Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013039.1 Kokia drynarioides strain JFW-HI SEQ_128057, 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: 11002
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35


Found at i:96 original size:13 final size:11

Alignment explanation


    Indices: 68--110  Score: 52
    Period size: 11  Copynumber: 3.8  Consensus size: 11

         58 AGTTAAATAT

                       
         68 TATTTTATTAA
          1 TATTTTATTAA

                         
         79 TATTTTACTTAGA
          1 TATTTTA-TTA-A

                      *
         92 TA-TTTATTAT
          1 TATTTTATTAA

                     
        102 TATTTTATT
          1 TATTTTATT

        111 TAGAAAATTG


Statistics
Matches: 28,  Mismatches: 1, Indels: 6
        0.80            0.03        0.17

Matches are distributed among these distances:
  10    2  0.07
  11   16  0.57
  12    7  0.25
  13    3  0.11

ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65


Consensus pattern (11 bp):   
TATTTTATTAA

Found at i:97 original size:23 final size:23

Alignment explanation


    Indices: 71--114  Score: 70
    Period size: 23  Copynumber: 1.9  Consensus size: 23

         61 TAAATATTAT

                                   
         71 TTTATTAATATTTTACTTAGATA
          1 TTTATTAATATTTTACTTAGATA

                   *       *     
         94 TTTATTATTATTTTATTTAGA
          1 TTTATTAATATTTTACTTAGA

        115 AAATTGTAGT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61


Consensus pattern (23 bp):   
TTTATTAATATTTTACTTAGATA

Found at i:6465 original size:17 final size:16

Alignment explanation


    Indices: 6432--6478  Score: 53
    Period size: 15  Copynumber: 2.9  Consensus size: 16

       6422 AATGTCCAAG

                              
       6432 CTTGAGAAAATCC-AACC
          1 CTTGA-AAAATCCGAA-C

                     *      
       6449 CTTGAAAAACCCGAAC
          1 CTTGAAAAATCCGAAC

                           
       6465 C-TGAAAAATCCGAA
          1 CTTGAAAAATCCGAA

       6479 TCTAAAATTA


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  15   12  0.44
  16    8  0.30
  17    7  0.26

ACGTcount: A:0.45, C:0.28, G:0.13, T:0.15


Consensus pattern (16 bp):   
CTTGAAAAATCCGAAC

Found at i:6654 original size:29 final size:29

Alignment explanation


    Indices: 6597--6653  Score: 78
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       6587 TGGTTGAATA

                        *                
       6597 TGCAATTGTATATATAAACTTTGATTTTG
          1 TGCAATTGTATACATAAACTTTGATTTTG

                       *       *        
       6626 TGCAATTGTATGCATGAAATTTTGATTT
          1 TGCAATTGTATACAT-AAACTTTGATTT

       6654 GATATAATTC


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  29   13  0.54
  30   11  0.46

ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47


Consensus pattern (29 bp):   
TGCAATTGTATACATAAACTTTGATTTTG

Found at i:6869 original size:29 final size:30

Alignment explanation


    Indices: 6835--6896  Score: 99
    Period size: 31  Copynumber: 2.1  Consensus size: 30

       6825 GCTTCACGTG

                                          
       6835 TATAATTACAC-TAAATTAAAATTCATGTA
          1 TATAATTACACATAAATTAAAATTCATGTA

                          *                
       6864 TATAATTACACATTGAATTAAAATTCATGTA
          1 TATAATTACACA-TAAATTAAAATTCATGTA

              
       6895 TA
          1 TA

       6897 ATTTTAAGAT


Statistics
Matches: 30,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  29   11  0.37
  31   19  0.63

ACGTcount: A:0.47, C:0.10, G:0.05, T:0.39


Consensus pattern (30 bp):   
TATAATTACACATAAATTAAAATTCATGTA

Found at i:6897 original size:29 final size:27

Alignment explanation


    Indices: 6833--6899  Score: 89
    Period size: 29  Copynumber: 2.3  Consensus size: 27

       6823 AAGCTTCACG

                                       
       6833 TGTATAATTACACTAAATTAAAATTCA
          1 TGTATAATTACACTAAATTAAAATTCA

                              *            
       6860 TGTATATAATTACACATTGAATTAAAATTCA
          1 TG--TATAATTACAC--TAAATTAAAATTCA

                     
       6891 TGTATAATT
          1 TGTATAATT

       6900 TTAAGATTTA


Statistics
Matches: 35,  Mismatches: 1, Indels: 6
        0.83            0.02        0.14

Matches are distributed among these distances:
  27    2  0.06
  29   18  0.51
  31   15  0.43

ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40


Consensus pattern (27 bp):   
TGTATAATTACACTAAATTAAAATTCA
Done.