Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001206.1 Kokia drynarioides strain JFW-HI SEQ_112554, 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, 652

Length: 1088
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30


Found at i:393 original size:24 final size:22

Alignment explanation


    Indices: 351--409  Score: 59
    Period size: 22  Copynumber: 2.6  Consensus size: 22

        341 ATTTAATGAT

                                   
        351 AAATAAATAAATAAA--CAAACA
          1 AAATAAA-AAATAAATTCAAACA

                                  **
        372 AAATAATAACAATAAATTCAAATT
          1 AAATAA-AA-AATAAATTCAAACA

                          
        396 AAATAAAAAATAAA
          1 AAATAAAAAATAAA

        410 AAAATAACAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 7
        0.78            0.05        0.17

Matches are distributed among these distances:
  21    7  0.22
  22   13  0.41
  23    2  0.06
  24   10  0.31

ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20


Consensus pattern (22 bp):   
AAATAAAAAATAAATTCAAACA

Found at i:515 original size:15 final size:15

Alignment explanation


    Indices: 495--525  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        485 TTCAATGCTA

                           
        495 ATAAACAATAAAAAT
          1 ATAAACAATAAAAAT

                           
        510 ATAAACAATAAAAAT
          1 ATAAACAATAAAAAT

             
        525 A
          1 A

        526 ATTGAGACTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19


Consensus pattern (15 bp):   
ATAAACAATAAAAAT

Found at i:622 original size:20 final size:20

Alignment explanation


    Indices: 561--619  Score: 55
    Period size: 20  Copynumber: 2.8  Consensus size: 20

        551 GACCAATTAA

                         *        *
        561 TAAATATACAAAAAACAATAAAT
          1 TAAATATA-AAAATA-AAT-AAC

                 *              
        584 TAAATGTAAAAATAAATAAC
          1 TAAATATAAAAATAAATAAC

                            
        604 TAAATATAAATAATAA
          1 TAAATATAAA-AATAA

        620 TAAAAAAGAA


Statistics
Matches: 31,  Mismatches: 4, Indels: 4
        0.79            0.10        0.10

Matches are distributed among these distances:
  20   11  0.35
  21    8  0.26
  22    5  0.16
  23    7  0.23

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


Consensus pattern (20 bp):   
TAAATATAAAAATAAATAAC

Found at i:991 original size:17 final size:17

Alignment explanation


    Indices: 969--1008  Score: 80
    Period size: 17  Copynumber: 2.4  Consensus size: 17

        959 TTGAGAATCT

                             
        969 ATTCTCAAATCTTGGAG
          1 ATTCTCAAATCTTGGAG

                             
        986 ATTCTCAAATCTTGGAG
          1 ATTCTCAAATCTTGGAG

                  
       1003 ATTCTC
          1 ATTCTC

       1009 TTGGCAAGGG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   23  1.00

ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38


Consensus pattern (17 bp):   
ATTCTCAAATCTTGGAG
Done.