Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004112.1 Kokia drynarioides strain JFW-HI SEQ_117294, 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: 25381
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:3172 original size:17 final size:18

Alignment explanation


    Indices: 3143--3179  Score: 51
    Period size: 17  Copynumber: 2.1  Consensus size: 18

       3133 AGTTTAAAGT

                              
       3143 AATAATATAATTTAT-AA
          1 AATAATATAATTTATCAA

                               
       3160 AATAA-ATAGATTTATCAA
          1 AATAATATA-ATTTATCAA

              
       3178 AA
          1 AA

       3180 ATCCCTATTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  16    3  0.17
  17   11  0.61
  18    4  0.22

ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35


Consensus pattern (18 bp):   
AATAATATAATTTATCAA

Found at i:4680 original size:14 final size:14

Alignment explanation


    Indices: 4643--4702  Score: 61
    Period size: 14  Copynumber: 4.4  Consensus size: 14

       4633 GGTTTAAAAA

                   *     *
       4643 GTCAACAATCAA-A
          1 GTCAACAGTCAATG

                          
       4656 GTCAA-AGTCAATG
          1 GTCAACAGTCAATG

                         *
       4669 GTCAACAGTCAATT
          1 GTCAACAGTCAATG

            * *           
       4683 ATAAACAGTCAATG
          1 GTCAACAGTCAATG

                  
       4697 GTCAAC
          1 GTCAAC

       4703 GGGTCGGGTC


Statistics
Matches: 37,  Mismatches: 8, Indels: 3
        0.77            0.17        0.06

Matches are distributed among these distances:
  12    5  0.14
  13   10  0.27
  14   22  0.59

ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22


Consensus pattern (14 bp):   
GTCAACAGTCAATG

Found at i:5873 original size:24 final size:24

Alignment explanation


    Indices: 5846--5970  Score: 97
    Period size: 24  Copynumber: 5.0  Consensus size: 24

       5836 TACGCTCACT

                       *            
       5846 AGCTTGCATACATTTACGCTCGTC
          1 AGCTTGCATACGTTTACGCTCGTC

                 **     *      *    * 
       5870 AGCTTATATATGTGTTTACACTCGGC
          1 AGCTTGCATA--CGTTTACGCTCGTC

                    *  *    *       
       5896 AGCTTGCACACTTTTATGCTCGTC
          1 AGCTTGCATACGTTTACGCTCGTC

                 **                 * 
       5920 AGCTTTTATATTCGTTTACGCTCGCC
          1 AGCTTGCATA--CGTTTACGCTCGTC

                    *               
       5946 AGCTTGCACACGTTTACGCTCGTC
          1 AGCTTGCATACGTTTACGCTCGTC

             
       5970 A
          1 A

       5971 ACTTATATAT


Statistics
Matches: 73,  Mismatches: 24, Indels: 8
        0.70            0.23        0.08

Matches are distributed among these distances:
  24   38  0.52
  26   35  0.48

ACGTcount: A:0.19, C:0.27, G:0.18, T:0.36


Consensus pattern (24 bp):   
AGCTTGCATACGTTTACGCTCGTC

Found at i:5917 original size:50 final size:51

Alignment explanation


    Indices: 5846--5981  Score: 186
    Period size: 50  Copynumber: 2.7  Consensus size: 51

       5836 TACGCTCACT

                    *                                        * 
       5846 AGCTTGCATACATTTACGCTCGTCAGCTTATATATGT-GTTTACACTCGGC
          1 AGCTTGCACACATTTACGCTCGTCAGCTTATATATGTCGTTTACACTCGCC

                       *    *            *              *      
       5896 AGCTTGCACACTTTTATGCTCGTCAGCTTTTATAT-TCGTTTACGCTCGCC
          1 AGCTTGCACACATTTACGCTCGTCAGCTTATATATGTCGTTTACACTCGCC

                       *             *          
       5946 AGCTTGCACACGTTTACGCTCGTCAACTTATATATG
          1 AGCTTGCACACATTTACGCTCGTCAGCTTATATATG

       5982 CATTACTTGA


Statistics
Matches: 74,  Mismatches: 10, Indels: 3
        0.85            0.11        0.03

Matches are distributed among these distances:
  49    1  0.01
  50   73  0.99

ACGTcount: A:0.21, C:0.26, G:0.17, T:0.37


Consensus pattern (51 bp):   
AGCTTGCACACATTTACGCTCGTCAGCTTATATATGTCGTTTACACTCGCC

Found at i:17085 original size:17 final size:18

Alignment explanation


    Indices: 17065--17099  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

      17055 AATTATTTTC

                              
      17065 ATTTTTAAAT-ATAAAAT
          1 ATTTTTAAATCATAAAAT

                   *          
      17082 ATTTTTATATCATAAAAT
          1 ATTTTTAAATCATAAAAT

      17100 TTAAAAATTA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    9  0.56
  18    7  0.44

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (18 bp):   
ATTTTTAAATCATAAAAT

Found at i:17790 original size:17 final size:17

Alignment explanation


    Indices: 17757--17800  Score: 54
    Period size: 18  Copynumber: 2.5  Consensus size: 17

      17747 ATAGCTTATT

                               
      17757 CTTTTTTGTTCAG-TTTTA
          1 CTTTTTT-TT-AGTTTTTA

                              
      17775 CTTTATTTTTAGTTTTTA
          1 CTTT-TTTTTAGTTTTTA

                    
      17793 CTTTTTTT
          1 CTTTTTTT

      17801 ATTTCCCAAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  17    6  0.25
  18   15  0.62
  19    3  0.12

ACGTcount: A:0.11, C:0.09, G:0.07, T:0.73


Consensus pattern (17 bp):   
CTTTTTTTTAGTTTTTA
Done.