Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004908.1 Kokia drynarioides strain JFW-HI SEQ_118602, 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: 16810
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33


Found at i:1876 original size:14 final size:14

Alignment explanation


    Indices: 1857--1891  Score: 52
    Period size: 14  Copynumber: 2.5  Consensus size: 14

       1847 ACCCGACCCA

                          
       1857 GATCGTTAACCGTT
          1 GATCGTTAACCGTT

                   *      
       1871 GATCGTTCACCGTT
          1 GATCGTTAACCGTT

              *    
       1885 GACCGTT
          1 GATCGTT

       1892 GACAGTAGAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.17, C:0.26, G:0.23, T:0.34


Consensus pattern (14 bp):   
GATCGTTAACCGTT

Found at i:9038 original size:18 final size:18

Alignment explanation


    Indices: 9015--9051  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       9005 GACTCGACTC

                               
       9015 ATTGACC-AACCCGAACCT
          1 ATTGACCTAACCCG-ACCT

                              
       9033 ATTGACCTAACCCGACCT
          1 ATTGACCTAACCCGACCT

             
       9051 A
          1 A

       9052 GACCATCGAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  18   12  0.67
  19    6  0.33

ACGTcount: A:0.32, C:0.38, G:0.11, T:0.19


Consensus pattern (18 bp):   
ATTGACCTAACCCGACCT

Found at i:10014 original size:48 final size:48

Alignment explanation


    Indices: 9956--10054  Score: 171
    Period size: 48  Copynumber: 2.1  Consensus size: 48

       9946 ATAACACTCA

                                                            
       9956 AATCCCGAACACCATTATCAGTTAGGATTCCAGTGTTACTATTCATTT
          1 AATCCCGAACACCATTATCAGTTAGGATTCCAGTGTTACTATTCATTT

                 *     *       *                            
      10004 AATCCTGAACATCATTATCGGTTAGGATTCCAGTGTTACTATTCATTT
          1 AATCCCGAACACCATTATCAGTTAGGATTCCAGTGTTACTATTCATTT

               
      10052 AAT
          1 AAT

      10055 ATCGTTCATC


Statistics
Matches: 48,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  48   48  1.00

ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37


Consensus pattern (48 bp):   
AATCCCGAACACCATTATCAGTTAGGATTCCAGTGTTACTATTCATTT

Found at i:16527 original size:24 final size:24

Alignment explanation


    Indices: 16497--16556  Score: 120
    Period size: 24  Copynumber: 2.5  Consensus size: 24

      16487 ATGCATGCAT

                                    
      16497 ACTACCGATACATTAATGCTAAAA
          1 ACTACCGATACATTAATGCTAAAA

                                    
      16521 ACTACCGATACATTAATGCTAAAA
          1 ACTACCGATACATTAATGCTAAAA

                        
      16545 ACTACCGATACA
          1 ACTACCGATACA

      16557 ACTCAAGTCA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   36  1.00

ACGTcount: A:0.45, C:0.23, G:0.08, T:0.23


Consensus pattern (24 bp):   
ACTACCGATACATTAATGCTAAAA
Done.