Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014833.1 Kokia drynarioides strain JFW-HI SEQ_129875, 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: 23324
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35

Warning! 7 characters in sequence are not A, C, G, or T


Found at i:4339 original size:25 final size:25

Alignment explanation


    Indices: 4311--4359  Score: 64
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       4301 ACTATATAAA

                                      
       4311 AAAATTAAATAAATA-AAAAATATAT
          1 AAAATT-AATAAATATAAAAATATAT

                   *       *        
       4336 AAAATTATTAAATATTAAAATATA
          1 AAAATTAATAAATATAAAAATATA

       4360 ATATAAATAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  24    7  0.33
  25   14  0.67

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (25 bp):   
AAAATTAATAAATATAAAAATATAT

Found at i:4339 original size:28 final size:27

Alignment explanation


    Indices: 4303--4366  Score: 74
    Period size: 28  Copynumber: 2.3  Consensus size: 27

       4293 TTAAGATAAC

                                        
       4303 TATATAAAAAAATTAAATAAATAAAAAA
          1 TATATAAAAAAATTAAAT-AATAAAAAA

                     **        *     * 
       4331 TATATAAAATTATTAAATATTAAAATA
          1 TATATAAAAAAATTAAATAATAAAAAA

                     
       4358 TAATATAAA
          1 T-ATATAAA

       4367 TATTTTTTTT


Statistics
Matches: 31,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  27    8  0.26
  28   23  0.74

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (27 bp):   
TATATAAAAAAATTAAATAATAAAAAA

Found at i:7467 original size:70 final size:69

Alignment explanation


    Indices: 7354--7519  Score: 233
    Period size: 70  Copynumber: 2.4  Consensus size: 69

       7344 ATATAATCAT

                                                                     *      *
       7354 GTCAGGTTACCTGTCCGGGCTAAACCTTTATCGACACATCAAATAGCTTGGCCAAAGCTGTAATG
          1 GTCAGGTTACCTGTCCGGGCTAAACCTTTATCGACACATCAAATAGCTTGGCCAAAGATGT-ATA

                 
       7419 TACAG
         65 TACAG

                                 **        *                                 
       7424 GTCAGGTTACCTGTCCGGGCTTGACCTTTATTGACACATCAAATAGCTTGGCCAAAGATGTATAT
          1 GTCAGGTTACCTGTCCGGGCTAAACCTTTATCGACACATCAAATAGCTTGGCCAAAGATGTATAT

               *
       7489 ACAT
         66 ACAG

              *       *     **         
       7493 GTAAGGTTACTTGTCCTAGCTAAACCT
          1 GTCAGGTTACCTGTCCGGGCTAAACCT

       7520 ATAAAACGAC


Statistics
Matches: 84,  Mismatches: 12, Indels: 1
        0.87            0.12        0.01

Matches are distributed among these distances:
  69   27  0.32
  70   57  0.68

ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29


Consensus pattern (69 bp):   
GTCAGGTTACCTGTCCGGGCTAAACCTTTATCGACACATCAAATAGCTTGGCCAAAGATGTATAT
ACAG

Found at i:13555 original size:3 final size:3

Alignment explanation


    Indices: 13549--13583  Score: 61
    Period size: 3  Copynumber: 11.7  Consensus size: 3

      13539 TGATGATGAT

                                                 *        
      13549 GAG GAG GAG GAG GAG GAG GAG GAG GAG GTG GAG GA
          1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA

      13584 TTCTTAGCTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.31, C:0.00, G:0.66, T:0.03


Consensus pattern (3 bp):   
GAG

Found at i:14199 original size:3 final size:3

Alignment explanation


    Indices: 14191--14222  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

      14181 TTAGACCAAG

                                                      
      14191 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
          1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA

      14223 AGATTATCAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31


Consensus pattern (3 bp):   
GAT

Found at i:14697 original size:6 final size:6

Alignment explanation


    Indices: 14686--14712  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      14676 AGCTGCCCTT

                                           
      14686 TCTCTA TCTCTA TCTCTA TCTCTA TCT
          1 TCTCTA TCTCTA TCTCTA TCTCTA TCT

      14713 GATGCCTTCT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52


Consensus pattern (6 bp):   
TCTCTA

Done.