Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010876.1 Kokia drynarioides strain JFW-HI SEQ_125844, 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: 13174
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35


Found at i:964 original size:7 final size:7

Alignment explanation


    Indices: 952--991  Score: 57
    Period size: 7  Copynumber: 6.0  Consensus size: 7

        942 ATTTTAAAAT

                   
        952 AAATTTA
          1 AAATTTA

                   
        959 AAATTTA
          1 AAATTTA

                *  
        966 AAA-ATA
          1 AAATTTA

                   
        972 AAATTT-
          1 AAATTTA

                   
        978 AAATTTA
          1 AAATTTA

                   
        985 AAATTTA
          1 AAATTTA

        992 TTTTTAGGTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
   6   11  0.38
   7   18  0.62

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (7 bp):   
AAATTTA

Found at i:964 original size:19 final size:19

Alignment explanation


    Indices: 942--988  Score: 62
    Period size: 19  Copynumber: 2.5  Consensus size: 19

        932 GTATTTGGAC

                                
        942 ATTTTAAAAT-AAATTTAAA
          1 ATTTTAAAATAAAATTT-AA

                *              
        961 ATTTAAAAATAAAATTTAA
          1 ATTTTAAAATAAAATTTAA

                      
        980 A-TTTAAAAT
          1 ATTTTAAAAT

        989 TTATTTTTAG


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  18    7  0.28
  19   12  0.48
  20    6  0.24

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (19 bp):   
ATTTTAAAATAAAATTTAA

Found at i:997 original size:13 final size:13

Alignment explanation


    Indices: 951--991  Score: 64
    Period size: 13  Copynumber: 3.2  Consensus size: 13

        941 CATTTTAAAA

                         
        951 TAAATTTAAAATT
          1 TAAATTTAAAATT

                **       
        964 TAAAAATAAAATT
          1 TAAATTTAAAATT

                         
        977 TAAATTTAAAATT
          1 TAAATTTAAAATT

              
        990 TA
          1 TA

        992 TTTTTAGGTT


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  13   24  1.00

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (13 bp):   
TAAATTTAAAATT

Found at i:2192 original size:21 final size:20

Alignment explanation


    Indices: 2164--2202  Score: 69
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       2154 CCATGCTATG

                                
       2164 TATTATAAAAATAATATATT
          1 TATTATAAAAATAATATATT

                               
       2184 TATTCATAAAAATAATATA
          1 TATT-ATAAAAATAATATA

       2203 GTTCAATAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20    4  0.22
  21   14  0.78

ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41


Consensus pattern (20 bp):   
TATTATAAAAATAATATATT

Found at i:9943 original size:16 final size:17

Alignment explanation


    Indices: 9922--9953  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       9912 ATCGAATTGA

                             
       9922 GAAAA-TTATTTATTTG
          1 GAAAATTTATTTATTTG

                            
       9938 GAAAATTTATTTATTT
          1 GAAAATTTATTTATTT

       9954 ATTTAAATTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    5  0.33
  17   10  0.67

ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53


Consensus pattern (17 bp):   
GAAAATTTATTTATTTG

Done.