Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009933.1 Kokia drynarioides strain JFW-HI SEQ_124674, 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, 910

Length: 1517
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36

Warning! 23 characters in sequence are not A, C, G, or T


Found at i:18 original size:6 final size:6

Alignment explanation


    Indices: 9--93  Score: 56
    Period size: 6  Copynumber: 15.0  Consensus size: 6

          1 TTTTAATT

                                   *         *      *     *       *
          9 TTAAAA TTAAAA TT-AAA TTTAAA TTAAAT TTAAAT TTAAGA TT-AAT
          1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA

                 *                     *                     
         55 TTAAAT TTAAAA -T-AAA TCTAAAT TTAAAA -T-AAA TTAAAA
          1 TTAAAA TTAAAA TTAAAA T-TAAAA TTAAAA TTAAAA TTAAAA

         94 AGGGGCTAGG


Statistics
Matches: 63,  Mismatches: 9, Indels: 14
        0.73            0.10        0.16

Matches are distributed among these distances:
   4    6  0.10
   5   11  0.17
   6   43  0.68
   7    3  0.05

ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40


Consensus pattern (6 bp):   
TTAAAA

Found at i:32 original size:11 final size:11

Alignment explanation


    Indices: 12--92  Score: 76
    Period size: 11  Copynumber: 7.3  Consensus size: 11

          2 TTTAATTTTA

                 *     
         12 AAATTAAAATT
          1 AAATTTAAATT

                       
         23 AAATTTAAATT
          1 AAATTTAAATT

                        
         34 AAATTTAAATTT
          1 AAATTTAAA-TT

                     *  
         46 AAGA-TTAATTT
          1 AA-ATTTAAATT

                     * 
         57 AAATTTAAAAT
          1 AAATTTAAATT

                *       
         68 AAATCTAAATTT
          1 AAATTTAAA-TT

                *      
         80 AAA-ATAAATT
          1 AAATTTAAATT

               
         90 AAA
          1 AAA

         93 AAGGGGCTAG


Statistics
Matches: 59,  Mismatches: 7, Indels: 9
        0.79            0.09        0.12

Matches are distributed among these distances:
  10    6  0.10
  11   40  0.68
  12   12  0.20
  13    1  0.02

ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40


Consensus pattern (11 bp):   
AAATTTAAATT

Found at i:34 original size:17 final size:16

Alignment explanation


    Indices: 12--92  Score: 99
    Period size: 17  Copynumber: 4.8  Consensus size: 16

          2 TTTAATTTTA

                             
         12 AAATTAAAATTAAATTT
          1 AAATT-AAATTAAATTT

                             
         29 AAATTAAATTTAAATTT
          1 AAATTAAA-TTAAATTT

                    *        
         46 AAGATTAATTTAAATTT
          1 AA-ATTAAATTAAATTT

               *             
         63 AAAATAAATCTAAATTT
          1 AAATTAAAT-TAAATTT

               *         
         80 AAAATAAATTAAA
          1 AAATTAAATTAAA

         93 AAGGGGCTAG


Statistics
Matches: 58,  Mismatches: 3, Indels: 7
        0.85            0.04        0.10

Matches are distributed among these distances:
  16   12  0.21
  17   41  0.71
  18    5  0.09

ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40


Consensus pattern (16 bp):   
AAATTAAATTAAATTT

Found at i:811 original size:205 final size:203

Alignment explanation


    Indices: 510--1045  Score: 749
    Period size: 205  Copynumber: 2.6  Consensus size: 203

        500 MCYRTATTTT

                            *       *      ** *     *   *   *            * * 
        510 CATCAGGAAGCTAAYCRTTTTATTRCTTCGAMYTRCTTCTYAGTRTCTMATCAGGAAGCTRRGRT
          1 CATCAGGAAGCTAA-CCTTTTATTACTTCGACCTACTTCTCAGTGTCTCATCAGGAAGCT-TGGT

              *                                                              
        575 TCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAG
         64 TCAAAGATTTGCTCACAT-GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAG

                                       *                                     
        640 ATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTATATCTCATCAAGAAGACGAATTTGATCCACT
        128 ATGACCGCGTCGTTTGTTTCAATTCGCCTCTCTATATCTCATCAAGAAGACGAATTTGATCCACT

                       
        705 TCTCAGTATCC
        193 TCTCAGTATCC

                                             *       *                       
        716 CATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAATGTCTCATCAGGAAGCTTGAGTT
          1 CATCAGGAAGCTAACCTTTTATTACTTCGACCTACTTCTCAGTGTCTCATCAGGAAGCTTG-GTT

                     *        *  * *                                         
        781 CAAAGATTTACTCACATTAAGTGCGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGA
         65 CAAAGATTTGCTCACA-TGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGA

                                   *        *          *             *       
        846 TGACCGCGTCGTTTGTTTCAATTTGCCTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTT
        129 TGACCGCGTCGTTTGTTTCAATTCGCCTCTCTATATCTCATCAAGAAGACGAATTTGATCCACTT

                     *
        911 CTCAGTATCT
        194 CTCAGTATCC

                                   *                                         
        921 CATCAGGAAGCTAACCTTTTATTGCTTCGACCTACTTCTCAGTGTCTCATCAGGAAG-TTGGGGT
          1 CATCAGGAAGCTAACCTTTTATTACTTCGACCTACTTCTCAGTGTCTCATCAGGAAGCTT--GGT

                                     *                                       
        985 TCAAAGATTTGCT--C--GAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGA
         64 TCAAAGATTTGCTCACATGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGA

       1046 CGAATTTGGT


Statistics
Matches: 296,  Mismatches: 30, Indels: 14
        0.87            0.09        0.04

Matches are distributed among these distances:
 200   43  0.15
 203    1  0.00
 204    3  0.01
 205  233  0.79
 206   16  0.05

ACGTcount: A:0.22, C:0.22, G:0.19, T:0.35


Consensus pattern (203 bp):   
CATCAGGAAGCTAACCTTTTATTACTTCGACCTACTTCTCAGTGTCTCATCAGGAAGCTTGGTTC
AAAGATTTGCTCACATGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATG
ACCGCGTCGTTTGTTTCAATTCGCCTCTCTATATCTCATCAAGAAGACGAATTTGATCCACTTCT
CAGTATCC
Done.