Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010651.1 Kokia drynarioides strain JFW-HI SEQ_125594, 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: 10735
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:413 original size:6 final size:6

Alignment explanation


    Indices: 402--467  Score: 57
    Period size: 6  Copynumber: 11.0  Consensus size: 6

        392 ATTATTTAAA

                                                             * *      
        402 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TAAAATA AAAATTT
          1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAA-TT

                 *              
        451 TAAA-A TAAATT TAAATT
          1 TAAATT TAAATT TAAATT

        468 CTACTGGGCC


Statistics
Matches: 48,  Mismatches: 6, Indels: 12
        0.73            0.09        0.18

Matches are distributed among these distances:
   4    2  0.04
   5    6  0.12
   6   30  0.62
   7   10  0.21

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (6 bp):   
TAAATT

Found at i:430 original size:17 final size:17

Alignment explanation


    Indices: 408--467  Score: 81
    Period size: 17  Copynumber: 3.7  Consensus size: 17

        398 TAAATAAATT

                          *  
        408 TAAATTTAAATTTATAA
          1 TAAATTTAAATTTAAAA

                             
        425 TAAATTTAAATTTAAAA
          1 TAAATTTAAATTTAAAA

                     *       
        442 TAAA---AATTTTAAAA
          1 TAAATTTAAATTTAAAA

                        
        456 TAAATTTAAATT
          1 TAAATTTAAATT

        468 CTACTGGGCC


Statistics
Matches: 37,  Mismatches: 3, Indels: 6
        0.80            0.07        0.13

Matches are distributed among these distances:
  14   13  0.35
  17   24  0.65

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (17 bp):   
TAAATTTAAATTTAAAA

Found at i:430 original size:23 final size:22

Alignment explanation


    Indices: 395--466  Score: 87
    Period size: 23  Copynumber: 3.4  Consensus size: 22

        385 ATTGGACATT

                                  
        395 ATTTAAATAAATTTAAATTTAA
          1 ATTTAAATAAATTTAAATTTAA

                                   
        417 ATTTATAATAAATTTAAATTTAA
          1 ATTTA-AATAAATTTAAATTTAA

              *       *       *   
        440 A-ATAAA-AATTTTAAA-ATAA
          1 ATTTAAATAAATTTAAATTTAA

                    
        459 ATTTAAAT
          1 ATTTAAAT

        467 TCTACTGGGC


Statistics
Matches: 43,  Mismatches: 4, Indels: 7
        0.80            0.07        0.13

Matches are distributed among these distances:
  19    4  0.09
  20   12  0.28
  21    2  0.05
  22    7  0.16
  23   18  0.42

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (22 bp):   
ATTTAAATAAATTTAAATTTAA

Found at i:1368 original size:205 final size:203

Alignment explanation


    Indices: 860--1385  Score: 692
    Period size: 195  Copynumber: 2.6  Consensus size: 203

        850 TCTCTGTGTT

                          *                *             *                 * 
        860 TCATCAGGAAGACGGATTTGGTTCTCTTCTCCGTATCTCATCAGGGAGCTAACCATTTTTATTAC
          1 TCATCAGGAAGACGAATTTGG-TC-CTTCTCAGTATCTCATCAGGAAGCTAACC--TTTTATTGC

                              *                                   *          
        925 TTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATATCGAGCGTG
         62 TTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTG

                **                                       *   *              *
        990 AGTTTTATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTTGTCTCAATCCG
        127 AGTTCGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCGTTTGTCTCAATCCA

             *          
       1055 CTTCTCTATACC
        192 CCTCTCTATACC

                         *                       *       *                   
       1067 TCATCAGGAAGACAAATTTGG--------AGTATCTCGTCAGGAAACTAACCTTTTATTGCTTCG
          1 TCATCAGGAAGACGAATTTGGTCCTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG

                                                                         *   
       1124 ACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTT
         66 ACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTT

                                     *      *                   *     *      
       1189 CGATTTGGTCTTCTTCTCAGTATCTTATCAGGGAGATGACCACGTCGTTTGTTTCAATTCACCTC
        131 CGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCGTTTGTCTCAATCCACCTC

             * *  * 
       1254 TTTGTATC
        196 TCTATACC

                                                                     *       
       1262 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTGATTGCTT
          1 TCATCAGGAAGACGAATTTGGT-C-CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTT

                                     *    *               *             
       1327 CGACCTGCTTCTCAGTGTCTCATCAAGAAGTTGGGGTTCGAAGA-TCGCTCACATCGAGC
         64 CGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC

       1386 CCTGAGTTGG


Statistics
Matches: 279,  Mismatches: 30, Indels: 23
        0.84            0.09        0.07

Matches are distributed among these distances:
 195  154  0.55
 197   19  0.07
 204   14  0.05
 205   73  0.26
 207   19  0.07

ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34


Consensus pattern (203 bp):   
TCATCAGGAAGACGAATTTGGTCCTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG
ACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTT
CGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCGTTTGTCTCAATCCACCTC
TCTATACC
Done.