Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008554.1 Kokia drynarioides strain JFW-HI SEQ_123232, 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: 10365
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32


Found at i:192 original size:98 final size:101

Alignment explanation


    Indices: 60--276  Score: 307
    Period size: 101  Copynumber: 2.2  Consensus size: 101

         50 AGTGATAACG

                                       *                  *                  
         60 TCTTCAAGTG-TTTTTTTACTTCAAGTGTCTTTCTAATAGCT-T-AGCTATTAGGTTCAATTCTA
          1 TCTTCAAGTGTTTTTTTTACTTCAAGTATCTTTCTAATAGCTCTCAACTATTAGGTTCAATTCTA

                      *                         
        122 CCTTCAATCCCTGTACGTTATGAACTTTT-ATTTAA
         66 CCTTCAATCCATGTACGTTATGAACTTTTAATTTAA

                                                *                            
        157 TCTTCAAGTGTTTTTTTTACTTCAAGTATCTTTCTAGTAGCTCCTCAACTATTAGGTTCAATTCT
          1 TCTTCAAGTGTTTTTTTTACTTCAAGTATCTTTCTAATAGCT-CTCAACTATTAGGTTCAATTCT

            *      *         *       *             
        222 TCCTTCAGTCCATGTACTTTATGAAGTTTTAAAATTTAA
         65 ACCTTCAATCCATGTACGTTATGAACTTTT--AATTTAA

                            
        261 TCTTCAAGTGTTTTTT
          1 TCTTCAAGTGTTTTTT

        277 ATTAAAGTCA


Statistics
Matches: 105,  Mismatches: 8, Indels: 7
        0.88            0.07        0.06

Matches are distributed among these distances:
  97   10  0.10
  98   29  0.28
 100    1  0.01
 101   43  0.41
 104   22  0.21

ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47


Consensus pattern (101 bp):   
TCTTCAAGTGTTTTTTTTACTTCAAGTATCTTTCTAATAGCTCTCAACTATTAGGTTCAATTCTA
CCTTCAATCCATGTACGTTATGAACTTTTAATTTAA

Found at i:3377 original size:18 final size:18

Alignment explanation


    Indices: 3354--3389  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       3344 TTTCAATCAA

                              
       3354 GCTTTACTGTAACAATAT
          1 GCTTTACTGTAACAATAT

                  *           
       3372 GCTTTATTGTAACAATAT
          1 GCTTTACTGTAACAATAT

       3390 TGCATTGCCA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42


Consensus pattern (18 bp):   
GCTTTACTGTAACAATAT

Found at i:7441 original size:27 final size:27

Alignment explanation


    Indices: 7411--7489  Score: 115
    Period size: 27  Copynumber: 2.9  Consensus size: 27

       7401 AAAGTCTAAG

                                       
       7411 GAAAGAGCAATACTCTATTTCTGGCTC
          1 GAAAGAGCAATACTCTATTTCTGGCTC

                          * *          
       7438 GAAAGAGCAATACTTTGTTTCTGGCTC
          1 GAAAGAGCAATACTCTATTTCTGGCTC

               *                      
       7465 GAAGGAG-AGATACTCTATTTCTGGC
          1 GAAAGAGCA-ATACTCTATTTCTGGC

       7490 CTGAATTAAT


Statistics
Matches: 46,  Mismatches: 5, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  26    1  0.02
  27   45  0.98

ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30


Consensus pattern (27 bp):   
GAAAGAGCAATACTCTATTTCTGGCTC
Done.