Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000435.1 Kokia drynarioides strain JFW-HI SEQ_111271, 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: 6747
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36


Found at i:377 original size:20 final size:21

Alignment explanation


    Indices: 354--393  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 21

        344 TTGGTACTTA

                     *           
        354 AATTTGATATAT-ATTTTTTT
          1 AATTTGATACATAATTTTTTT

                                
        374 AATTTGATACATAATTTTTT
          1 AATTTGATACATAATTTTTT

        394 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:1763 original size:9 final size:9

Alignment explanation


    Indices: 1743--1771  Score: 51
    Period size: 9  Copynumber: 3.3  Consensus size: 9

       1733 ACAAATAAAA

                     
       1743 TATTTA-TT
          1 TATTTATTT

                     
       1751 TATTTATTT
          1 TATTTATTT

                     
       1760 TATTTATTT
          1 TATTTATTT

               
       1769 TAT
          1 TAT

       1772 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:2902 original size:18 final size:17

Alignment explanation


    Indices: 2869--2902  Score: 50
    Period size: 18  Copynumber: 1.9  Consensus size: 17

       2859 TATCTATAAA

                     *       
       2869 TAAGAAAAATATTATTG
          1 TAAGAAAAAAATTATTG

                             
       2886 TAAGAATAAAAATTATT
          1 TAAGAA-AAAAATTATT

       2903 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:4256 original size:17 final size:17

Alignment explanation


    Indices: 4224--4256  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       4214 TTTTAAATTT

                             
       4224 ATTTTTTTAATGTTTTC
          1 ATTTTTTTAATGTTTTC

                             
       4241 ATTTTCTTTAAT-TTTT
          1 ATTTT-TTTAATGTTTT

       4257 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.