Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008448.1 Kokia drynarioides strain JFW-HI SEQ_123120, 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: 15778
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:3971 original size:18 final size:18

Alignment explanation


    Indices: 3948--3983  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       3938 TCATACTCAT

                              
       3948 ACACTTCATATGAAAGCG
          1 ACACTTCATATGAAAGCG

                              
       3966 ACACTTCATATGAAAGCG
          1 ACACTTCATATGAAAGCG

       3984 TATATAAATG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22


Consensus pattern (18 bp):   
ACACTTCATATGAAAGCG

Found at i:10875 original size:41 final size:42

Alignment explanation


    Indices: 10818--10898  Score: 137
    Period size: 41  Copynumber: 2.0  Consensus size: 42

      10808 TTTTCTTTGT

                       *                              
      10818 TTGGTTAATAATTATTAGTTTTTTTTTT-ATATTACTAAATA
          1 TTGGTTAATAAATATTAGTTTTTTTTTTCATATTACTAAATA

                   *                                
      10859 TTGGTTACTAAATATTAGTTTTTTTTTTCATATTACTAAA
          1 TTGGTTAATAAATATTAGTTTTTTTTTTCATATTACTAAA

      10899 AAAATTACAT


Statistics
Matches: 37,  Mismatches: 2, Indels: 1
        0.93            0.05        0.03

Matches are distributed among these distances:
  41   26  0.70
  42   11  0.30

ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57


Consensus pattern (42 bp):   
TTGGTTAATAAATATTAGTTTTTTTTTTCATATTACTAAATA

Found at i:14051 original size:17 final size:17

Alignment explanation


    Indices: 14016--14048  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      14006 TTAATTCAAC

                    *        
      14016 TTTTTTATTTTAATAAA
          1 TTTTTTATATTAATAAA

                             
      14033 TTTTTTATATT-ATAAA
          1 TTTTTTATATTAATAAA

      14049 ATTATATTTT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16    5  0.33
  17   10  0.67

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (17 bp):   
TTTTTTATATTAATAAA

Found at i:15223 original size:22 final size:22

Alignment explanation


    Indices: 15198--15239  Score: 59
    Period size: 22  Copynumber: 1.9  Consensus size: 22

      15188 CGAATTTGGC

                                   
      15198 TCGATAATTTTTT-GAATTGAGT
          1 TCGA-AATTTTTTGGAATTGAGT

                 *              
      15220 TCGAATTTTTTTGGAATTGA
          1 TCGAAATTTTTTGGAATTGA

      15240 ACTCGAGTAG


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21    7  0.39
  22   11  0.61

ACGTcount: A:0.26, C:0.05, G:0.19, T:0.50


Consensus pattern (22 bp):   
TCGAAATTTTTTGGAATTGAGT

Found at i:15245 original size:22 final size:21

Alignment explanation


    Indices: 15205--15245  Score: 55
    Period size: 22  Copynumber: 1.9  Consensus size: 21

      15195 GGCTCGATAA

                         **      
      15205 TTTTTTGAATTGAGTTCGAAT
          1 TTTTTTGAATTGAACTCGAAT

                                
      15226 TTTTTTGGAATTGAACTCGA
          1 TTTTTT-GAATTGAACTCGA

      15246 GTAGCTTGCG


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    6  0.35
  22   11  0.65

ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49


Consensus pattern (21 bp):   
TTTTTTGAATTGAACTCGAAT
Done.