Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002705.1 Kokia drynarioides strain JFW-HI SEQ_114991, 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: 3970
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33


Found at i:386 original size:17 final size:17

Alignment explanation


    Indices: 360--396  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 17

        350 AAGTAATTAC

                 *           
        360 AAGAATATGAAACGTTA
          1 AAGAAGATGAAACGTTA

                        *    
        377 AAGAAGATGAAAGGTTA
          1 AAGAAGATGAAACGTTA

               
        394 AAG
          1 AAG

        397 GTCAAAGGAG


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:0.54, C:0.03, G:0.24, T:0.19


Consensus pattern (17 bp):   
AAGAAGATGAAACGTTA

Found at i:463 original size:8 final size:8

Alignment explanation


    Indices: 452--483  Score: 57
    Period size: 8  Copynumber: 4.1  Consensus size: 8

        442 ACAAAATAAA

                    
        452 ATTTTTTT
          1 ATTTTTTT

                    
        460 ATTTTTTT
          1 ATTTTTTT

                    
        468 A-TTTTTT
          1 ATTTTTTT

                    
        475 ATTTTTTT
          1 ATTTTTTT

             
        483 A
          1 A

        484 GAATTAATAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   7    7  0.30
   8   16  0.70

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


Consensus pattern (8 bp):   
ATTTTTTT

Found at i:474 original size:15 final size:15

Alignment explanation


    Indices: 454--483  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        444 AAAATAAAAT

                           
        454 TTTTTTATTTTTTTA
          1 TTTTTTATTTTTTTA

                           
        469 TTTTTTATTTTTTTA
          1 TTTTTTATTTTTTTA

        484 GAATTAATAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87


Consensus pattern (15 bp):   
TTTTTTATTTTTTTA

Found at i:889 original size:21 final size:21

Alignment explanation


    Indices: 857--914  Score: 59
    Period size: 21  Copynumber: 2.8  Consensus size: 21

        847 TGAAAAATGA

                                  
        857 TAAAATAAATAATACATTAAAT
          1 TAAAA-AAATAATACATTAAAT

                                * 
        879 TAAAAAAATAACT-C-TTAATT
          1 TAAAAAAATAA-TACATTAAAT

                             
        899 TAAAGAAAATAA-ACAT
          1 TAAA-AAAATAATACAT

        915 AATTATCTAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 9
        0.76            0.02        0.22

Matches are distributed among these distances:
  20   10  0.32
  21   15  0.48
  22    6  0.19

ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29


Consensus pattern (21 bp):   
TAAAAAAATAATACATTAAAT

Found at i:917 original size:20 final size:20

Alignment explanation


    Indices: 857--918  Score: 54
    Period size: 20  Copynumber: 3.0  Consensus size: 20

        847 TGAAAAATGA

                        *       * 
        857 TAAAATAAATAATACATTAAAT
          1 TAAAA-AAATAACACA-TAATT

                        * *     
        879 TAAAAAAATAACTCTTAATT
          1 TAAAAAAATAACACATAATT

                                 
        899 TAAAGAAAATAA-ACATAATT
          1 TAAA-AAAATAACACATAATT

        919 ATCTAAACAA


Statistics
Matches: 33,  Mismatches: 6, Indels: 4
        0.77            0.14        0.09

Matches are distributed among these distances:
  20   14  0.42
  21   14  0.42
  22    5  0.15

ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31


Consensus pattern (20 bp):   
TAAAAAAATAACACATAATT
Done.