Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004064.1 Kokia drynarioides strain JFW-HI SEQ_117219, 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: 10964
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35


Found at i:4284 original size:15 final size:16

Alignment explanation


    Indices: 4264--4293  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       4254 ATAACAATAA

                            
       4264 TTTAATCATT-AAATC
          1 TTTAATCATTCAAATC

                           
       4279 TTTAATCATTCAAAT
          1 TTTAATCATTCAAAT

       4294 ATCATGCATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15   10  0.71
  16    4  0.29

ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47


Consensus pattern (16 bp):   
TTTAATCATTCAAATC

Found at i:7823 original size:20 final size:20

Alignment explanation


    Indices: 7795--7851  Score: 59
    Period size: 20  Copynumber: 3.0  Consensus size: 20

       7785 TCACGTTAGC

                *               
       7795 AAATGATTTTAAAATTATTA
          1 AAATTATTTTAAAATTATTA

                                  
       7815 AAATTATTTTTTAAAA-TA-TA
          1 AAATTA--TTTTAAAATTATTA

                               
       7835 AAATTA--TTAAAATTATT
          1 AAATTATTTTAAAATTATT

       7852 TTTTGAAATA


Statistics
Matches: 32,  Mismatches: 1, Indels: 10
        0.74            0.02        0.23

Matches are distributed among these distances:
  16    6  0.19
  17    2  0.06
  18    1  0.03
  20   13  0.41
  21    2  0.06
  22    8  0.25

ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47


Consensus pattern (20 bp):   
AAATTATTTTAAAATTATTA

Found at i:7846 original size:29 final size:30

Alignment explanation


    Indices: 7804--7875  Score: 128
    Period size: 29  Copynumber: 2.4  Consensus size: 30

       7794 CAAATGATTT

                                          
       7804 TAAAATTATTAAAATTATTTTTTAAAAT-A
          1 TAAAATTATTAAAATTATTTTTTAAAATAA

                                   *      
       7833 TAAAATTATTAAAATTATTTTTTGAAATAA
          1 TAAAATTATTAAAATTATTTTTTAAAATAA

                         
       7863 TAAAATTATTAAA
          1 TAAAATTATTAAA

       7876 TAATTTTAAT


Statistics
Matches: 41,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  29   27  0.66
  30   14  0.34

ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46


Consensus pattern (30 bp):   
TAAAATTATTAAAATTATTTTTTAAAATAA

Found at i:9069 original size:20 final size:22

Alignment explanation


    Indices: 9044--9085  Score: 70
    Period size: 20  Copynumber: 2.0  Consensus size: 22

       9034 AAATAATTTT

                                  
       9044 AATAATTTT-AT-ATTTTAAAA
          1 AATAATTTTAATAATTTTAAAA

                                  
       9064 AATAATTTTAATAATTTTAAAA
          1 AATAATTTTAATAATTTTAAAA

       9086 TCATTTGCTG


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

Matches are distributed among these distances:
  20    9  0.45
  21    2  0.10
  22    9  0.45

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (22 bp):   
AATAATTTTAATAATTTTAAAA

Found at i:9073 original size:29 final size:31

Alignment explanation


    Indices: 9010--9082  Score: 123
    Period size: 29  Copynumber: 2.4  Consensus size: 31

       9000 ATTAAAATTA

                                           
       9010 TTTAATAATTTTATTATTTCAAAAAAATAAT
          1 TTTAATAATTTTATTATTTCAAAAAAATAAT

                                *          
       9041 TTTAATAATTTTA-TATTT-TAAAAAATAAT
          1 TTTAATAATTTTATTATTTCAAAAAAATAAT

                         
       9070 TTTAATAATTTTA
          1 TTTAATAATTTTA

       9083 AAATCATTTG


Statistics
Matches: 41,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  29   23  0.56
  30    5  0.12
  31   13  0.32

ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52


Consensus pattern (31 bp):   
TTTAATAATTTTATTATTTCAAAAAAATAAT

Found at i:9086 original size:20 final size:20

Alignment explanation


    Indices: 9035--9091  Score: 59
    Period size: 20  Copynumber: 3.0  Consensus size: 20

       9025 ATTTCAAAAA

                                
       9035 AATAATTTT--AATAATTTT
          1 AATAATTTTAAAATAATTTT

                                  
       9053 -AT-ATTTTAAAAAATAATTTT
          1 AATAATTTT--AAAATAATTTT

                          *    
       9073 AATAATTTTAAAATCATTT
          1 AATAATTTTAAAATAATTT

       9092 GCTGACATGA


Statistics
Matches: 32,  Mismatches: 1, Indels: 10
        0.74            0.02        0.23

Matches are distributed among these distances:
  16    5  0.16
  17    2  0.06
  20   18  0.56
  21    2  0.06
  22    5  0.16

ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51


Consensus pattern (20 bp):   
AATAATTTTAAAATAATTTT
Done.