Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006696.1 Kokia drynarioides strain JFW-HI SEQ_121290, 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: 7963
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40


Found at i:1592 original size:20 final size:20

Alignment explanation


    Indices: 1567--1608  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       1557 ACAACTTTAA

                    *           
       1567 AATCAAATTAAAATGATTTT
          1 AATCAAATCAAAATGATTTT

                  *             
       1587 AATCAAGTCAAAATGATTTT
          1 AATCAAATCAAAATGATTTT

              
       1607 AA
          1 AA

       1609 CTAAGGCAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36


Consensus pattern (20 bp):   
AATCAAATCAAAATGATTTT

Found at i:1618 original size:20 final size:20

Alignment explanation


    Indices: 1576--1632  Score: 80
    Period size: 20  Copynumber: 2.9  Consensus size: 20

       1566 AAATCAAATT

                               * 
       1576 AAAATGATTTTAA-TCAAGTC
          1 AAAATGATTTTAACT-AAGGC

                                
       1596 AAAATGATTTTAACTAAGGC
          1 AAAATGATTTTAACTAAGGC

                 *           
       1616 AAAATCATTTTAACTAA
          1 AAAATGATTTTAACTAA

       1633 TCAAATTGCT


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  20   33  0.97
  21    1  0.03

ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33


Consensus pattern (20 bp):   
AAAATGATTTTAACTAAGGC

Found at i:5558 original size:46 final size:44

Alignment explanation


    Indices: 5506--5599  Score: 125
    Period size: 46  Copynumber: 2.1  Consensus size: 44

       5496 GGTTCGTTGT

                                                *         
       5506 AATGGAATAGAGCTGTAATCAGTATTCCAATTGTTTGGTTGAATGA
          1 AATGGAATAGAGCTGTAAT-AGTATTCCAA-TGTTTAGTTGAATGA

                       *              **               *
       5552 AATGGAATAGATCTGTAATAGTATTCTTATGTTTAGTTGAATGG
          1 AATGGAATAGAGCTGTAATAGTATTCCAATGTTTAGTTGAATGA

                
       5596 AATG
          1 AATG

       5600 ATGCTGTAAT


Statistics
Matches: 43,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  44   17  0.40
  45    8  0.19
  46   18  0.42

ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37


Consensus pattern (44 bp):   
AATGGAATAGAGCTGTAATAGTATTCCAATGTTTAGTTGAATGA

Found at i:5769 original size:56 final size:56

Alignment explanation


    Indices: 5693--5847  Score: 195
    Period size: 56  Copynumber: 2.7  Consensus size: 56

       5683 TTGTTATTAA

                     *                                            * *
       5693 ATTTTAATAAGATTATTATTAAATATAATTTAATAAAAAATA-AGTAATTAAATCAT
          1 ATTTTAATATGATTATTATTAAATATAATTTAATAAAAAATATA-TAATTAAATAAC

                   *                 *                        *      
       5749 ATTTTAACATGATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAAC
          1 ATTTTAATATGATTATTATTAAATATAATTTAATAAAA-AATATATAATTAAATAAC

                       *                *             
       5806 ATTCTTAATATAATTATTATTAAAATATGATTTAATAAAAAA
          1 ATT-TTAATATGATTATTATT-AAATATAATTTAATAAAAAA

       5848 CATAATATAT


Statistics
Matches: 85,  Mismatches: 10, Indels: 6
        0.84            0.10        0.06

Matches are distributed among these distances:
  56   35  0.41
  57   16  0.19
  58   18  0.21
  59   16  0.19

ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42


Consensus pattern (56 bp):   
ATTTTAATATGATTATTATTAAATATAATTTAATAAAAAATATATAATTAAATAAC
Done.