Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008487.1 Kokia drynarioides strain JFW-HI SEQ_123162, 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: 12705
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36


Found at i:4940 original size:16 final size:17

Alignment explanation


    Indices: 4908--4941  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       4898 GTTAATTTAA

                             
       4908 TTTAAATAAATTAATTT
          1 TTTAAATAAATTAATTT

                 *           
       4925 TTTAATTAAA-TAATTT
          1 TTTAAATAAATTAATTT

             
       4941 T
          1 T

       4942 CTCAACACAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    7  0.44
  17    9  0.56

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (17 bp):   
TTTAAATAAATTAATTT

Found at i:6335 original size:20 final size:21

Alignment explanation


    Indices: 6312--6351  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       6302 TTGGTACTTA

                     *           
       6312 AATTTGATATAT-ATTTTTTT
          1 AATTTGATACATAATTTTTTT

                                
       6332 AATTTGATACATAATTTTTT
          1 AATTTGATACATAATTTTTT

       6352 GTTTTTGTCT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20   11  0.61
  21    7  0.39

ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60


Consensus pattern (21 bp):   
AATTTGATACATAATTTTTTT

Found at i:7721 original size:9 final size:9

Alignment explanation


    Indices: 7701--7729  Score: 51
    Period size: 9  Copynumber: 3.3  Consensus size: 9

       7691 ACAAATAAAA

                     
       7701 TATTTA-TT
          1 TATTTATTT

                     
       7709 TATTTATTT
          1 TATTTATTT

                     
       7718 TATTTATTT
          1 TATTTATTT

               
       7727 TAT
          1 TAT

       7730 GTAGTTTGAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
   8    6  0.30
   9   14  0.70

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (9 bp):   
TATTTATTT

Found at i:8860 original size:18 final size:17

Alignment explanation


    Indices: 8827--8860  Score: 50
    Period size: 18  Copynumber: 1.9  Consensus size: 17

       8817 TATCTATAAA

                     *       
       8827 TAAGAAAAATATTATTG
          1 TAAGAAAAAAATTATTG

                             
       8844 TAAGAATAAAAATTATT
          1 TAAGAA-AAAAATTATT

       8861 AAATAATGTT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    6  0.40
  18    9  0.60

ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35


Consensus pattern (17 bp):   
TAAGAAAAAAATTATTG

Found at i:10214 original size:17 final size:17

Alignment explanation


    Indices: 10182--10214  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      10172 TTTTAAATTT

                             
      10182 ATTTTTTTAATGTTTTC
          1 ATTTTTTTAATGTTTTC

                             
      10199 ATTTTCTTTAAT-TTTT
          1 ATTTT-TTTAATGTTTT

      10215 AAGCTTATTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  17    9  0.60
  18    6  0.40

ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73


Consensus pattern (17 bp):   
ATTTTTTTAATGTTTTC
Done.