Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000192.1 Kokia drynarioides strain JFW-HI SEQ_110876, 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: 12210
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1943 original size:23 final size:23

Alignment explanation


    Indices: 1846--1945  Score: 112
    Period size: 23  Copynumber: 4.3  Consensus size: 23

       1836 AGTGTTGGGC

                             *     
       1846 AACAGAGAGCACACACAATGCTA
          1 AACAGAGAGCACACACAGTGCTA

             *             *    *  
       1869 ATCAGAGAGCACACAAAGTGTTA
          1 AACAGAGAGCACACACAGTGCTA

             *                      
       1892 ATCAGAGAGCACACACAGTGCTAA
          1 AACAGAGAGCACACACAGTGCT-A

                           *         
       1916 TAACAGAGAGCACGAGAC-GTGCTA
          1 -AACAGAGAGCAC-ACACAGTGCTA

                  
       1940 AACAGA
          1 AACAGA

       1946 TAGCGCGCTA


Statistics
Matches: 66,  Mismatches: 8, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  23   45  0.68
  24    2  0.03
  25   16  0.24
  26    3  0.05

ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12


Consensus pattern (23 bp):   
AACAGAGAGCACACACAGTGCTA

Found at i:5459 original size:29 final size:29

Alignment explanation


    Indices: 5426--5481  Score: 85
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       5416 TTTGACTCTT

                   *                     
       5426 TTTAATAGTATAGAGACTAAATTGATCCA
          1 TTTAATAATATAGAGACTAAATTGATCCA

                         *      *      
       5455 TTTAATAATATAGGGACTAATTTGATC
          1 TTTAATAATATAGAGACTAAATTGATC

       5482 TGTCCGTATA


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  29   24  1.00

ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38


Consensus pattern (29 bp):   
TTTAATAATATAGAGACTAAATTGATCCA

Found at i:7568 original size:9 final size:9

Alignment explanation


    Indices: 7554--7579  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

       7544 GATACTAACA

                     
       7554 TTTCTTCGG
          1 TTTCTTCGG

                     
       7563 TTTCTTCGG
          1 TTTCTTCGG

                    
       7572 TTTCTTCG
          1 TTTCTTCG

       7580 ACCCCCATTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.00, C:0.23, G:0.19, T:0.58


Consensus pattern (9 bp):   
TTTCTTCGG

Found at i:9907 original size:34 final size:36

Alignment explanation


    Indices: 9844--9925  Score: 89
    Period size: 34  Copynumber: 2.4  Consensus size: 36

       9834 GCTTTTAATA

                      *                    *   *
       9844 TTTTTTTAAAAT-TTAATTTGCATTCTATATGT-TT
          1 TTTTTTTAAATTATTAATTTGCATTCTATATATATG

                                  *  *          
       9878 TTTTTTTAAATTATTAATTT-CTTTGTATATATATG
          1 TTTTTTTAAATTATTAATTTGCATTCTATATATATG

            *            
       9913 GTTTTTTAAATTA
          1 TTTTTTTAAATTA

       9926 ATTTTATTTT


Statistics
Matches: 40,  Mismatches: 6, Indels: 3
        0.82            0.12        0.06

Matches are distributed among these distances:
  34   20  0.50
  35   20  0.50

ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62


Consensus pattern (36 bp):   
TTTTTTTAAATTATTAATTTGCATTCTATATATATG

Found at i:11374 original size:105 final size:104

Alignment explanation


    Indices: 11200--11434  Score: 242
    Period size: 105  Copynumber: 2.2  Consensus size: 104

      11190 AGCACAATAC

                              *    *             *     * *    **             
      11200 TGAGCCTGATGTTGTCACTTATAATATATTGGTTGATGCGTATTGTAAGGCTGGGATCATTTCTA
          1 TGAGCCTGATGTTGTCACGTATAGTATATTGGTTGATACGTATGGCAAGGAGGGGATCATTTCTA

                    *     *     *                 *  
      11265 AAGCTGTAGACACTGTTGACGCAATGAGAAA-TCAAGATAT
         66 AAGCTGTAAACACTATTGACACAATGAGAAACTC-AG-CAT

                   *                               *                         
      11305 TGAGCCTAATGTTGTCACGTATAGTATATTGGTTGATACTTATGGCAAGGAGGGGA-CGATTT-T
          1 TGAGCCTGATGTTGTCACGTATAGTATATTGGTTGATACGTATGGCAAGGAGGGGATC-ATTTCT

             *          *        *                    
      11368 CCAAGCTGTAAATACTATTGATACAATGAGAAAGCTCAGCAT
         65 -AAAGCTGTAAACACTATTGACACAATGAGAAA-CTCAGCAT

               *           *         
      11410 TGAACCTGATGTTGTTACGTATAGT
          1 TGAGCCTGATGTTGTCACGTATAGT

      11435 GCGTTAATAA


Statistics
Matches: 107,  Mismatches: 19, Indels: 8
        0.80            0.14        0.06

Matches are distributed among these distances:
 104    2  0.02
 105  101  0.94
 106    2  0.02
 107    2  0.02

ACGTcount: A:0.30, C:0.14, G:0.24, T:0.33


Consensus pattern (104 bp):   
TGAGCCTGATGTTGTCACGTATAGTATATTGGTTGATACGTATGGCAAGGAGGGGATCATTTCTA
AAGCTGTAAACACTATTGACACAATGAGAAACTCAGCAT
Done.