Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007062.1 Kokia drynarioides strain JFW-HI SEQ_121671, 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: 16756
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:6648 original size:17 final size:17

Alignment explanation


    Indices: 6628--6712  Score: 66
    Period size: 17  Copynumber: 5.1  Consensus size: 17

       6618 TATATATATG

                             
       6628 TAAAAAAAATATGTATA
          1 TAAAAAAAATATGTATA

                 * *         
       6645 TAAAAGAGATATGTATA
          1 TAAAAAAAATATGTATA

                * **    * *  
       6662 -AAACAGTATATATGTA
          1 TAAAAAAAATATGTATA

                             
       6678 T-AAAAAAATATGTATA
          1 TAAAAAAAATATGTATA

                 * *   *     
       6694 TAAAATAGATAGGTATA
          1 TAAAAAAAATATGTATA

              
       6711 TA
          1 TA

       6713 TATATATATA


Statistics
Matches: 50,  Mismatches: 16, Indels: 4
        0.71            0.23        0.06

Matches are distributed among these distances:
  16   21  0.42
  17   29  0.58

ACGTcount: A:0.56, C:0.01, G:0.12, T:0.31


Consensus pattern (17 bp):   
TAAAAAAAATATGTATA

Found at i:6721 original size:49 final size:48

Alignment explanation


    Indices: 6610--6722  Score: 165
    Period size: 49  Copynumber: 2.3  Consensus size: 48

       6600 ATCCCCAATA

                                                          * 
       6610 TATATATATATATATATGTAAAAAAAATATGTATATAAAAGAGATATG
          1 TATATATATATATATATGTAAAAAAAATATGTATATAAAAGAGATAGG

                  * *                                 *       
       6658 TATA-AAACAGTATATATGTATAAAAAAATATGTATATAAAATAGATAGG
          1 TATATATATA-TATATATGTA-AAAAAAATATGTATATAAAAGAGATAGG

                            
       6707 TATATATATATATATA
          1 TATATATATATATATA

       6723 AAATATAGTA


Statistics
Matches: 56,  Mismatches: 6, Indels: 5
        0.84            0.09        0.07

Matches are distributed among these distances:
  47    3  0.05
  48   14  0.25
  49   36  0.64
  50    3  0.05

ACGTcount: A:0.54, C:0.01, G:0.10, T:0.35


Consensus pattern (48 bp):   
TATATATATATATATATGTAAAAAAAATATGTATATAAAAGAGATAGG

Found at i:6736 original size:20 final size:19

Alignment explanation


    Indices: 6613--6752  Score: 67
    Period size: 18  Copynumber: 7.4  Consensus size: 19

       6603 CCCAATATAT

                          *    
       6613 ATATATATATATATGTAAA
          1 ATATATATATATATATAAA

                 *    *        
       6632 A-A-AAATATGTATATAAA
          1 ATATATATATATATATAAA

             * *    *           
       6649 AGAGATATGTATA-A-AACA
          1 ATATATATATATATATAA-A

            *       *      *   
       6667 GTATATATGTATA-AAAAA
          1 ATATATATATATATATAAA

                *        *       
       6685 ATATGTATATA-AAATAGATA
          1 ATATATATATATATATA-A-A

             *                  
       6705 GGTATATATATATATATAAA
          1 -ATATATATATATATATAAA

                         *      
       6725 ATATAGTATATATTTATAAA
          1 ATATA-TATATATATATAAA

             *      
       6745 AAATATAT
          1 ATATATAT

       6753 GTTTAAAATA


Statistics
Matches: 92,  Mismatches: 19, Indels: 20
        0.70            0.15        0.15

Matches are distributed among these distances:
  17   16  0.17
  18   26  0.28
  19   17  0.18
  20   19  0.21
  21   10  0.11
  22    4  0.04

ACGTcount: A:0.55, C:0.01, G:0.09, T:0.36


Consensus pattern (19 bp):   
ATATATATATATATATAAA

Found at i:6752 original size:15 final size:15

Alignment explanation


    Indices: 6732--6791  Score: 50
    Period size: 15  Copynumber: 3.9  Consensus size: 15

       6722 AAAATATAGT

                           
       6732 ATATATTTATAAAAA
          1 ATATATTTATAAAAA

                           *
       6747 ATATATGTT-TAAAAT
          1 ATATAT-TTATAAAAA

                *    *      
       6762 ATACAATTTGTAAAAA
          1 ATA-TATTTATAAAAA

                * *       
       6778 ATATGTATATAAAA
          1 ATATATTTATAAAA

       6792 TTACTAATCT


Statistics
Matches: 35,  Mismatches: 7, Indels: 6
        0.73            0.15        0.12

Matches are distributed among these distances:
  15   23  0.66
  16   12  0.34

ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38


Consensus pattern (15 bp):   
ATATATTTATAAAAA

Found at i:8011 original size:108 final size:108

Alignment explanation


    Indices: 7822--8039  Score: 382
    Period size: 108  Copynumber: 2.0  Consensus size: 108

       7812 TTTTATTTCT

                                                         *                  *
       7822 TAGAGAACCAAGAAACAAGCATGTTGCCTAAGAGTTAACAAGTTCTGGAAGTGCTTTTTCTATCT
          1 TAGAGAACCAAGAAACAAGCATGTTGCCTAAGAGTTAACAAGTTCCGGAAGTGCTTTTTCTATCC

                      *        *                       
       7887 AACTTGCATCTTCCAAAATTCACATCGGAGTAAGCATGCAAAC
         66 AACTTGCATCCTCCAAAATCCACATCGGAGTAAGCATGCAAAC

                                                *                            
       7930 TAGAGAACCAAGAAACAAGCATGTTGCCTAAGAGTTGACAAGTTCCGGAAGTGCTTTTTCTATCC
          1 TAGAGAACCAAGAAACAAGCATGTTGCCTAAGAGTTAACAAGTTCCGGAAGTGCTTTTTCTATCC

                                 *                     
       7995 AACTTGCATCCTCCAAAATCCGCATCGGAGTAAGCATGCAAAC
         66 AACTTGCATCCTCCAAAATCCACATCGGAGTAAGCATGCAAAC

              
       8038 TA
          1 TA

       8040 AATGATGAAT


Statistics
Matches: 104,  Mismatches: 6, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 108  104  1.00

ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25


Consensus pattern (108 bp):   
TAGAGAACCAAGAAACAAGCATGTTGCCTAAGAGTTAACAAGTTCCGGAAGTGCTTTTTCTATCC
AACTTGCATCCTCCAAAATCCACATCGGAGTAAGCATGCAAAC
Done.