Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002210.1 Kokia drynarioides strain JFW-HI SEQ_114200, 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, 867

Length: 1446
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38


Found at i:24 original size:17 final size:16

Alignment explanation


    Indices: 2--69  Score: 91
    Period size: 17  Copynumber: 4.1  Consensus size: 16

          1 C

                     *       
          2 TAAATTTAATTTTATAA
          1 TAAATTTAAATTTA-AA

                             
         19 TAAATTTAAATTTCAAA
          1 TAAATTTAAATTT-AAA

                             
         36 TAAATTTAAATTTAAAA
          1 TAAATTTAAATTT-AAA

                *           
         53 TAAACTTAAATTTAAA
          1 TAAATTTAAATTTAAA

             
         69 T
          1 T

         70 TCAATTTCCA


Statistics
Matches: 47,  Mismatches: 3, Indels: 3
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    4  0.09
  17   42  0.89
  18    1  0.02

ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44


Consensus pattern (16 bp):   
TAAATTTAAATTTAAA

Found at i:53 original size:7 final size:6

Alignment explanation


    Indices: 2--70  Score: 58
    Period size: 6  Copynumber: 12.0  Consensus size: 6

          1 C

                      *                                              
          2 TAAATT TAATTT TATAA-- TAAATT TAAATT TCAAA-- TAAATT TAAATT
          1 TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT TAAATT

                 *     *               
         48 TAAA-A TAAACT TAAATT TAAATT
          1 TAAATT TAAATT TAAATT TAAATT

         71 CAATTTCCAT


Statistics
Matches: 51,  Mismatches: 5, Indels: 14
        0.73            0.07        0.20

Matches are distributed among these distances:
   4    5  0.10
   5    7  0.14
   6   35  0.69
   7    4  0.08

ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45


Consensus pattern (6 bp):   
TAAATT

Found at i:76 original size:34 final size:34

Alignment explanation


    Indices: 2--69  Score: 102
    Period size: 34  Copynumber: 2.0  Consensus size: 34

          1 C

                     *    *      *            
          2 TAAATTTAATTTTATAATAAATTTAAATTTCAAA
          1 TAAATTTAAATTTAAAATAAACTTAAATTTCAAA

                                              
         36 TAAATTTAAATTTAAAATAAACTTAAATTT-AAA
          1 TAAATTTAAATTTAAAATAAACTTAAATTTCAAA

             
         69 T
          1 T

         70 TCAATTTCCA


Statistics
Matches: 31,  Mismatches: 3, Indels: 1
        0.89            0.09        0.03

Matches are distributed among these distances:
  33    4  0.13
  34   27  0.87

ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44


Consensus pattern (34 bp):   
TAAATTTAAATTTAAAATAAACTTAAATTTCAAA

Found at i:785 original size:136 final size:138

Alignment explanation


    Indices: 494--906  Score: 543
    Period size: 136  Copynumber: 3.0  Consensus size: 138

        484 GCTGGGGTTC

                        * *      *  *                *   *                 * 
        494 GAAGATTTGCTCATATCGAGCGTGGGTTT-GGTCTTCTTCTTAGTATCTCATCAGGAAGATGACC
          1 GAAGATTTGCTCGTTTCGAGCCT-CGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATC

                  *    *                                              *    * 
        558 ACATCGTCTGTCTCAAAT-CGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCATTTCTCA
         65 ACATC-ACTGTTTC-AATCCGCTTCTCTGTA--TCATCAGGAAGACGAATTTGGTTCACTTCTTA

               *        *
        622 GT-CCCTCATCTG
        126 GTATCCTCATCTA

                                                               *            *
        634 GAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATTAGGAAGATGATCT
          1 GAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCA

                                                                             
        699 CATCACTGTTTCAATCCGCTTCTCTGTA-CATCAGGAAGACGAATTTGGTTCACTTCTTAGTATC
         66 CATCACTGTTTCAATCCGCTTCTCTGTATCATCAGGAAGACGAATTTGGTTCACTTCTTAGTATC

                    
        763 CT-ATCTA
        131 CTCATCTA

                                                                            *
        770 GAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCC
          1 GAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCA

                            *                                          *     
        835 CATCACTGTTTCAATCTGCTTCTCTGTATC-TCACTAGGAAGACGAATTTGGTTCACTTTTTAGT
         66 CATCACTGTTTCAATCCGCTTCTCTGTATCAT--C-AGGAAGACGAATTTGGTTCACTTCTTAGT

                     
        899 AT-CTCATC
        128 ATCCTCATC

        907 AGGAAGCTAA


Statistics
Matches: 246,  Mismatches: 19, Indels: 17
        0.87            0.07        0.06

Matches are distributed among these distances:
 136  126  0.51
 137    4  0.02
 138    6  0.02
 139   55  0.22
 140   55  0.22

ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37


Consensus pattern (138 bp):   
GAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCA
CATCACTGTTTCAATCCGCTTCTCTGTATCATCAGGAAGACGAATTTGGTTCACTTCTTAGTATC
CTCATCTA
Done.