Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009689.1 Kokia drynarioides strain JFW-HI SEQ_124407, 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: 355750
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 50 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:325559 original size:15 final size:15

Alignment explanation


    Indices: 325541--325585  Score: 72
    Period size: 15  Copynumber: 3.0  Consensus size: 15

     325531 AGGACAAATA

                    *      
     325541 TTAAATTGGTTTAAT
          1 TTAAATTGATTTAAT

                        *  
     325556 TTAAATTGATTTTAT
          1 TTAAATTGATTTAAT

                           
     325571 TTAAATTGATTTAAT
          1 TTAAATTGATTTAAT

     325586 AACTCCTTTA


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   27  1.00

ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56


Consensus pattern (15 bp):   
TTAAATTGATTTAAT

Found at i:328422 original size:23 final size:25

Alignment explanation


    Indices: 328396--328443  Score: 64
    Period size: 23  Copynumber: 2.0  Consensus size: 25

     328386 TTTTCTCTCG

                                     
     328396 AATTTTT-CCTGCAAA-ATTTCAAA
          1 AATTTTTGCCTGCAAATATTTCAAA

                     *       *       
     328419 AATTTTTGCTTGCAAATTTTTCAAA
          1 AATTTTTGCCTGCAAATATTTCAAA

     328444 CAGTTGTGCT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  23    7  0.33
  24    7  0.33
  25    7  0.33

ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44


Consensus pattern (25 bp):   
AATTTTTGCCTGCAAATATTTCAAA

Found at i:339297 original size:57 final size:57

Alignment explanation


    Indices: 339236--339460  Score: 182
    Period size: 57  Copynumber: 4.1  Consensus size: 57

     339226 GACAGCAGCA

                                     * *      * *                    
     339236 TCAACACCCTCTCCACCTAAACCTTTAACACCTTTATCACCTTTACTGCCAGCAACC
          1 TCAACACCCTCTCCACCTAAACCTTCACCACCTTCACCACCTTTACTGCCAGCAACC

                      * *   *            *                           
     339293 TCAACACCCTTTTCACTTAAACCTTCACCGCCTT-A--A-C--TA-T--CAGCAACC
          1 TCAACACCCTCTCCACCTAAACCTTCACCACCTTCACCACCTTTACTGCCAGCAACC

                          *             *    *      *     *     *     
     339341 TCAACACCCTGC-CAACCTAAACCTTCAGCACCATCACCATCTTTATTGCCAACAACC
          1 TCAACACCCT-CTCCACCTAAACCTTCACCACCTTCACCACCTTTACTGCCAGCAACC

               *    *  *                                       *        
     339398 TCACCACCTTCCCCACCTAAACCTTCACCACCATCCTCACCACCTTTACTGGCAGCAACC
          1 TCAACACCCTCTCCACCTAAACCTTCACCACC-T--TCACCACCTTTACTGCCAGCAACC

               
     339458 TCA
          1 TCA

     339461 CCACTTTTAT


Statistics
Matches: 131,  Mismatches: 23, Indels: 25
        0.73            0.13        0.14

Matches are distributed among these distances:
  48   34  0.26
  49    1  0.01
  50    1  0.01
  51    3  0.02
  52    1  0.01
  53    1  0.01
  54    3  0.02
  55    1  0.01
  56    2  0.02
  57   61  0.47
  60   23  0.18

ACGTcount: A:0.28, C:0.44, G:0.04, T:0.24


Consensus pattern (57 bp):   
TCAACACCCTCTCCACCTAAACCTTCACCACCTTCACCACCTTTACTGCCAGCAACC

Found at i:339425 original size:24 final size:23

Alignment explanation


    Indices: 339394--339438  Score: 63
    Period size: 24  Copynumber: 1.9  Consensus size: 23

     339384 TATTGCCAAC

                        *          
     339394 AACCTCACCACCTTCCCCACCTA
          1 AACCTCACCACCATCCCCACCTA

                             *    
     339417 AACCTTCACCACCATCCTCACC
          1 AACC-TCACCACCATCCCCACC

     339439 ACCTTTACTG


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  23    4  0.21
  24   15  0.79

ACGTcount: A:0.27, C:0.56, G:0.00, T:0.18


Consensus pattern (23 bp):   
AACCTCACCACCATCCCCACCTA

Found at i:339480 original size:24 final size:24

Alignment explanation


    Indices: 339432--339480  Score: 62
    Period size: 24  Copynumber: 2.0  Consensus size: 24

     339422 TCACCACCAT

                             *  *   
     339432 CCTCACCACCTTTACTGGCAGCAA
          1 CCTCACCACCTTTACTGCCAACAA

                     *    *         
     339456 CCTCACCACTTTTATTGCCAACAA
          1 CCTCACCACCTTTACTGCCAACAA

             
     339480 C
          1 C

     339481 TTTAACACCT


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  24   21  1.00

ACGTcount: A:0.27, C:0.41, G:0.08, T:0.24


Consensus pattern (24 bp):   
CCTCACCACCTTTACTGCCAACAA

Found at i:340358 original size:29 final size:29

Alignment explanation


    Indices: 340229--340358  Score: 97
    Period size: 30  Copynumber: 4.4  Consensus size: 29

     340219 AAAAAATACA

                 *           **           
     340229 CAAAAATCCTAAACAAATGTCT-CACAAAT
          1 CAAAACTCCTAAACAAAAATCTCCA-AAAT

                     *             *       
     340258 CGAAAAC-CATAAA-AGAAAATCCCCAAAAT
          1 C-AAAACTCCTAAACA-AAAATCTCCAAAAT

            *     *       *         *     
     340287 TAGAAAATCCTAAATAAAAATCTCGAAAAT
          1 CA-AAACTCCTAAACAAAAATCTCCAAAAT

                                           
     340317 CAAATTAC-CCTAAACAAAAATCTCCAAAAT
          1 CAAA--ACTCCTAAACAAAAATCTCCAAAAT

                        
     340347 CAAAACTCCTAA
          1 CAAAACTCCTAA

     340359 CCCAAGATCC


Statistics
Matches: 78,  Mismatches: 14, Indels: 18
        0.71            0.13        0.16

Matches are distributed among these distances:
  28    4  0.05
  29   24  0.31
  30   48  0.62
  31    2  0.03

ACGTcount: A:0.55, C:0.23, G:0.04, T:0.18


Consensus pattern (29 bp):   
CAAAACTCCTAAACAAAAATCTCCAAAAT

Done.