Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004159.1 Kokia drynarioides strain JFW-HI SEQ_117377, 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: 2914
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36


Found at i:656 original size:28 final size:28

Alignment explanation


    Indices: 628--703  Score: 73
    Period size: 28  Copynumber: 2.7  Consensus size: 28

        618 TGGACAAAAA

                                  *       
        628 TAAATTTTAAAGTTAAATTTATGATAAATT
          1 TAAATTTTAAA-TTAAATTTATAATAAA-T

                    * *                *
        658 TAAA-TTTCATTTAAATTTATAATAAAC
          1 TAAATTTTAAATTAAATTTATAATAAAT

             *         *       
        685 TCAATTTTAAAATAAATTT
          1 TAAATTTTAAATTAAATTT

        704 TAAGTTTATT


Statistics
Matches: 37,  Mismatches: 8, Indels: 4
        0.76            0.16        0.08

Matches are distributed among these distances:
  27    3  0.08
  28   26  0.70
  29    4  0.11
  30    4  0.11

ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46


Consensus pattern (28 bp):   
TAAATTTTAAATTAAATTTATAATAAAT

Found at i:672 original size:17 final size:16

Alignment explanation


    Indices: 633--676  Score: 52
    Period size: 17  Copynumber: 2.6  Consensus size: 16

        623 AAAAATAAAT

                  *         
        633 TTTAAAGTTAAATTTA
          1 TTTAAATTTAAATTTA

              *               
        649 TGATAAATTTAAATTTCA
          1 T-TTAAATTTAAATTT-A

                      
        667 TTTAAATTTA
          1 TTTAAATTTA

        677 TAATAAACTC


Statistics
Matches: 23,  Mismatches: 3, Indels: 3
        0.79            0.10        0.10

Matches are distributed among these distances:
  16    1  0.04
  17   20  0.87
  18    2  0.09

ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50


Consensus pattern (16 bp):   
TTTAAATTTAAATTTA

Found at i:1425 original size:204 final size:202

Alignment explanation


    Indices: 1111--1613  Score: 735
    Period size: 204  Copynumber: 2.5  Consensus size: 202

       1101 TTTCATCAGG

                            *                                      *         
       1111 ATTTGGTTCACTTCTCGGTATCTTATCAGGGAGCTAACCATTTTATGGCTTCGACTTGCTTCTCA
          1 ATTTGGTTCACTTCTCAGTATCTTATCAGGGAGCTAACCATTTTATGGCTTCGACCTGCTTCTCA

             *       *           *                **                         
       1176 GCGTCTCATTAGGAAGCTGGGATTCGAAGA-TTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTC
         66 GTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCCCTTTGAGCCTCGTTTGGGTCTTCTTC

                                               *                             
       1240 TCAGTGCCTCATCAGGAAGATGATTACATCGC-T-GTTTGTTTCAATTCGCTCCTCCGTATCTCA
        131 TCAGTGCCTCATCAGGAAGATG---AC--CGCGTCATTTGTTTCAATTCGCTCCTCCGTATCTCA

              *         
       1303 TCCGGAAGACGA
        191 TCAGGAAGACGA

                    *      *    *         *               *    *             
       1315 ATTTGGTTGACTTCTTAGTACCTTATCAGGAAGCTAACC-TTTTATTGCTTTGACCTGCTTCTCA
          1 ATTTGGTTCACTTCTCAGTATCTTATCAGGGAGCTAACCATTTTATGGCTTCGACCTGCTTCTCA

                       *                                                     
       1379 GTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTTGCTCCCTTTGAGCCTCGTTTGGGTCTTCTTC
         66 GTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCCCTTTGAGCCTCGTTTGGGTCTTCTTC

                  *                                        *   *             
       1444 TCAGTGTCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATTCGCTTCTCTGTATCTCATCAGG
        131 TCAGTGCCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATTCGCTCCTCCGTATCTCATCAGG

                   
       1509 AAGACGA
        196 AAGACGA

                                   *                *                       *
       1516 ATTTGGTTCACTTCTCAGTATCTCATCAGGGAGCTAACCACTTTATGGCTTCGACCTGCTTCTCT
          1 ATTTGGTTCACTTCTCAGTATCTTATCAGGGAGCTAACCATTTTATGGCTTCGACCTGCTTCTCA

                                             
       1581 GTGTCTCATCAGGAAGCTGGGGTTCGAAGATTT
         66 GTGTCTCATCAGGAAGCTGGGGTTCGAAGATTT

       1614 GCTTACATAG


Statistics
Matches: 266,  Mismatches: 29, Indels: 10
        0.87            0.10        0.03

Matches are distributed among these distances:
 199    3  0.01
 200    1  0.00
 201   74  0.28
 202   53  0.20
 203   48  0.18
 204   87  0.33

ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36


Consensus pattern (202 bp):   
ATTTGGTTCACTTCTCAGTATCTTATCAGGGAGCTAACCATTTTATGGCTTCGACCTGCTTCTCA
GTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCCCTTTGAGCCTCGTTTGGGTCTTCTTC
TCAGTGCCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATTCGCTCCTCCGTATCTCATCAGG
AAGACGA
Done.