Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003536.1 Kokia drynarioides strain JFW-HI SEQ_116381, 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: 5691
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:2345 original size:28 final size:24

Alignment explanation


    Indices: 2288--2338  Score: 77
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       2278 ATAAATAATC

                 *                  
       2288 TTTCAGTTAAACTCTGTTTGTTTG
          1 TTTCAATTAAACTCTGTTTGTTTG

                                     
       2312 TTTCAATTAAACTCTGTTTAG-TTG
          1 TTTCAATTAAACTCTGTTT-GTTTG

               
       2336 TTT
          1 TTT

       2339 TAGTCAAATT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  24   24  0.96
  25    1  0.04

ACGTcount: A:0.20, C:0.12, G:0.14, T:0.55


Consensus pattern (24 bp):   
TTTCAATTAAACTCTGTTTGTTTG

Found at i:3513 original size:41 final size:41

Alignment explanation


    Indices: 3417--3570  Score: 151
    Period size: 41  Copynumber: 3.9  Consensus size: 41

       3407 CTTTAGCTAT

                  *                *             **  
       3417 GCTTTACCATAAACGCCGCTAAAAGTCAGAGCATTAGTTGC
          1 GCTTTATCATAAACGCCGCTAAAGGTCAGAGCATTAGCGGC

                    * *                          *    
       3458 GC-TTATGGACAAACGCCGCTAAAGGTCAGAGCATTAACGGC
          1 GCTTTAT-CATAAACGCCGCTAAAGGTCAGAGCATTAGCGGC

                                                    *
       3499 GCTTTATCATAAA---CGC---AGGTCAGAGCATTAGCGGT
          1 GCTTTATCATAAACGCCGCTAAAGGTCAGAGCATTAGCGGC

                 * *                  *          
       3534 GCTTTCTAATAAACGCCGCTAAAGGTTAGAGCATTAG
          1 GCTTTATCATAAACGCCGCTAAAGGTCAGAGCATTAG

       3571 GAGGTGTTTA


Statistics
Matches: 91,  Mismatches: 14, Indels: 16
        0.75            0.12        0.13

Matches are distributed among these distances:
  35   28  0.31
  38    6  0.07
  40    3  0.03
  41   50  0.55
  42    4  0.04

ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23


Consensus pattern (41 bp):   
GCTTTATCATAAACGCCGCTAAAGGTCAGAGCATTAGCGGC

Found at i:3526 original size:35 final size:35

Alignment explanation


    Indices: 3480--3549  Score: 104
    Period size: 35  Copynumber: 2.0  Consensus size: 35

       3470 ACGCCGCTAA

                                      *        
       3480 AGGTCAGAGCATTAACGGCGCTTTATCATAAACGC
          1 AGGTCAGAGCATTAACGGCGCTTTATAATAAACGC

                          *   *     *          
       3515 AGGTCAGAGCATTAGCGGTGCTTTCTAATAAACGC
          1 AGGTCAGAGCATTAACGGCGCTTTATAATAAACGC

       3550 CGCTAAAGGT


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  35   31  1.00

ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24


Consensus pattern (35 bp):   
AGGTCAGAGCATTAACGGCGCTTTATAATAAACGC
Done.