Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000688.1 Kokia drynarioides strain JFW-HI SEQ_111687, 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: 9592
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37


Found at i:3820 original size:103 final size:102

Alignment explanation


    Indices: 3663--3857  Score: 300
    Period size: 103  Copynumber: 1.9  Consensus size: 102

       3653 AAGCTTATTC

                                                           *                 
       3663 TTTTTTAATCACTAGTCTGATGTGACAAATTTAAGTGCTCCTATAATTAGTGCATGATACAGATC
          1 TTTTTTAATCACTAGTCTGATGTGACAAATTTAAGTGCTCCTATAATCAGTGCATGATACAGATC

                                                 
       3728 AAGATTATGAAGTTGCAAGGAAATGAAAGGACTGTTT
         66 AAGATTATGAAGTTGCAAGGAAATGAAAGGACTGTTT

                         *  *  *    *       *                 *        *     
       3765 TTTTTTAATCACTGGTTTGTTGTGGCAAATTTGAGTTGCTCCTATAATCATTGCATGATGCAGAT
          1 TTTTTTAATCACTAGTCTGATGTGACAAATTTAAG-TGCTCCTATAATCAGTGCATGATACAGAT

                                  *     
       3830 CAAGATTATGAAGTTGCAAGGAGATGAA
         65 CAAGATTATGAAGTTGCAAGGAAATGAA

       3858 TGAACTGCTT


Statistics
Matches: 83,  Mismatches: 9, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
 102   30  0.36
 103   53  0.64

ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35


Consensus pattern (102 bp):   
TTTTTTAATCACTAGTCTGATGTGACAAATTTAAGTGCTCCTATAATCAGTGCATGATACAGATC
AAGATTATGAAGTTGCAAGGAAATGAAAGGACTGTTT

Found at i:4172 original size:88 final size:88

Alignment explanation


    Indices: 3998--4173  Score: 210
    Period size: 88  Copynumber: 2.0  Consensus size: 88

       3988 TTTTATTCGA

                              *               *              *   *     *     
       3998 TTCTAAGTCATTATGTCCGTTGCTTTAGTCATTCTGAGCTCAAACAAACCAGGGCATAATTATAG
          1 TTCTAAGTCATTATGTCCATTGCTTTAGTCATTCCGAGCTCAAACAAACAAGGACATAACTATAG

                   **    *  *      
       4063 ATGGAAATGTGACGGATATAATT
         66 ATGGAAACATGACAGAAATAATT

                     *      *                            *                   
       4086 TTCTAAGTCGTTATGTTCATTGCTTTCA-TCATTCCGAGCTCAAAGAAACAAGGACATAACTATA
          1 TTCTAAGTCATTATGTCCATTGCTTT-AGTCATTCCGAGCTCAAACAAACAAGGACATAACTATA

             *          *           
       4150 GTTGGAAACATGGCAGAAATAATT
         65 GATGGAAACATGACAGAAATAATT

       4174 CTTGTTTGTA


Statistics
Matches: 73,  Mismatches: 14, Indels: 2
        0.82            0.16        0.02

Matches are distributed among these distances:
  88   72  0.99
  89    1  0.01

ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Consensus pattern (88 bp):   
TTCTAAGTCATTATGTCCATTGCTTTAGTCATTCCGAGCTCAAACAAACAAGGACATAACTATAG
ATGGAAACATGACAGAAATAATT

Found at i:5177 original size:70 final size:67

Alignment explanation


    Indices: 5051--5183  Score: 185
    Period size: 70  Copynumber: 1.9  Consensus size: 67

       5041 ATAAGCATTA

                       *            *                      *          *      
       5051 TAATGGTTTTGCCTTTTAACTTAATGGGTAAACATTTATCAAAATGATATAATTTTACTTTTTAA
          1 TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA

              
       5116 CT
         66 CT

                                                               *  *          
       5118 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAACATTTATCAAAATGACGTAGTTTTACCTTT
          1 TAATGGTTTTGACTTTTAAC-TT--AAAGGGTAAACATTTATCAAAATGACATAATTTTACCTTT

             
       5183 T
         63 T

       5184 CTTATTTGGA


Statistics
Matches: 57,  Mismatches: 6, Indels: 3
        0.86            0.09        0.05

Matches are distributed among these distances:
  67   19  0.33
  68    2  0.04
  70   36  0.63

ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44


Consensus pattern (67 bp):   
TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
CT

Found at i:6582 original size:15 final size:16

Alignment explanation


    Indices: 6562--6591  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       6552 ATAATATCGC

                            
       6562 TTTATGAT-TTATGAT
          1 TTTATGATCTTATGAT

                           
       6577 TTTATGATCTTATGA
          1 TTTATGATCTTATGA

       6592 AATTAATAAG


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

Matches are distributed among these distances:
  15    8  0.57
  16    6  0.43

ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57


Consensus pattern (16 bp):   
TTTATGATCTTATGAT

Found at i:7170 original size:51 final size:51

Alignment explanation


    Indices: 7094--7195  Score: 204
    Period size: 51  Copynumber: 2.0  Consensus size: 51

       7084 TTATGTGCTC

                                                               
       7094 TTCTTCCTTTTGCCTAGGATGAGTACTTACAATGGGTTGTTGGAAGTCAAA
          1 TTCTTCCTTTTGCCTAGGATGAGTACTTACAATGGGTTGTTGGAAGTCAAA

                                                               
       7145 TTCTTCCTTTTGCCTAGGATGAGTACTTACAATGGGTTGTTGGAAGTCAAA
          1 TTCTTCCTTTTGCCTAGGATGAGTACTTACAATGGGTTGTTGGAAGTCAAA

       7196 GAAGTCTTCT


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  51   51  1.00

ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37


Consensus pattern (51 bp):   
TTCTTCCTTTTGCCTAGGATGAGTACTTACAATGGGTTGTTGGAAGTCAAA
Done.