Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007983.1 Kokia drynarioides strain JFW-HI SEQ_122634, 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: 4527
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:2239 original size:17 final size:18

Alignment explanation


    Indices: 2215--2250  Score: 56
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       2205 TAATGTAAAG

                               
       2215 GAAAAAAAATTAAA-AGAA
          1 GAAAAAAAA-TAAAGAGAA

                              
       2233 GAAAAAAAATAAAGAGAA
          1 GAAAAAAAATAAAGAGAA

       2251 TCGTATCTAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    4  0.24
  18   13  0.76

ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08


Consensus pattern (18 bp):   
GAAAAAAAATAAAGAGAA

Found at i:2250 original size:15 final size:16

Alignment explanation


    Indices: 2210--2250  Score: 50
    Period size: 18  Copynumber: 2.6  Consensus size: 16

       2200 TAAGTTAATG

                            
       2210 TAAAG-GAAAAAAAAT
          1 TAAAGAGAAAAAAAAT

                              
       2225 TAAAAGAAGAAAAAAAA-
          1 T-AAAG-AGAAAAAAAAT

                     
       2242 TAAAGAGAA
          1 TAAAGAGAA

       2251 TCGTATCTAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 6
        0.79            0.00        0.21

Matches are distributed among these distances:
  15    5  0.22
  16    8  0.35
  17    1  0.04
  18    9  0.39

ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10


Consensus pattern (16 bp):   
TAAAGAGAAAAAAAAT

Found at i:3943 original size:53 final size:52

Alignment explanation


    Indices: 3872--4140  Score: 159
    Period size: 54  Copynumber: 4.9  Consensus size: 52

       3862 TTTTTAAACA

                      *  *           *                           
       3872 GATAAAAGGGATGCCGACCATCAATATCCCAACACCCAAAATTTTTTTGAATT
          1 GATAAAAGGGGTGTCGACCATCAATGTCCCAACACCCAAAATTTTTTT-AATT

                                   *    *         *                
       3925 GATAAAAGGGGTGTCGACCATCAGTGTCTCAACACCCCCAAATTTTTTTAATTTT
          1 GATAAAAGGGGTGTCGACCATCAATGTCCCAACA-CCCAAAATTTTTTTAA--TT

              **           *               *        **              
       3980 G-GGAAAGGGGTGTCAACCATCAATGTCCCAGCAACCCAATTTTTTTTTAAATTCT
          1 GATAAAAGGGGTGTCGACCATCAATGTCCCAAC-ACCCAAAATTTTTTT-AA-T-T

              *          * *              *                            
       4035 G-GAAAAGGGGTATTTG-CCATCAATGTCCTAACACCCTAAAAAAGATTTTTTTTAATT
          1 GATAAAAGGGGT-GTCGACCATCAATGTCCCAACACCC----AAA-A-TTTTTTTAATT

              *              *    * *                   *     
       4092 -AAATAAAGGGGTGTCGGCCATTAGTGTCCCAACATCTCCAAAAGTTTTT
          1 GATA-AAAGGGGTGTCGACCATCAATGTCCCAACA-C-CCAAAATTTTTT

       4141 CTAAATATTG


Statistics
Matches: 168,  Mismatches: 30, Indels: 35
        0.72            0.13        0.15

Matches are distributed among these distances:
  53   31  0.18
  54   60  0.36
  55   32  0.19
  56    4  0.02
  57    4  0.02
  58   25  0.15
  59    3  0.02
  60    9  0.05

ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30


Consensus pattern (52 bp):   
GATAAAAGGGGTGTCGACCATCAATGTCCCAACACCCAAAATTTTTTTAATT

Done.