Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002525.1 Kokia drynarioides strain JFW-HI SEQ_114694, 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: 6696
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34


Found at i:2598 original size:18 final size:19

Alignment explanation


    Indices: 2577--2617  Score: 57
    Period size: 18  Copynumber: 2.2  Consensus size: 19

       2567 AAATTAAGTT

                            *  
       2577 TTAAATATGAATT-TTTCA
          1 TTAAATATGAATTATTACA

                     *         
       2595 TTAAATATGTATTATTACA
          1 TTAAATATGAATTATTACA

                
       2614 TTAA
          1 TTAA

       2618 TTACAAATTC


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

Matches are distributed among these distances:
  18   12  0.60
  19    8  0.40

ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49


Consensus pattern (19 bp):   
TTAAATATGAATTATTACA

Found at i:3543 original size:5 final size:5

Alignment explanation


    Indices: 3527--3569  Score: 52
    Period size: 5  Copynumber: 8.6  Consensus size: 5

       3517 AATATTCTAG

                    *             *                             
       3527 TTTAA TTAAA TTTAA TTT-T TTCTAA TTTAA TTTAA TTTAA TTT
          1 TTTAA TTTAA TTTAA TTTAA TT-TAA TTTAA TTTAA TTTAA TTT

       3570 CAAAAAATAT


Statistics
Matches: 32,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
   4    2  0.06
   5   28  0.88
   6    2  0.06

ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63


Consensus pattern (5 bp):   
TTTAA

Found at i:3550 original size:25 final size:25

Alignment explanation


    Indices: 3521--3569  Score: 80
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       3511 GTTAGAAATA

                 *                   
       3521 TTCTAGTTTAATTAAATTTAATTTT
          1 TTCTAATTTAATTAAATTTAATTTT

                         *          
       3546 TTCTAATTTAATTTAATTTAATTT
          1 TTCTAATTTAATTAAATTTAATTT

       3570 CAAAAAATAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61


Consensus pattern (25 bp):   
TTCTAATTTAATTAAATTTAATTTT

Found at i:4416 original size:18 final size:19

Alignment explanation


    Indices: 4393--4436  Score: 56
    Period size: 17  Copynumber: 2.4  Consensus size: 19

       4383 CATGTGGTCC

                           **  
       4393 TAAAAAAATTAT-ATTCTT
          1 TAAAAAAATTATAATAATT

                               
       4411 T-AAAAAATTATAATAATT
          1 TAAAAAAATTATAATAATT

                    
       4429 TAAAAAAA
          1 TAAAAAAA

       4437 AAATCTAAAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  17   10  0.45
  18    6  0.27
  19    6  0.27

ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36


Consensus pattern (19 bp):   
TAAAAAAATTATAATAATT

Found at i:4715 original size:24 final size:24

Alignment explanation


    Indices: 4669--4715  Score: 58
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       4659 GTTTAATTTT

                  *        *  *     
       4669 TTAATTTAACTCGAACAATTTCAC
          1 TTAATTCAACTCGAAAAAATTCAC

                     *             
       4693 TTAATTCAATTCGAAAAAATTCA
          1 TTAATTCAACTCGAAAAAATTCA

       4716 AATCAAGTTA


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36


Consensus pattern (24 bp):   
TTAATTCAACTCGAAAAAATTCAC
Done.