Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007780.1 Kokia drynarioides strain JFW-HI SEQ_122414, 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: 19669
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36


Found at i:620 original size:15 final size:16

Alignment explanation


    Indices: 597--626  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

        587 AAATTTTTTT

                            
        597 TATATAAAAATAATAA
          1 TATATAAAAATAATAA

                           
        613 TATA-AAAAATAATA
          1 TATATAAAAATAATA

        627 TAGGTGGGCT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15   10  0.71
  16    4  0.29

ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30


Consensus pattern (16 bp):   
TATATAAAAATAATAA

Found at i:5040 original size:29 final size:28

Alignment explanation


    Indices: 4998--5065  Score: 75
    Period size: 29  Copynumber: 2.4  Consensus size: 28

       4988 ACTTAGTGTG

                 *   *                    
       4998 ATATATTTATTTTAATTT-TGTATATTTAT
          1 ATATAATTAATTTAATTTATGT-T-TTTAT

                                        
       5027 ATATAATTAATTTAATTTATGTTTTTAT
          1 ATATAATTAATTTAATTTATGTTTTTAT

             *  *      
       5055 AAATCATTAAT
          1 ATATAATTAAT

       5066 ACCATTATTA


Statistics
Matches: 34,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  28   14  0.41
  29   17  0.50
  30    3  0.09

ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59


Consensus pattern (28 bp):   
ATATAATTAATTTAATTTATGTTTTTAT

Found at i:5063 original size:28 final size:29

Alignment explanation


    Indices: 5008--5065  Score: 75
    Period size: 28  Copynumber: 2.0  Consensus size: 29

       4998 ATATATTTAT

                                *        
       5008 TTTAATTTTGTATATTTATATATAATTAA
          1 TTTAATTTTGTATATTTATAAATAATTAA

                                    *     
       5037 TTTAATTTATGT-T-TTTATAAATCATTAA
          1 TTTAATTT-TGTATATTTATAAATAATTAA

             
       5065 T
          1 T

       5066 ACCATTATTA


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  28   14  0.54
  29    9  0.35
  30    3  0.12

ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59


Consensus pattern (29 bp):   
TTTAATTTTGTATATTTATAAATAATTAA

Found at i:5494 original size:19 final size:20

Alignment explanation


    Indices: 5472--5510  Score: 62
    Period size: 19  Copynumber: 2.0  Consensus size: 20

       5462 AATGTGTTTT

                *               
       5472 AAATCACATAATA-TATAAA
          1 AAATAACATAATATTATAAA

                                
       5491 AAATAACATAATATTATAAA
          1 AAATAACATAATATTATAAA

       5511 CTTAAAATGG


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  19   12  0.67
  20    6  0.33

ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28


Consensus pattern (20 bp):   
AAATAACATAATATTATAAA

Found at i:7216 original size:31 final size:31

Alignment explanation


    Indices: 7181--7239  Score: 75
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       7171 TTAAAAAAGG

                               *            
       7181 TTAATATATT-ATTTGGTATCTGAATTTGGTT
          1 TTAATAT-TTAATTTGGTACCTGAATTTGGTT

                 *                 *    
       7212 TTAATGTTTAATTTGGTACCTGAGTTTG
          1 TTAATATTTAATTTGGTACCTGAATTTG

       7240 TTGTCACAAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  30    2  0.08
  31   22  0.92

ACGTcount: A:0.24, C:0.05, G:0.19, T:0.53


Consensus pattern (31 bp):   
TTAATATTTAATTTGGTACCTGAATTTGGTT

Found at i:15442 original size:63 final size:63

Alignment explanation


    Indices: 15346--15481  Score: 245
    Period size: 63  Copynumber: 2.2  Consensus size: 63

      15336 TAAAAAAAAA

                     *                                 *                   
      15346 TTATTTTATCGGAGACACCTTGACTAATGCCAAATTATTCCACTATAGTTGATTTTCAAGATT
          1 TTATTTTATTGGAGACACCTTGACTAATGCCAAATTATTCCACCATAGTTGATTTTCAAGATT

                           *                                               
      15409 TTATTTTATTGGAGAGACCTTGACTAATGCCAAATTATTCCACCATAGTTGATTTTCAAGATT
          1 TTATTTTATTGGAGACACCTTGACTAATGCCAAATTATTCCACCATAGTTGATTTTCAAGATT

                      
      15472 TTATTTTATT
          1 TTATTTTATT

      15482 AGACATACAT


Statistics
Matches: 70,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  63   70  1.00

ACGTcount: A:0.29, C:0.15, G:0.12, T:0.43


Consensus pattern (63 bp):   
TTATTTTATTGGAGACACCTTGACTAATGCCAAATTATTCCACCATAGTTGATTTTCAAGATT

Found at i:17486 original size:15 final size:16

Alignment explanation


    Indices: 17468--17497  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

      17458 TTATATTAAT

                            
      17468 AATTTATA-AAAATTA
          1 AATTTATATAAAATTA

                           
      17483 AATTTATATAAAATT
          1 AATTTATATAAAATT

      17498 CATATGTAAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    8  0.57
  16    6  0.43

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (16 bp):   
AATTTATATAAAATTA

Done.