Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008213.1 Kokia drynarioides strain JFW-HI SEQ_122877, 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: 15097
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36

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


Found at i:5015 original size:59 final size:59

Alignment explanation


    Indices: 4923--5037  Score: 212
    Period size: 59  Copynumber: 1.9  Consensus size: 59

       4913 ATTCTCGTTG

                                                                       
       4923 AAGTTTGCTTATATGAAACATTGTAGTTCAGTTCAAGAATAGCCGTTATTTTCATAAGA
          1 AAGTTTGCTTATATGAAACATTGTAGTTCAGTTCAAGAATAGCCGTTATTTTCATAAGA

                   *                                   *            
       4982 AAGTTTGGTTATATGAAACATTGTAGTTCAGTTCAAGAATAGCTGTTATTTTCATA
          1 AAGTTTGCTTATATGAAACATTGTAGTTCAGTTCAAGAATAGCCGTTATTTTCATA

       5038 TTTCTTGACA


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  59   54  1.00

ACGTcount: A:0.33, C:0.10, G:0.17, T:0.39


Consensus pattern (59 bp):   
AAGTTTGCTTATATGAAACATTGTAGTTCAGTTCAAGAATAGCCGTTATTTTCATAAGA

Found at i:5565 original size:23 final size:23

Alignment explanation


    Indices: 5539--5583  Score: 56
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       5529 TTTTATTGAT

                                    
       5539 AACA-TTTAAAAGAAAATAGTTTC
          1 AACACTTTAAAAG-AAATAGTTTC

                    *  *          
       5562 AACACTTTGAATGAAATAGTTT
          1 AACACTTTAAAAGAAATAGTTT

       5584 TTAAATATAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  23   13  0.68
  24    6  0.32

ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33


Consensus pattern (23 bp):   
AACACTTTAAAAGAAATAGTTTC

Found at i:8044 original size:78 final size:78

Alignment explanation


    Indices: 7939--8156  Score: 201
    Period size: 78  Copynumber: 2.8  Consensus size: 78

       7929 CATTGTAGTT

                  *          *     *          *                        *     
       7939 TTTACATTGTCACTGCTAAG-TCGGTATAGCTTCACAGTGTTTACAGTGTCACTAT-C-TGTTCA
          1 TTTACAGTGTCACTG-TCAGTTCAGTATAGCTTCGCAGTGTTTACAGTGTCA-T-TGCAAGTTCA

            *       *    *  
       8001 GTATAGTTTCGCATTA
         63 ATATAGTTCCGCAGTA

                                         *          *  *  *                  
       8017 TTTACAGTGTCACTGTCAGTTCAGTATAGTTTCGCAGTGTGTATAGAGTCATTGCAAGTTCAATA
          1 TTTACAGTGTCACTGTCAGTTCAGTATAGCTTCGCAGTGTTTACAGTGTCATTGCAAGTTCAATA

                        *
       8082 TAGTTCCGCAGTG
         66 TAGTTCCGCAGTA

                           *  *          *   * *                    *      
       8095 TTTACAGTGTCACT-ACTTGTTCAGTATAACTTTGTAGTGTTTACAGTGTCATTGCTAGTTCA
          1 TTTACAGTGTCACTGTC-AGTTCAGTATAGCTTCGCAGTGTTTACAGTGTCATTGCAAGTTCA

       8157 GTATTTTGAT


Statistics
Matches: 113,  Mismatches: 23, Indels: 8
        0.78            0.16        0.06

Matches are distributed among these distances:
  76    1  0.01
  77    6  0.05
  78  106  0.94

ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39


Consensus pattern (78 bp):   
TTTACAGTGTCACTGTCAGTTCAGTATAGCTTCGCAGTGTTTACAGTGTCATTGCAAGTTCAATA
TAGTTCCGCAGTA

Found at i:8156 original size:39 final size:38

Alignment explanation


    Indices: 7858--8160  Score: 168
    Period size: 39  Copynumber: 7.8  Consensus size: 38

       7848 ATGTTTAAGT

                               * **         *  *   
       7858 AGTGTTTACAGTGTCACT-ATTTTTCAGTATAGTCGTGC
          1 AGTGTTTACAGTGTCACTGCTAGTTCAGTATACT-TTGC

                         *    *           *     *   *
       7896 -GATGTTTACAGTATCACCG-TCAGTTCAGAATAACATTGT
          1 AG-TGTTTACAGTGTCACTGCT-AGTTCAGTAT-ACTTTGC

               *      *                *         ** 
       7935 AGTTTTTACATTGTCACTGCTAAG-TCGGTATAGCTTCAC
          1 AGTGTTTACAGTGTCACTGCT-AGTTCAGTATA-CTTTGC

                               *             *      
       7974 AGTGTTTACAGTGTCACTATCT-GTTCAGTATAGTTTCGC
          1 AGTGTTTACAGTGTCACT-GCTAGTTCAGTATACTTT-GC

             * *                             *      
       8013 ATTATTTACAGTGTCACTG-TCAGTTCAGTATAGTTTCGC
          1 AGTGTTTACAGTGTCACTGCT-AGTTCAGTATACTTT-GC

                 *  *  *    *   *      *    *   *  
       8052 AGTGTGTATAGAGTCATTGCAAGTTCAATATAGTTCCGC
          1 AGTGTTTACAGTGTCACTGCTAGTTCAGTATACTT-TGC

                              *  *                *
       8091 AGTGTTTACAGTGTCACTACTTGTTCAGTATAACTTTGT
          1 AGTGTTTACAGTGTCACTGCTAGTTCAGTAT-ACTTTGC

                            *              
       8130 AGTGTTTACAGTGTCATTGCTAGTTCAGTAT
          1 AGTGTTTACAGTGTCACTGCTAGTTCAGTAT

       8161 TTTGATCACT


Statistics
Matches: 197,  Mismatches: 53, Indels: 29
        0.71            0.19        0.10

Matches are distributed among these distances:
  37    2  0.01
  38   19  0.10
  39  166  0.84
  40   10  0.05

ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39


Consensus pattern (38 bp):   
AGTGTTTACAGTGTCACTGCTAGTTCAGTATACTTTGC

Found at i:9611 original size:24 final size:24

Alignment explanation


    Indices: 9584--9631  Score: 87
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       9574 CTCAGTCTCT

                       *            
       9584 GGTACTAATTCGGGACCTAGTACC
          1 GGTACTAATTCAGGACCTAGTACC

                                    
       9608 GGTACTAATTCAGGACCTAGTACC
          1 GGTACTAATTCAGGACCTAGTACC

       9632 CGTCTCTCCC


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25


Consensus pattern (24 bp):   
GGTACTAATTCAGGACCTAGTACC
Done.