Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011623.1 Kokia drynarioides strain JFW-HI SEQ_126614, 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: 32935
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:14294 original size:13 final size:13

Alignment explanation


    Indices: 14277--14324  Score: 51
    Period size: 13  Copynumber: 3.6  Consensus size: 13

      14267 TGAGTTTTTA

                         
      14277 AATTTTTAAGTTT
          1 AATTTTTAAGTTT

            *      **    
      14290 CATTTTTTTGTTT
          1 AATTTTTAAGTTT

                      *   
      14303 AAATTTTTAATTTT
          1 -AATTTTTAAGTTT

                    
      14317 AATTTTTA
          1 AATTTTTA

      14325 TGTTAATAAA


Statistics
Matches: 27,  Mismatches: 7, Indels: 2
        0.75            0.19        0.06

Matches are distributed among these distances:
  13   18  0.67
  14    9  0.33

ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67


Consensus pattern (13 bp):   
AATTTTTAAGTTT

Found at i:14303 original size:27 final size:27

Alignment explanation


    Indices: 14273--14328  Score: 85
    Period size: 27  Copynumber: 2.1  Consensus size: 27

      14263 TAATTGAGTT

                             *      *  
      14273 TTTAAATTTTTAAGTTTCATTTTTTTG
          1 TTTAAATTTTTAAGTTTAATTTTTATG

                         *             
      14300 TTTAAATTTTTAATTTTAATTTTTATG
          1 TTTAAATTTTTAAGTTTAATTTTTATG

              
      14327 TT
          1 TT

      14329 AATAAAAGGG


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68


Consensus pattern (27 bp):   
TTTAAATTTTTAAGTTTAATTTTTATG

Found at i:14723 original size:28 final size:28

Alignment explanation


    Indices: 14679--14733  Score: 85
    Period size: 28  Copynumber: 2.0  Consensus size: 28

      14669 CACACTGCCG

                        *                
      14679 TTGCTGTCGCACTTTGT-AGTCACCGCCA
          1 TTGCTGTCGCACGTTGTCA-TCACCGCCA

                                       
      14707 TTGCTGTCGCACGTTGTCATCACCGCC
          1 TTGCTGTCGCACGTTGTCATCACCGCC

      14734 GCAGCATCCT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  28   24  0.96
  29    1  0.04

ACGTcount: A:0.13, C:0.35, G:0.22, T:0.31


Consensus pattern (28 bp):   
TTGCTGTCGCACGTTGTCATCACCGCCA

Found at i:21090 original size:22 final size:22

Alignment explanation


    Indices: 21065--21107  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      21055 AAAATATTTC

                     *             
      21065 ATTA-ATAATTTGGGTTTAATTA
          1 ATTATATAAATTGGG-TTAATTA

                 *               
      21087 ATTATTTAAATTGGGTTAATT
          1 ATTATATAAATTGGGTTAATT

      21108 TTATTCTTTG


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  22   10  0.56
  23    8  0.44

ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51


Consensus pattern (22 bp):   
ATTATATAAATTGGGTTAATTA
Done.