Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014796.1 Kokia drynarioides strain JFW-HI SEQ_129838, 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: 53614
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35


Found at i:14082 original size:22 final size:23

Alignment explanation


    Indices: 14057--14105  Score: 57
    Period size: 22  Copynumber: 2.2  Consensus size: 23

      14047 TAAAAAAAAT

                            *      
      14057 AACAAG-AAGAAAATAGTAACAA
          1 AACAAGTAAGAAAATAATAACAA

                   *            *  
      14079 AAC-AGTGAGAAAATAATAAGAA
          1 AACAAGTAAGAAAATAATAACAA

                 
      14101 AACAA
          1 AACAA

      14106 ATTCAAGCCG


Statistics
Matches: 22,  Mismatches: 3, Indels: 3
        0.79            0.11        0.11

Matches are distributed among these distances:
  21    2  0.09
  22   19  0.86
  23    1  0.05

ACGTcount: A:0.67, C:0.08, G:0.14, T:0.10


Consensus pattern (23 bp):   
AACAAGTAAGAAAATAATAACAA

Found at i:14715 original size:3 final size:3

Alignment explanation


    Indices: 14690--14736  Score: 67
    Period size: 3  Copynumber: 15.7  Consensus size: 3

      14680 AAAATCGTCG

                  *         *    *                                        
      14690 TCA TCG TCA TCA CCA TTA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
          1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC

      14737 CTGTTCTCCG


Statistics
Matches: 38,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   3   38  1.00

ACGTcount: A:0.30, C:0.34, G:0.02, T:0.34


Consensus pattern (3 bp):   
TCA

Found at i:20152 original size:21 final size:21

Alignment explanation


    Indices: 20122--20174  Score: 65
    Period size: 20  Copynumber: 2.6  Consensus size: 21

      20112 TTCGACATTG

                 *               
      20122 AATAACATTACAAAAA-TACA
          1 AATAAAATTACAAAAATTACA

                                  
      20142 TAATAAAATTA-AAAAATTACA
          1 -AATAAAATTACAAAAATTACA

                *       
      20163 AATATAATTACA
          1 AATAAAATTACA

      20175 CACAATAATT


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  20   14  0.50
  21   14  0.50

ACGTcount: A:0.64, C:0.09, G:0.00, T:0.26


Consensus pattern (21 bp):   
AATAAAATTACAAAAATTACA

Found at i:33590 original size:21 final size:23

Alignment explanation


    Indices: 33566--33610  Score: 67
    Period size: 21  Copynumber: 2.0  Consensus size: 23

      33556 AATTGATCCG

                        *          
      33566 AATTCAAAA-AACTC-AACAAGT
          1 AATTCAAAATAAATCAAACAAGT

                                   
      33587 AATTCAAAATAAATCAAACAAGT
          1 AATTCAAAATAAATCAAACAAGT

             
      33610 A
          1 A

      33611 GCCTAAAATA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    9  0.43
  22    4  0.19
  23    8  0.38

ACGTcount: A:0.60, C:0.16, G:0.04, T:0.20


Consensus pattern (23 bp):   
AATTCAAAATAAATCAAACAAGT

Found at i:39944 original size:31 final size:31

Alignment explanation


    Indices: 39881--39945  Score: 87
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      39871 AATAGTTCAA

                                       *   
      39881 TGAATTAAATAAAACCTCTCGAATAGTTTAG
          1 TGAATTAAATAAAACCTCTCGAATAGTATAG

                                * *         
      39912 TGAATTAAATGAAAACCT-TTGGATAGTATAG
          1 TGAATTAAAT-AAAACCTCTCGAATAGTATAG

               
      39943 TGA
          1 TGA

      39946 CCATTTTGTA


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  31   23  0.77
  32    7  0.23

ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32


Consensus pattern (31 bp):   
TGAATTAAATAAAACCTCTCGAATAGTATAG
Done.