Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004505.1 Kokia drynarioides strain JFW-HI SEQ_117946, 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: 17635
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:347 original size:11 final size:11

Alignment explanation


    Indices: 327--357  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

        317 ACGTTAGGGT

                       
        327 TATT-TTTTTG
          1 TATTATTTTTG

                       
        337 TATTATTTTTG
          1 TATTATTTTTG

                      
        348 TATTATTTTT
          1 TATTATTTTT

        358 TGGTAAATAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  10    4  0.20
  11   16  0.80

ACGTcount: A:0.16, C:0.00, G:0.06, T:0.77


Consensus pattern (11 bp):   
TATTATTTTTG

Found at i:934 original size:2 final size:2

Alignment explanation


    Indices: 927--954  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

        917 TGTCACTTAA

                                                     
        927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        955 TAATTATTAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:2270 original size:13 final size:14

Alignment explanation


    Indices: 2247--2275  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

       2237 GAAATTGATT

                          
       2247 AAAATATAACTTTG
          1 AAAATATAACTTTG

                          
       2261 AAAA-ATAACTTTG
          1 AAAATATAACTTTG

              
       2274 AA
          1 AA

       2276 TCGATTAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.73
  14    4  0.27

ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31


Consensus pattern (14 bp):   
AAAATATAACTTTG

Found at i:5074 original size:22 final size:23

Alignment explanation


    Indices: 5021--5064  Score: 79
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       5011 ACTTCTTAAG

                          *        
       5021 AATTTTATGTTTTTTTTTTTGGA
          1 AATTTTATGTTTTTCTTTTTGGA

                                 
       5044 AATTTTATGTTTTTCTTTTTG
          1 AATTTTATGTTTTTCTTTTTG

       5065 CATTTCTATG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.16, C:0.02, G:0.11, T:0.70


Consensus pattern (23 bp):   
AATTTTATGTTTTTCTTTTTGGA

Found at i:15945 original size:60 final size:59

Alignment explanation


    Indices: 15825--15945  Score: 136
    Period size: 60  Copynumber: 2.0  Consensus size: 59

      15815 ATACTTGAAC

                                    *            *          *    * *   
      15825 TTGACATTTTTTCTTAATTCGGTATTTAAACTTTTTTGGACTCAATTTGGTACTTGAAT
          1 TTGACATTTTTTCTTAATTCGGTACTTAAACTTTTTTAGACTCAATTTAGTACATAAAT

                            *  *         *            *                  
      15884 TTGACA-TTTTTCTTATTTTGGTACTTAAGCTTTATTTTAGATTCAATTTAGTACATAAAT
          1 TTGACATTTTTTCTTAATTCGGTACTTAAAC-TT-TTTTAGACTCAATTTAGTACATAAAT

              
      15944 TT
          1 TT

      15946 ATTAAATATT


Statistics
Matches: 51,  Mismatches: 9, Indels: 3
        0.81            0.14        0.05

Matches are distributed among these distances:
  58   20  0.39
  59    8  0.16
  60   23  0.45

ACGTcount: A:0.26, C:0.11, G:0.12, T:0.52


Consensus pattern (59 bp):   
TTGACATTTTTTCTTAATTCGGTACTTAAACTTTTTTAGACTCAATTTAGTACATAAAT

Found at i:16233 original size:28 final size:28

Alignment explanation


    Indices: 16180--16233  Score: 65
    Period size: 28  Copynumber: 1.9  Consensus size: 28

      16170 AAAAAGTGTT

                              *  *      
      16180 AAGTTTGAGTATCAAATTGGATAAAAAA
          1 AAGTTTGAGTATCAAATTAGAAAAAAAA

                           *           
      16208 AAGTTT-AGATATCAGATTAGAAAAAA
          1 AAGTTTGAG-TATCAAATTAGAAAAAA

      16234 GTTTTAAGTT


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  27    2  0.09
  28   20  0.91

ACGTcount: A:0.52, C:0.04, G:0.17, T:0.28


Consensus pattern (28 bp):   
AAGTTTGAGTATCAAATTAGAAAAAAAA
Done.