Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012301.1 Kokia drynarioides strain JFW-HI SEQ_127302, 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: 25234
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32


Found at i:111 original size:41 final size:40

Alignment explanation


    Indices: 63--162  Score: 98
    Period size: 38  Copynumber: 2.5  Consensus size: 40

         53 TCGACCTTGA

                                   * *              
         63 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
          1 GTCGATGAGACACTGGGTGTCATCACTTTACTTCGGATAG

             *        **       *                 *   
        103 ATTCGATGAGGTACT-GG-AT-ATCACTTTACTTCGGCTAG
          1 -GTCGATGAGACACTGGGTGTCATCACTTTACTTCGGATAG

             *                    
        141 GCCGATGAGACACTGGGTGTCA
          1 GTCGATGAGACACTGGGTGTCA

        163 CTTTATTGCT


Statistics
Matches: 44,  Mismatches: 12, Indels: 7
        0.70            0.19        0.11

Matches are distributed among these distances:
  37   10  0.23
  38   18  0.41
  39    2  0.05
  40    3  0.07
  41   11  0.25

ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31


Consensus pattern (40 bp):   
GTCGATGAGACACTGGGTGTCATCACTTTACTTCGGATAG

Found at i:4694 original size:70 final size:70

Alignment explanation


    Indices: 4546--4683  Score: 249
    Period size: 70  Copynumber: 2.0  Consensus size: 70

       4536 ATCCACATAA

                                                               *             
       4546 TGTGGTTAATTTGGCTTGGTGGATGATAATGGTAGAAATGTCTAGAACAAGTCTTAGGTGGCTTG
          1 TGTGGTTAATTTGGCTTGGTGGATGATAATGGTAGAAATGTCTAGAACAAGCCTTAGGTGGCTTG

                 
       4611 TTAAT
         66 TTAAT

                          *                      *                           
       4616 TGTGGTTAATTTGGTTTGGTGGATGATAATGGTAGAATTGTCTAGAACAAGCCTTAGGTGGCTTG
          1 TGTGGTTAATTTGGCTTGGTGGATGATAATGGTAGAAATGTCTAGAACAAGCCTTAGGTGGCTTG

               
       4681 TTA
         66 TTA

       4684 TTATTGGTTA


Statistics
Matches: 65,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  70   65  1.00

ACGTcount: A:0.25, C:0.07, G:0.30, T:0.38


Consensus pattern (70 bp):   
TGTGGTTAATTTGGCTTGGTGGATGATAATGGTAGAAATGTCTAGAACAAGCCTTAGGTGGCTTG
TTAAT

Found at i:20051 original size:27 final size:28

Alignment explanation


    Indices: 20008--20072  Score: 73
    Period size: 27  Copynumber: 2.4  Consensus size: 28

      19998 CATTTATAAA

                    *           *        
      20008 AATTTAA-ATTAATAAT-ATTAAAATTAT
          1 AATTTAATTTTAATAATAATAAAAATT-T

             *                          
      20035 ATTTTAATTTTAA-AATAATAAAAATTT
          1 AATTTAATTTTAATAATAATAAAAATTT

                       
      20062 AATTTAATTTT
          1 AATTTAATTTT

      20073 TTAAAATTTA


Statistics
Matches: 32,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  27   20  0.62
  28   12  0.38

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (28 bp):   
AATTTAATTTTAATAATAATAAAAATTT

Found at i:20073 original size:28 final size:30

Alignment explanation


    Indices: 20018--20079  Score: 76
    Period size: 29  Copynumber: 2.1  Consensus size: 30

      20008 AATTTAAATT

                              *            
      20018 AATAATATTAAAATTATATTTTAA-TTTTAA
          1 AATAATA-TAAAATTATAATTTAATTTTTAA

                                           
      20048 AATAATA-AAAATT-TAATTTAATTTTTTAA
          1 AATAATATAAAATTATAATTTAA-TTTTTAA

               
      20077 AAT
          1 AAT

      20080 TTATATTAAT


Statistics
Matches: 29,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  27    7  0.24
  28    6  0.21
  29    9  0.31
  30    7  0.24

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (30 bp):   
AATAATATAAAATTATAATTTAATTTTTAA

Found at i:24752 original size:18 final size:19

Alignment explanation


    Indices: 24721--24757  Score: 51
    Period size: 18  Copynumber: 2.0  Consensus size: 19

      24711 TGTTACTAAT

                                
      24721 TTTTATTTTAACTTTATAAA
          1 TTTTATTTTAACTTT-TAAA

                               
      24741 TTTT-TTTT-ACTTTTAAA
          1 TTTTATTTTAACTTTTAAA

      24758 AAATATATAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  17    4  0.24
  18    5  0.29
  19    4  0.24
  20    4  0.24

ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65


Consensus pattern (19 bp):   
TTTTATTTTAACTTTTAAA
Done.