Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009942.1 Kokia drynarioides strain JFW-HI SEQ_124684, 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: 2439
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.23

Warning! 59 characters in sequence are not A, C, G, or T


Found at i:1691 original size:139 final size:139

Alignment explanation


    Indices: 1114--1676  Score: 739
    Period size: 139  Copynumber: 4.1  Consensus size: 139

       1104 ATCCACAAAG

                                             *           *               *   
       1114 CAGATTCGTCTTCCTGATGAGATACAGAGAAACTGATCGAAACAGTGATGGGATCATCTTCTTGA
          1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGCGATGGGATCATCTTCCTGA

                     *                *                                      
       1179 TGAGACACTAAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
         66 TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA

                     
       1244 GAAGTGAAC
        131 GAAGTGAAC

                                  * *          *                             
       1253 CAGATTCGTCTTCCTGATGAGACATAGAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGA
          1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGCGATGGGATCATCTTCCTGA

                                     *                                     * 
       1318 TGAGACACTGAGAAGAAAACCCAAATGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGAA
         66 TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA

                     
       1383 GAAGTGAAC
        131 GAAGTGAAC

                                      *        *                             
       1392 CAGATTCGTCTTCCTGATGAGATACAAAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGA
          1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGCGATGGGATCATCTTCCTGA

                                     *****************                       
       1457 TGAGACACTGAGAAGAAAACCCAAANNNNNNNNNNNNNNNNNAAATCTTCCTGATGAGATACGGA
         66 TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA

                     
       1522 GAAGTGAAC
        131 GAAGTGAAC

                           *                      *      *                *  
       1531 CAGATTCGTCTTCCTAATGAGATACAGAGAAACGGATCAAAACAGTGATGGGATCATCTTCCCGA
          1 CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGCGATGGGATCATCTTCCTGA

                  *        * *              *          *    *  *      *   *  
       1596 TGAGACGCTGAGAAGGAGACCCAAACGAGGCTTGAAACGAGCAGATCTACCAGATGAGGTACTGA
         66 TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA

                     
       1661 GAAGTGAAC
        131 GAAGTGAAC

              *    
       1670 CAAATTC
          1 CAGATTC

       1677 ATAAGCGAAT


Statistics
Matches: 361,  Mismatches: 63, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
 139  361  1.00

ACGTcount: A:0.35, C:0.19, G:0.24, T:0.19


Consensus pattern (139 bp):   
CAGATTCGTCTTCCTGATGAGATACAGAGAAACGGATCGAAACAGCGATGGGATCATCTTCCTGA
TGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGA
GAAGTGAAC

Found at i:2280 original size:15 final size:15

Alignment explanation


    Indices: 2262--2326  Score: 69
    Period size: 15  Copynumber: 4.3  Consensus size: 15

       2252 AGTCCAAATT

                           
       2262 ACAAATGGCCCAATA
          1 ACAAATGGCCCAATA

                        * *
       2277 ACAAATGGCCCAGTT
          1 ACAAATGGCCCAATA

               *           
       2292 ACAGATGGCCCAA-A
          1 ACAAATGGCCCAATA

                    *      *
       2306 TACAAATGACCCAATT
          1 -ACAAATGGCCCAATA

                 
       2322 ACAAA
          1 ACAAA

       2327 GTGCCCGAAA


Statistics
Matches: 40,  Mismatches: 8, Indels: 4
        0.77            0.15        0.08

Matches are distributed among these distances:
  15   40  1.00

ACGTcount: A:0.45, C:0.26, G:0.14, T:0.15


Consensus pattern (15 bp):   
ACAAATGGCCCAATA

Found at i:2280 original size:30 final size:29

Alignment explanation


    Indices: 2242--2326  Score: 98
    Period size: 30  Copynumber: 2.9  Consensus size: 29

       2232 ACAAAAAAAT

                      * *  *             
       2242 CCAAAACAAAAGTCCAAATTACAAATGGC
          1 CCAAAACAAATGACCCAATTACAAATGGC

                         *    *     *     
       2271 CCAATAACAAATGGCCCAGTTACAGATGGC
          1 CCAA-AACAAATGACCCAATTACAAATGGC

                                      
       2301 CCAAATACAAATGACCCAATTACAAA
          1 CCAAA-ACAAATGACCCAATTACAAA

       2327 GTGCCCGAAA


Statistics
Matches: 46,  Mismatches: 8, Indels: 3
        0.81            0.14        0.05

Matches are distributed among these distances:
  29    5  0.11
  30   41  0.89

ACGTcount: A:0.47, C:0.26, G:0.12, T:0.15


Consensus pattern (29 bp):   
CCAAAACAAATGACCCAATTACAAATGGC
Done.