Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009535.1 Kokia drynarioides strain JFW-HI SEQ_124247, 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: 6706
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37


Found at i:1947 original size:5 final size:6

Alignment explanation


    Indices: 1930--1954  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

       1920 ACAGTTTATG

                                         
       1930 TATTTT TATTTT TATTTT TATTTT T
          1 TATTTT TATTTT TATTTT TATTTT T

       1955 TTGATTGAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84


Consensus pattern (6 bp):   
TATTTT

Found at i:4638 original size:69 final size:69

Alignment explanation


    Indices: 4555--4693  Score: 260
    Period size: 69  Copynumber: 2.0  Consensus size: 69

       4545 CAGGAAAGAT

                     *                                                       
       4555 GCTCAAACAGCTGCTGATATTATTGAAGAAATAGATGCTGAGGATGTAGCTACTACAAATACTCA
          1 GCTCAAACAACTGCTGATATTATTGAAGAAATAGATGCTGAGGATGTAGCTACTACAAATACTCA

                
       4620 TGAA
         66 TGAA

                                                                *            
       4624 GCTCAAACAACTGCTGATATTATTGAAGAAATAGATGCTGAGGATGTAGCTAGTACAAATACTCA
          1 GCTCAAACAACTGCTGATATTATTGAAGAAATAGATGCTGAGGATGTAGCTACTACAAATACTCA

                
       4689 TGAA
         66 TGAA

             
       4693 G
          1 G

       4694 AAAGAAACAA


Statistics
Matches: 68,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  69   68  1.00

ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26


Consensus pattern (69 bp):   
GCTCAAACAACTGCTGATATTATTGAAGAAATAGATGCTGAGGATGTAGCTACTACAAATACTCA
TGAA

Found at i:5566 original size:56 final size:56

Alignment explanation


    Indices: 5450--5613  Score: 172
    Period size: 56  Copynumber: 2.8  Consensus size: 56

       5440 TTTTTCTAAT

                         *      *                                *      
       5450 ATTATATATTATAATTTTACTAATTCATATTTTAATAATAATTATTAAAAATGTTATTAA
          1 ATTATATATTAT-TTTTTA-AAATT-ATA-TTTAATAATAATTATTAAAAATGATATTAA

                                    *                    *             
       5510 ATTATATATTATTTTATT-AAATTTTATTTAATAATAATTATGT-TAAAT-ATAGTTAA
          1 ATTATATATTATTTT-TTAAAATTATATTTAATAATAATTAT-TAAAAATGATA-TTAA

                 *                                          
       5566 ATTATTTATTATTTTTTAAAATTATATTTAATAATAATCTTATTAAAA
          1 ATTATATATTATTTTTTAAAATTATATTTAATAATAA--TTATTAAAA

       5614 TTTAATAACA


Statistics
Matches: 89,  Mismatches: 8, Indels: 16
        0.79            0.07        0.14

Matches are distributed among these distances:
  55    4  0.04
  56   55  0.62
  57    4  0.04
  58   10  0.11
  59    2  0.02
  60   14  0.16

ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52


Consensus pattern (56 bp):   
ATTATATATTATTTTTTAAAATTATATTTAATAATAATTATTAAAAATGATATTAA

Found at i:6690 original size:3 final size:3

Alignment explanation


    Indices: 6682--6706  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       6672 GATGGTTTCG

                                             
       6682 ATA ATA ATA ATA ATA ATA ATA ATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA A


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
ATA

Done.