Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008854.1 Kokia drynarioides strain JFW-HI SEQ_123540, 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: 3822
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32


Found at i:2752 original size:15 final size:15

Alignment explanation


    Indices: 2732--2782  Score: 50
    Period size: 15  Copynumber: 3.3  Consensus size: 15

       2722 CATAAAAAAA

                           
       2732 TAAATATAAAATTAT
          1 TAAATATAAAATTAT

                           *
       2747 TAAATATTAAAA-TAA
          1 TAAATA-TAAAATTAT

                           * 
       2762 TATAATATAAATATTTT
          1 TA-AATATAAA-ATTAT

                
       2779 TAAA
          1 TAAA

       2783 AAATAATATG


Statistics
Matches: 29,  Mismatches: 3, Indels: 7
        0.74            0.08        0.18

Matches are distributed among these distances:
  15   14  0.48
  16   12  0.41
  17    3  0.10

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (15 bp):   
TAAATATAAAATTAT

Found at i:2771 original size:31 final size:31

Alignment explanation


    Indices: 2724--2782  Score: 84
    Period size: 30  Copynumber: 1.9  Consensus size: 31

       2714 GATTTTTTCA

                                           
       2724 TAAAAAAATAAATATAAA-ATTATTAAATAT
          1 TAAAAAAATAAATATAAATATTATTAAATAT

                 *                 *     
       2754 TAAAATAATATAATATAAATATTTTTAAA
          1 TAAAAAAATA-AATATAAATATTATTAAA

       2783 AAATAATATG


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  30    9  0.36
  31    8  0.32
  32    8  0.32

ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37


Consensus pattern (31 bp):   
TAAAAAAATAAATATAAATATTATTAAATAT

Found at i:3137 original size:17 final size:17

Alignment explanation


    Indices: 3107--3146  Score: 53
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       3097 AGACATAATT

                              
       3107 TTTTGTGAAATTTTAAAA
          1 TTTT-TGAAATTTTAAAA

                    *       *
       3125 TTTTTGAACTTTTAAAC
          1 TTTTTGAAATTTTAAAA

                 
       3142 TTTTT
          1 TTTTT

       3147 TTTTAAATTG


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  17   16  0.80
  18    4  0.20

ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57


Consensus pattern (17 bp):   
TTTTTGAAATTTTAAAA

Found at i:3301 original size:17 final size:17

Alignment explanation


    Indices: 3279--3315  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       3269 AAATTTTATT

                   *         
       3279 TTTGAATTTTTTAAATA
          1 TTTGAATATTTTAAATA

                          *  
       3296 TTTGAATATTTTAATTA
          1 TTTGAATATTTTAAATA

               
       3313 TTT
          1 TTT

       3316 ATAAATTATT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62


Consensus pattern (17 bp):   
TTTGAATATTTTAAATA
Done.