Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008825.1 Kokia drynarioides strain JFW-HI SEQ_123509, 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: 8300
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32


Found at i:800 original size:21 final size:21

Alignment explanation


    Indices: 776--818  Score: 77
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        766 CATCTCAACC

                         *       
        776 TGTTCGTGATGCGTAACCACA
          1 TGTTCGTGATGCGCAACCACA

                                 
        797 TGTTCGTGATGCGCAACCACA
          1 TGTTCGTGATGCGCAACCACA

             
        818 T
          1 T

        819 TTAAAGGGCT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28


Consensus pattern (21 bp):   
TGTTCGTGATGCGCAACCACA

Found at i:4363 original size:36 final size:36

Alignment explanation


    Indices: 4316--4388  Score: 146
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       4306 TCTTTCAATA

                                                
       4316 TAAAGCAATCCCTTTAGCTAGCCTATGAGTATTCTT
          1 TAAAGCAATCCCTTTAGCTAGCCTATGAGTATTCTT

                                                
       4352 TAAAGCAATCCCTTTAGCTAGCCTATGAGTATTCTT
          1 TAAAGCAATCCCTTTAGCTAGCCTATGAGTATTCTT

             
       4388 T
          1 T

       4389 TTCTTTTGTT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   37  1.00

ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37


Consensus pattern (36 bp):   
TAAAGCAATCCCTTTAGCTAGCCTATGAGTATTCTT

Found at i:4501 original size:21 final size:22

Alignment explanation


    Indices: 4462--4510  Score: 64
    Period size: 21  Copynumber: 2.3  Consensus size: 22

       4452 TATTCACATG

                *                 
       4462 CTTTCTTACTCATGATTCTT-T
          1 CTTTTTTACTCATGATTCTTCT

                         **       
       4483 CTTTTTTACTCATTTTTCTTCT
          1 CTTTTTTACTCATGATTCTTCT

                  
       4505 CTTTTT
          1 CTTTTT

       4511 GATTTTTTCT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  21   17  0.71
  22    7  0.29

ACGTcount: A:0.10, C:0.22, G:0.02, T:0.65


Consensus pattern (22 bp):   
CTTTTTTACTCATGATTCTTCT

Done.