Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004634.1 Kokia drynarioides strain JFW-HI SEQ_118158, 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: 8411
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:799 original size:18 final size:17

Alignment explanation


    Indices: 740--800  Score: 61
    Period size: 18  Copynumber: 3.4  Consensus size: 17

        730 CACCGTGGAA

                 *            
        740 AGGAGGGATCTTGGGAAG
          1 AGGAGCGATCTTGGG-AG

                       *      
        758 AGGAGCGATCTCGAGGAG
          1 AGGAGCGATCTTG-GGAG

                               
        776 AGGAGC-AGTCTTGGGTAG
          1 AGGAGCGA-TCTTGGG-AG

                   
        794 AGGAGCG
          1 AGGAGCG

        801 GTCAATCGTC


Statistics
Matches: 36,  Mismatches: 3, Indels: 7
        0.78            0.07        0.15

Matches are distributed among these distances:
  17    3  0.08
  18   31  0.86
  19    2  0.06

ACGTcount: A:0.26, C:0.11, G:0.48, T:0.15


Consensus pattern (17 bp):   
AGGAGCGATCTTGGGAG

Found at i:1856 original size:49 final size:48

Alignment explanation


    Indices: 1762--1856  Score: 118
    Period size: 49  Copynumber: 2.0  Consensus size: 48

       1752 TGCTTAATTT

                       *          *      *       * **       
       1762 TTTCCCTTCATTTTCTGAGGTATAAGGTTCGCCGTTGTGGTTTAAATC
          1 TTTCCCTTCATCTTCTGAGGTACAAGGTTAGCCGTTGCGACTTAAATC

                                             *             
       1810 TTTCCCTTCATGCTTCTGAGGTACAAGGTTAGCTGTTGCGACTTAAA
          1 TTTCCCTTCAT-CTTCTGAGGTACAAGGTTAGCCGTTGCGACTTAAA

       1857 CCTTCCTCTC


Statistics
Matches: 39,  Mismatches: 7, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  48   11  0.28
  49   28  0.72

ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40


Consensus pattern (48 bp):   
TTTCCCTTCATCTTCTGAGGTACAAGGTTAGCCGTTGCGACTTAAATC

Found at i:2360 original size:18 final size:19

Alignment explanation


    Indices: 2337--2372  Score: 65
    Period size: 18  Copynumber: 1.9  Consensus size: 19

       2327 TGTCGAATAT

                               
       2337 TTACAAGGAACAA-ATTAA
          1 TTACAAGGAACAATATTAA

                              
       2355 TTACAAGGAACAATATTA
          1 TTACAAGGAACAATATTA

       2373 GATTCTAGAT


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

Matches are distributed among these distances:
  18   13  0.76
  19    4  0.24

ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25


Consensus pattern (19 bp):   
TTACAAGGAACAATATTAA
Done.