Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006934.1 Kokia drynarioides strain JFW-HI SEQ_121537, 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: 8115
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34


Found at i:1106 original size:30 final size:32

Alignment explanation


    Indices: 1070--1136  Score: 102
    Period size: 30  Copynumber: 2.2  Consensus size: 32

       1060 AATAGTTTAT

                                       *    
       1070 ATTTTTATAATTTTT-AAAAAATTAAATTA-A
          1 ATTTTTATAATTTTTGAAAAAATTAAAATATA

                              *             
       1100 ATTTTTATAATTTTTGAAGAAATTAAAATATA
          1 ATTTTTATAATTTTTGAAAAAATTAAAATATA

                 
       1132 ATTTT
          1 ATTTT

       1137 ATCATTAAAA


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

Matches are distributed among these distances:
  30   15  0.45
  31   12  0.36
  32    6  0.18

ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51


Consensus pattern (32 bp):   
ATTTTTATAATTTTTGAAAAAATTAAAATATA

Found at i:1137 original size:31 final size:30

Alignment explanation


    Indices: 1067--1138  Score: 92
    Period size: 31  Copynumber: 2.4  Consensus size: 30

       1057 TTTAATAGTT

                *                        *
       1067 TATATTTTTATAATTTTTAAAAAATTAAAT
          1 TATAATTTTATAATTTTTAAAAAATTAAAA

                                  *         
       1097 TA-AATTTTTATAATTTTTGAAGAAATTAAAA
          1 TATAA-TTTTATAATTTTT-AAAAAATTAAAA

                       
       1128 TATAATTTTAT
          1 TATAATTTTAT

       1139 CATTAAAATT


Statistics
Matches: 36,  Mismatches: 3, Indels: 5
        0.82            0.07        0.11

Matches are distributed among these distances:
  29    1  0.03
  30   15  0.42
  31   18  0.50
  32    2  0.06

ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51


Consensus pattern (30 bp):   
TATAATTTTATAATTTTTAAAAAATTAAAA

Found at i:4467 original size:25 final size:25

Alignment explanation


    Indices: 4439--4521  Score: 130
    Period size: 25  Copynumber: 3.3  Consensus size: 25

       4429 ATTTTAGCTT

                                  *  
       4439 GAAAGAGCGTAATTTTGTCTGGCTC
          1 GAAAGAGCGTAATTTTGTCTGGGTC

                        * *   *      
       4464 GAAAGAGCGTAAATCTGTATGGGTC
          1 GAAAGAGCGTAATTTTGTCTGGGTC

                                     
       4489 GAAAGAGCGTAATTTTGTCTGGGTC
          1 GAAAGAGCGTAATTTTGTCTGGGTC

                    
       4514 GAAAGAGC
          1 GAAAGAGC

       4522 ATAAATTTAT


Statistics
Matches: 51,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  25   51  1.00

ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27


Consensus pattern (25 bp):   
GAAAGAGCGTAATTTTGTCTGGGTC

Found at i:4535 original size:50 final size:50

Alignment explanation


    Indices: 4439--4535  Score: 158
    Period size: 50  Copynumber: 1.9  Consensus size: 50

       4429 ATTTTAGCTT

                                             *       *        
       4439 GAAAGAGCGTAATTTTGTCTGGCTCGAAAGAGCGTAAATCTGTATGGGTC
          1 GAAAGAGCGTAATTTTGTCTGGCTCGAAAGAGCATAAATCTATATGGGTC

                                  *                *       
       4489 GAAAGAGCGTAATTTTGTCTGGGTCGAAAGAGCATAAATTTATATGG
          1 GAAAGAGCGTAATTTTGTCTGGCTCGAAAGAGCATAAATCTATATGG

       4536 CTCAAGAGAG


Statistics
Matches: 43,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  50   43  1.00

ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29


Consensus pattern (50 bp):   
GAAAGAGCGTAATTTTGTCTGGCTCGAAAGAGCATAAATCTATATGGGTC
Done.