAT
          1 TAAGGGAGAATCATATTAAGATTAGATTGATAT

                                               
      25554 TAAGGGAGAATCATATCTTAAGATTAGATTGATAT
          1 TAAGGGAGAATCATA--TTAAGATTAGATTGATAT

             
      25589 T
          1 T

      25590 GTAATCTTGT


Statistics
Matches: 33,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  32   15  0.45
  35   18  0.55

ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34


Consensus pattern (33 bp):   
TAAGGGAGAATCATATTAAGATTAGATTGATAT

Found at i:31182 original size:63 final size:63

Alignment explanation


    Indices: 31083--31210  Score: 220
    Period size: 63  Copynumber: 2.0  Consensus size: 63

      31073 GGTCTGTCTG

                                *                                 *        
      31083 CTGGCACTGATATTGAGCTAGAAGAAAAAATGGATAATTTGTCTCTTGAAGAGCGTAGCAAAA
          1 CTGGCACTGATATTGAGCTACAAGAAAAAATGGATAATTTGTCTCTTGAAGAGCATAGCAAAA

                           * *                                             
      31146 CTGGCACTGATATTGTGGTACAAGAAAAAATGGATAATTTGTCTCTTGAAGAGCATAGCAAAA
          1 CTGGCACTGATATTGAGCTACAAGAAAAAATGGATAATTTGTCTCTTGAAGAGCATAGCAAAA

              
      31209 CT
          1 CT

      31211 ATGGTAGAAA


Statistics
Matches: 61,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  63   61  1.00

ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27


Consensus pattern (63 bp):   
CTGGCACTGATATTGAGCTACAAGAAAAAATGGATAATTTGTCTCTTGAAGAGCATAGCAAAA
Done.