Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007417.1 Kokia drynarioides strain JFW-HI SEQ_122036, 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: 5631
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35


Found at i:2875 original size:30 final size:30

Alignment explanation


    Indices: 2809--2865  Score: 93
    Period size: 27  Copynumber: 2.0  Consensus size: 30

       2799 GAACATTAAC

                                          
       2809 AAACGAACATGAACACACATAATTTAAAAT
          1 AAACGAACATGAACACACATAATTTAAAAT

                                          
       2839 AAACGAACAT-AA-ACACA-AATTTAAAAT
          1 AAACGAACATGAACACACATAATTTAAAAT

       2866 TCTTAACGAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  27   10  0.37
  28    5  0.19
  29    2  0.07
  30   10  0.37

ACGTcount: A:0.60, C:0.16, G:0.05, T:0.19


Consensus pattern (30 bp):   
AAACGAACATGAACACACATAATTTAAAAT

Found at i:3554 original size:37 final size:39

Alignment explanation


    Indices: 3491--3564  Score: 116
    Period size: 37  Copynumber: 1.9  Consensus size: 39

       3481 TTATTTTAAA

                                                   
       3491 ATTATTAAAATTATTTTTTTAAAATATAAAATTATTATG
          1 ATTATTAAAATTATTTTTTTAAAATATAAAATTATTATG

                    *           *                
       3530 ATTATT-ATATTA-TTTTTTGAAATATAAAATTATTA
          1 ATTATTAAAATTATTTTTTTAAAATATAAAATTATTA

       3565 AATAATTTTA


Statistics
Matches: 33,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  37   22  0.67
  38    5  0.15
  39    6  0.18

ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53


Consensus pattern (39 bp):   
ATTATTAAAATTATTTTTTTAAAATATAAAATTATTATG

Found at i:3705 original size:46 final size:46

Alignment explanation


    Indices: 3638--3742  Score: 156
    Period size: 46  Copynumber: 2.3  Consensus size: 46

       3628 AAATGAAATA

                   *      * *         *                   
       3638 TGGGTTTCTGAAATTTGAATTTTTTTTAAAATCAAACCTAAAAACT
          1 TGGGTTTTTGAAATCTAAATTTTTTTAAAAATCAAACCTAAAAACT

                                                 *  *     
       3684 TGGGTTTTTGAAATCTAAATTTTTTTAAAAATCAAACTTAGAAACT
          1 TGGGTTTTTGAAATCTAAATTTTTTTAAAAATCAAACCTAAAAACT

                         
       3730 TGGGTTTTTGAAA
          1 TGGGTTTTTGAAA

       3743 CCTGTTCTTT


Statistics
Matches: 53,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  46   53  1.00

ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42


Consensus pattern (46 bp):   
TGGGTTTTTGAAATCTAAATTTTTTTAAAAATCAAACCTAAAAACT
Done.