Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002262.1 Kokia drynarioides strain JFW-HI SEQ_114276, 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: 13231
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37


Found at i:1447 original size:31 final size:27

Alignment explanation


    Indices: 1382--1436  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       1372 TAGAAAAAAT

                                       
       1382 AATAATAATAAAGAGAGAGAATTTAAC
          1 AATAATAATAAAGAGAGAGAATTTAAC

                                       
       1409 AATAATAATAAAGAGAGAGAATTTAAC
          1 AATAATAATAAAGAGAGAGAATTTAAC

             
       1436 A
          1 A

       1437 GTGTTTAATA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.60, C:0.04, G:0.15, T:0.22


Consensus pattern (27 bp):   
AATAATAATAAAGAGAGAGAATTTAAC

Found at i:2275 original size:33 final size:34

Alignment explanation


    Indices: 2238--2301  Score: 85
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       2228 AATTTTTATA

                                 *            
       2238 ATATTATTAATGC-TTTTTAATTTTTAAAAAAAT
          1 ATATTATTAATGCATTTTTAAATTTTAAAAAAAT

                 *  **                     
       2271 ATATTTTTTTTGCATTTTTAAATTTTAAAAA
          1 ATATTATTAATGCATTTTTAAATTTTAAAAA

       2302 TTAATTAAAT


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  33   10  0.38
  34   16  0.62

ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55


Consensus pattern (34 bp):   
ATATTATTAATGCATTTTTAAATTTTAAAAAAAT

Found at i:7562 original size:30 final size:30

Alignment explanation


    Indices: 7508--7568  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       7498 AATAGTCTAT

                                      *   
       7508 ATTTTTATAATTTTTAAAAAATTAAATTAC
          1 ATTTTTATAATTTTTAAAAAATTAAAATAC

                    *        ***          
       7538 ATTTTTATCATTTTTAAGGGATTAAAATAC
          1 ATTTTTATAATTTTTAAAAAATTAAAATAC

             
       7568 A
          1 A

       7569 AATTTTTTTA


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48


Consensus pattern (30 bp):   
ATTTTTATAATTTTTAAAAAATTAAAATAC

Found at i:9308 original size:20 final size:20

Alignment explanation


    Indices: 9283--9324  Score: 84
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       9273 GCTTCTCATT

                                
       9283 ATCACCACTCAGGTACTAAA
          1 ATCACCACTCAGGTACTAAA

                                
       9303 ATCACCACTCAGGTACTAAA
          1 ATCACCACTCAGGTACTAAA

              
       9323 AT
          1 AT

       9325 AACTTAGAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.40, C:0.29, G:0.10, T:0.21


Consensus pattern (20 bp):   
ATCACCACTCAGGTACTAAA

Found at i:10582 original size:29 final size:29

Alignment explanation


    Indices: 10540--10597  Score: 80
    Period size: 29  Copynumber: 2.0  Consensus size: 29

      10530 TAAGGTTTTA

                 *                 *     
      10540 ACCCTTATCTTTCAAGTACCAACGAAGTG
          1 ACCCTCATCTTTCAAGTACCAACCAAGTG

                    *        *           
      10569 ACCCTCATTTTTCAAGTGCCAACCAAGTG
          1 ACCCTCATCTTTCAAGTACCAACCAAGTG

      10598 TACGACACCG


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  29   25  1.00

ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28


Consensus pattern (29 bp):   
ACCCTCATCTTTCAAGTACCAACCAAGTG

Found at i:12011 original size:16 final size:15

Alignment explanation


    Indices: 11990--12045  Score: 67
    Period size: 16  Copynumber: 3.5  Consensus size: 15

      11980 GTGTAACATT

                            
      11990 ATTAAATTTAATTTTA
          1 ATTAAATTT-ATTTTA

                      *     
      12006 ATTAAATATTTTTTTA
          1 ATTAAAT-TTATTTTA

               *            
      12022 ATTTAATTTGATTTTA
          1 ATTAAATTT-ATTTTA

                    
      12038 ATTAAATT
          1 ATTAAATT

      12046 ACTTAAAATA


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
  15    2  0.06
  16   30  0.88
  17    2  0.06

ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59


Consensus pattern (15 bp):   
ATTAAATTTATTTTA
Done.