Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004787.1 Kokia drynarioides strain JFW-HI SEQ_118403, 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: 11018
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:126 original size:15 final size:15

Alignment explanation


    Indices: 93--148  Score: 69
    Period size: 15  Copynumber: 3.7  Consensus size: 15

         83 TTTCCTCTCC

                           *
         93 TTCTTCC-TCTTCTCC
          1 TTCTTCCTTCTT-TCT

                           
        108 TTCTTCCTTCTTTCT
          1 TTCTTCCTTCTTTCT

                            
        123 TTCTTTCCTTCTTTCT
          1 TTC-TTCCTTCTTTCT

              *       
        139 TTTTTCCTTC
          1 TTCTTCCTTC

        149 ATTTTTCGTT


Statistics
Matches: 37,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
  15   19  0.51
  16   18  0.49

ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64


Consensus pattern (15 bp):   
TTCTTCCTTCTTTCT

Found at i:130 original size:16 final size:15

Alignment explanation


    Indices: 111--148  Score: 67
    Period size: 16  Copynumber: 2.5  Consensus size: 15

        101 CTTCTCCTTC

                            
        111 TTCCTTCTTTCTTTCT
          1 TTCCTTCTTTCTTT-T

                           
        127 TTCCTTCTTTCTTTT
          1 TTCCTTCTTTCTTTT

                   
        142 TTCCTTC
          1 TTCCTTC

        149 ATTTTTCGTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15    8  0.36
  16   14  0.64

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (15 bp):   
TTCCTTCTTTCTTTT

Found at i:135 original size:23 final size:24

Alignment explanation


    Indices: 100--144  Score: 65
    Period size: 23  Copynumber: 1.9  Consensus size: 24

         90 TCCTTCTTCC

                                    
        100 TCTTCTCCTTCTTCCTTCTTTCTT
          1 TCTTCTCCTTCTTCCTTCTTTCTT

                         *   *    
        124 TCTT-TCCTTCTTTCTTTTTTC
          1 TCTTCTCCTTCTTCCTTCTTTC

        145 CTTCATTTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  23   15  0.79
  24    4  0.21

ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67


Consensus pattern (24 bp):   
TCTTCTCCTTCTTCCTTCTTTCTT

Found at i:136 original size:12 final size:12

Alignment explanation


    Indices: 90--140  Score: 50
    Period size: 12  Copynumber: 4.1  Consensus size: 12

         80 TTTTTTCCTC

                          
         90 TCCTTCTTCCTCTT
          1 TCCTTCTT--TCTT

                       * 
        104 CTCCTTC-TTCCT
          1 -TCCTTCTTTCTT

              *         
        116 TCTTTCTTTCTT
          1 TCCTTCTTTCTT

                        
        128 TCCTTCTTTCTT
          1 TCCTTCTTTCTT

             
        140 T
          1 T

        141 TTTCCTTCAT


Statistics
Matches: 31,  Mismatches: 4, Indels: 5
        0.77            0.10        0.12

Matches are distributed among these distances:
  11    5  0.16
  12   19  0.61
  14    1  0.03
  15    6  0.19

ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63


Consensus pattern (12 bp):   
TCCTTCTTTCTT

Found at i:3388 original size:154 final size:154

Alignment explanation


    Indices: 3108--3566  Score: 701
    Period size: 154  Copynumber: 3.0  Consensus size: 154

       3098 ATAATGCTCG

                    *                                   *            *  *    
       3108 AGTCAGGGTATCGACTAATCTTGAAAATATGTTAACAAGTTTATGCATATATATATATATAGCTT
          1 AGTCAGGGCATCGACTAATCTTGAAAATATGTTAACAAGTTTATCCATATATATATACATGGCTT

              *                                                              
       3173 GATTAACTTCAATGAAGTGCTATGAGTAGTTGGTATTTGCCATATTTATTTTGAATGTTTAACCT
         66 GAGTAACTTCAATGAAGTGCTATGAGTAGTTGGTATTTGCCATATTTATTTTGAATGTTTAACCT

                                    
       3238 GCAGGAGAGACTCGAAGTTTATCA
        131 GCAGGAGAGACTCGAAGTTTATCA

                                 *      *                                    
       3262 AGTCAGGGCATCGACTAATCTCGAAAATTTGTTAACAAGTTTATCCATATATATATACATGGCTT
          1 AGTCAGGGCATCGACTAATCTTGAAAATATGTTAACAAGTTTATCCATATATATATACATGGCTT

                                                                             
       3327 GAGTAACTTCAATGAAGTGCTATGAGTAGTTGGTATTTGCCATATTTATTTTGAATGTTTAACCT
         66 GAGTAACTTCAATGAAGTGCTATGAGTAGTTGGTATTTGCCATATTTATTTTGAATGTTTAACCT

                                     *
       3392 GCAGGAGAAAGA-T-GAAG-TTATCG
        131 GCAGGAG--AGACTCGAAGTTTATCA

                        *               *      *             *               
       3415 AGTCAGGGCATCAACTAATCTTGAAAATGTGTTAATAAGTTTATGCATATATATATATATACATG
          1 AGTCAGGGCATCGACTAATCTTGAAAATATGTTAACAAGTTTAT-C---CATATATATATACATG

                                              *                              
       3480 GCTTGAGTAACTTCAATGAAGTGCTATGAGTAGTAGGTATTTGCCATATTTA-TTTGAATGTTTA
         62 GCTTGAGTAACTTCAATGAAGTGCTATGAGTAGTTGGTATTTGCCATATTTATTTTGAATGTTTA

            * *                    
       3544 TCATGCAGGAGAGACTCGAAGTT
        127 ACCTGCAGGAGAGACTCGAAGTT

       3567 ATCGAGAAAG


Statistics
Matches: 280,  Mismatches: 16, Indels: 15
        0.90            0.05        0.05

Matches are distributed among these distances:
 153   45  0.16
 154  138  0.49
 155    2  0.01
 156   28  0.10
 157   67  0.24

ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36


Consensus pattern (154 bp):   
AGTCAGGGCATCGACTAATCTTGAAAATATGTTAACAAGTTTATCCATATATATATACATGGCTT
GAGTAACTTCAATGAAGTGCTATGAGTAGTTGGTATTTGCCATATTTATTTTGAATGTTTAACCT
GCAGGAGAGACTCGAAGTTTATCA
Done.