Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013593.1 Kokia drynarioides strain JFW-HI SEQ_128620, 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: 11272
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33

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


Found at i:6207 original size:99 final size:99

Alignment explanation


    Indices: 6078--6259  Score: 249
    Period size: 99  Copynumber: 1.8  Consensus size: 99

       6068 CGTGTGTCAG

                     *   *    *                         *  *                 
       6078 CCCGTGTGCTTCAGAACAGTATACACACACCCTGACACACG-CTTGTGTGCCAGCCTATGTGCCT
          1 CCCGTGTGCCTCAAAACAATATACACACACCCTGACACACGTC-CGTATGCCAGCCTATGTGCCT

                 * *                           
       6142 CAAAATAGTATACACACACACACCCTTGACACATT
         65 CAAAACAATATACACACACACACCCTTGACACATT

                                           *                 *      *        
       6177 CCCGTGTGCCTCAAAACAATATACACACACCTTGACACACGTCCGTATGTCAGCCTGTGTGCCTC
          1 CCCGTGTGCCTCAAAACAATATACACACACCCTGACACACGTCCGTATGCCAGCCTATGTGCCTC

                       *      
       6242 AAAACAATATATACACAC
         66 AAAACAATATACACACAC

       6260 CCTGACACAC


Statistics
Matches: 71,  Mismatches: 11, Indels: 2
        0.85            0.13        0.02

Matches are distributed among these distances:
  99   70  0.99
 100    1  0.01

ACGTcount: A:0.31, C:0.33, G:0.14, T:0.22


Consensus pattern (99 bp):   
CCCGTGTGCCTCAAAACAATATACACACACCCTGACACACGTCCGTATGCCAGCCTATGTGCCTC
AAAACAATATACACACACACACCCTTGACACATT

Found at i:6215 original size:41 final size:41

Alignment explanation


    Indices: 6157--6329  Score: 139
    Period size: 43  Copynumber: 3.9  Consensus size: 41

       6147 TAGTATACAC

                               *                      
       6157 ACACACACCCTTGACACATTCCCGTGTGCCTCAAAACAATAT
          1 ACACACA-CCTTGACACATGCCCGTGTGCCTCAAAACAATAT

                                                                 
       6199 ACACACACCTTGACACACGTCCGTATGTCAGCCTGTGTGCCTCAAAACAATAT
          1 ACACACACCTTG--ACA----C--ATG-C--CC-GTGTGCCTCAAAACAATAT

             *       *       *  **    *               *
       6252 ATACACACCCTGACACACGCTTGTGTACCTCAAAACAGTATAC
          1 ACACACACCTTGACACATGCCCGTGTGCCTCAAAACA--ATAT

                                               
       6295 ACACACACCTTGACACATGCCCGTGTGCCTCAAAA
          1 ACACACACCTTGACACATGCCCGTGTGCCTCAAAA

       6330 TAGCACCATT


Statistics
Matches: 103,  Mismatches: 14, Indels: 27
        0.72            0.10        0.19

Matches are distributed among these distances:
  41   19  0.18
  42    7  0.07
  43   35  0.34
  44    1  0.01
  45    2  0.02
  47    2  0.02
  49    2  0.02
  50    1  0.01
  51    3  0.03
  52    2  0.02
  53   29  0.28

ACGTcount: A:0.32, C:0.34, G:0.13, T:0.21


Consensus pattern (41 bp):   
ACACACACCTTGACACATGCCCGTGTGCCTCAAAACAATAT

Found at i:7325 original size:24 final size:24

Alignment explanation


    Indices: 7298--7348  Score: 66
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       7288 CCATACAAAA

                            * *     
       7298 TTAGCTCTCACAAGCCTAGAAAGG
          1 TTAGCTCTCACAAGCCCAAAAAGG

                    *  *            
       7322 TTAGCTCTTACGAGCCCAAAAAGG
          1 TTAGCTCTCACAAGCCCAAAAAGG

               
       7346 TTA
          1 TTA

       7349 ACCATTATAC


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24


Consensus pattern (24 bp):   
TTAGCTCTCACAAGCCCAAAAAGG

Found at i:10283 original size:16 final size:16

Alignment explanation


    Indices: 10262--10294  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      10252 ACTTAATGTG

                             
      10262 TAATTC-TATTGTATGA
          1 TAATTCTTA-TGTATGA

                            
      10278 TAATTCTTATGTATGA
          1 TAATTCTTATGTATGA

             
      10294 T
          1 T

      10295 GATATAGTAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16   14  0.88
  17    2  0.12

ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52


Consensus pattern (16 bp):   
TAATTCTTATGTATGA
Done.