Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006491.1 Kokia drynarioides strain JFW-HI SEQ_121075, 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: 41331
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:11066 original size:41 final size:41

Alignment explanation


    Indices: 10999--11094  Score: 129
    Period size: 41  Copynumber: 2.3  Consensus size: 41

      10989 GAATTTTATT

                             *            *     *    
      10999 TTAACAAGAATTCTAGTTACCCAATTCTAATAATCTTCACC
          1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC

                        *        *                   
      11040 TTAACAAGAATTTTAGTCACCTAATTCTAACAATCTCCACC
          1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC

            * *           
      11081 ATGACAAGAATTCT
          1 TTAACAAGAATTCT

      11095 CTACGAACAA


Statistics
Matches: 47,  Mismatches: 8, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  41   47  1.00

ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32


Consensus pattern (41 bp):   
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC

Found at i:11106 original size:17 final size:17

Alignment explanation


    Indices: 11084--11122  Score: 60
    Period size: 17  Copynumber: 2.3  Consensus size: 17

      11074 CTCCACCATG

                   *    *    
      11084 ACAAGAATTCTCTACGA
          1 ACAAGAACTCTCAACGA

                             
      11101 ACAAGAACTCTCAACGA
          1 ACAAGAACTCTCAACGA

                 
      11118 ACAAG
          1 ACAAG

      11123 TTCTCCACTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  17   20  1.00

ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15


Consensus pattern (17 bp):   
ACAAGAACTCTCAACGA

Found at i:19099 original size:28 final size:28

Alignment explanation


    Indices: 19024--19145  Score: 113
    Period size: 29  Copynumber: 4.2  Consensus size: 28

      19014 TAGAGGTCTA

                      *                 
      19024 AACCATCCACTTCTTTCCCCAAATCAAG
          1 AACCATCCACCTCTTTCCCCAAATCAAG

                    * *                    
      19052 AAACCAT-TATCTC-TTCTCCCAAATCAATG
          1 -AACCATCCACCTCTTTC-CCCAAATCAA-G

               *                         
      19081 AACTATCCACCTCTTTCCCCCAAATCAAG
          1 AACCATCCACCTCTTT-CCCCAAATCAAG

            *   *               *         
      19110 GACCGTCCACCTCTTTCCCTAAAATCAAGG
          1 AACCATCCACCTCTTTCCC-CAAATCAA-G

                  
      19140 AACCAT
          1 AACCAT

      19146 TCAATTACAT


Statistics
Matches: 74,  Mismatches: 12, Indels: 13
        0.75            0.12        0.13

Matches are distributed among these distances:
  27    3  0.04
  28   21  0.28
  29   32  0.43
  30   17  0.23
  31    1  0.01

ACGTcount: A:0.32, C:0.37, G:0.06, T:0.25


Consensus pattern (28 bp):   
AACCATCCACCTCTTTCCCCAAATCAAG

Found at i:19124 original size:58 final size:57

Alignment explanation


    Indices: 19028--19142  Score: 126
    Period size: 57  Copynumber: 2.0  Consensus size: 57

      19018 GGTCTAAACC

                  *                        * *                  *     
      19028 ATCCACTTCTTTCCCCAAATCAAGAAACCATTATCTCTTCTCCC-AAATCAATGAACT
          1 ATCCACCTCTTTCCCCAAATCAAGAAACCATCACCTCTT-TCCCAAAATCAAGGAACT

                                      *   *                            
      19085 ATCCACCTCTTTCCCCCAAATCAAG-GACCGTCCACCTCTTTCCCTAAAATCAAGGAAC
          1 ATCCACCTCTTT-CCCCAAATCAAGAAACCAT-CACCTCTTTCCC-AAAATCAAGGAAC

      19143 CATTCAATTA


Statistics
Matches: 48,  Mismatches: 6, Indels: 6
        0.80            0.10        0.10

Matches are distributed among these distances:
  57   19  0.40
  58   18  0.38
  59   11  0.23

ACGTcount: A:0.31, C:0.37, G:0.06, T:0.26


Consensus pattern (57 bp):   
ATCCACCTCTTTCCCCAAATCAAGAAACCATCACCTCTTTCCCAAAATCAAGGAACT

Found at i:27404 original size:16 final size:16

Alignment explanation


    Indices: 27383--27413  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      27373 TTGAAAGAGT

                            
      27383 TTTCAAATATATATGG
          1 TTTCAAATATATATGG

                    *      
      27399 TTTCAAATTTATATG
          1 TTTCAAATATATATG

      27414 CTCTAACATG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48


Consensus pattern (16 bp):   
TTTCAAATATATATGG

Found at i:38334 original size:2 final size:2

Alignment explanation


    Indices: 38327--38392  Score: 114
    Period size: 2  Copynumber: 33.0  Consensus size: 2

      38317 TATGAATAAC

                                                               *          
      38327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                *                              
      38369 AT AC AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT

      38393 TTGCCTTGCG


Statistics
Matches: 60,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   60  1.00

ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.