Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014028.1 Kokia drynarioides strain JFW-HI SEQ_129059, 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: 23986
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:4377 original size:21 final size:20

Alignment explanation


    Indices: 4335--4377  Score: 50
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       4325 AATTAAGTTT

                            **  
       4335 ATTTAAAATAAAAATATTAA
          1 ATTTAAAATAAAAATAGAAA

                    *            
       4355 ATTTAAATTTAAAAATAGAAA
          1 ATTTAAA-ATAAAAATAGAAA

              
       4376 AT
          1 AT

       4378 AATATTAATA


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  20    7  0.37
  21   12  0.63

ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35


Consensus pattern (20 bp):   
ATTTAAAATAAAAATAGAAA

Found at i:9519 original size:23 final size:23

Alignment explanation


    Indices: 9467--9519  Score: 54
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       9457 TTAAGGGTCG

                     *           **
       9467 AAATT-AAATTATAATTTTTACG
          1 AAATTAAAAATATAATTTTTAAA

             * *                   
       9489 ATAGTAAAAATATAATTTTTAAA
          1 AAATTAAAAATATAATTTTTAAA

                    
       9512 AAATTAAA
          1 AAATTAAA

       9520 CCAAAATTTT


Statistics
Matches: 23,  Mismatches: 7, Indels: 1
        0.74            0.23        0.03

Matches are distributed among these distances:
  22    3  0.13
  23   20  0.87

ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40


Consensus pattern (23 bp):   
AAATTAAAAATATAATTTTTAAA

Found at i:14056 original size:23 final size:23

Alignment explanation


    Indices: 14026--14115  Score: 69
    Period size: 23  Copynumber: 3.9  Consensus size: 23

      14016 TGTGCTCAGT

                                   
      14026 ACTTTGTGTACTCTCTGTTTAGC
          1 ACTTTGTGTACTCTCTGTTTAGC

                     *    *       * * 
      14049 ACTTTGTGTGCTCTTTGTTGCCCAAC
          1 ACTTTGTGTACTCTCTGTT---TAGC

                                   *
      14075 ACTTATGTG--CTCTCTGTTTAGT
          1 ACTT-TGTGTACTCTCTGTTTAGC

                        *       
      14097 ACTTTG-GTACTTTCTGTTT
          1 ACTTTGTGTACTCTCTGTTT

      14116 GTTCCGTTTA


Statistics
Matches: 52,  Mismatches: 9, Indels: 13
        0.70            0.12        0.18

Matches are distributed among these distances:
  20    1  0.02
  21    2  0.04
  22   14  0.27
  23   17  0.33
  25    8  0.15
  26    6  0.12
  27    4  0.08

ACGTcount: A:0.12, C:0.21, G:0.18, T:0.49


Consensus pattern (23 bp):   
ACTTTGTGTACTCTCTGTTTAGC

Found at i:16085 original size:3 final size:3

Alignment explanation


    Indices: 16077--16106  Score: 60
    Period size: 3  Copynumber: 10.0  Consensus size: 3

      16067 CGATGGTAAC

                                                   
      16077 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
          1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT

      16107 ATGCTTTGGG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33


Consensus pattern (3 bp):   
GAT

Found at i:19123 original size:3 final size:3

Alignment explanation


    Indices: 19115--19144  Score: 60
    Period size: 3  Copynumber: 10.0  Consensus size: 3

      19105 GTTAGTTCAC

                                                   
      19115 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

      19145 GCAGTAACAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
ATT

Done.