Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014918.1 Kokia drynarioides strain JFW-HI SEQ_129961, 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: 24425
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:8968 original size:14 final size:14

Alignment explanation


    Indices: 8936--8975  Score: 57
    Period size: 14  Copynumber: 3.0  Consensus size: 14

       8926 AACCCTAAAC

                      *   
       8936 AGAAA-GGAAAGGG
          1 AGAAAGGGAAGGGG

                          
       8949 -GAAAGGGAAGGGG
          1 AGAAAGGGAAGGGG

                          
       8962 AGAAAGGGAAGGGG
          1 AGAAAGGGAAGGGG

       8976 GAAGGTAACA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  12    4  0.17
  13    7  0.29
  14   13  0.54

ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00


Consensus pattern (14 bp):   
AGAAAGGGAAGGGG

Found at i:9075 original size:17 final size:17

Alignment explanation


    Indices: 9018--9077  Score: 57
    Period size: 17  Copynumber: 3.3  Consensus size: 17

       9008 ATGATGATGA

                             
       9018 TTTAATAATTTTATATT
          1 TTTAATAATTTTATATT

              *                * 
       9035 TTAAATTAATTTTAAAATAGT
          1 TTTAA-TAATTTT---ATATT

                 *           
       9056 TTTAACAATTTTATATT
          1 TTTAATAATTTTATATT

                 
       9073 TTTAA
          1 TTTAA

       9078 AAATAATTTT


Statistics
Matches: 34,  Mismatches: 5, Indels: 8
        0.72            0.11        0.17

Matches are distributed among these distances:
  17   13  0.38
  18    7  0.21
  20    6  0.18
  21    8  0.24

ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57


Consensus pattern (17 bp):   
TTTAATAATTTTATATT

Found at i:19223 original size:5 final size:5

Alignment explanation


    Indices: 19213--19241  Score: 58
    Period size: 5  Copynumber: 5.8  Consensus size: 5

      19203 AAATAAATAA

                                              
      19213 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
          1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA

      19242 CCTCAATCTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   24  1.00

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (5 bp):   
AAAAG

Found at i:21184 original size:23 final size:21

Alignment explanation


    Indices: 21140--21185  Score: 65
    Period size: 23  Copynumber: 2.1  Consensus size: 21

      21130 GGTCCACCCA

                                 
      21140 TATTTTAGTTTATTAAATATT
          1 TATTTTAGTTTATTAAATATT

                            *      
      21161 TATTTTATGTTTAATTTAATATT
          1 TATTTTA-GTTT-ATTAAATATT

              
      21184 TA
          1 TA

      21186 ATACTCAGGG


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    7  0.32
  22    4  0.18
  23   11  0.50

ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63


Consensus pattern (21 bp):   
TATTTTAGTTTATTAAATATT

Found at i:21757 original size:15 final size:15

Alignment explanation


    Indices: 21707--21758  Score: 50
    Period size: 15  Copynumber: 3.2  Consensus size: 15

      21697 ACTAAAAACC

                        *  
      21707 ATTTATTATTAATAT
          1 ATTTATTATTAAAAT

                  *            
      21722 ATTTATAATTGTAACAAAT
          1 ATTTATTA-T-T-A-AAAT

                           
      21741 ATTTATTATTAAAAT
          1 ATTTATTATTAAAAT

               
      21756 ATT
          1 ATT

      21759 AATATTTATT


Statistics
Matches: 30,  Mismatches: 3, Indels: 8
        0.73            0.07        0.20

Matches are distributed among these distances:
  15   14  0.47
  16    2  0.07
  17    2  0.07
  18    2  0.07
  19   10  0.33

ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52


Consensus pattern (15 bp):   
ATTTATTATTAAAAT

Found at i:21877 original size:16 final size:16

Alignment explanation


    Indices: 21835--21886  Score: 51
    Period size: 16  Copynumber: 3.6  Consensus size: 16

      21825 TTAAATATTT

                            
      21835 TATTAA-AA-TAA-TA
          1 TATTAATAATTAATTA

                            
      21848 TATT-AT-ATTAATTA
          1 TATTAATAATTAATTA

                       *    
      21862 TATTAATAATTTATTA
          1 TATTAATAATTAATTA

               *     
      21878 TATGAATAA
          1 TATTAATAA

      21887 ATATAAATAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 7
        0.78            0.05        0.17

Matches are distributed among these distances:
  12    2  0.06
  13    7  0.22
  14    6  0.19
  15    2  0.06
  16   15  0.47

ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48


Consensus pattern (16 bp):   
TATTAATAATTAATTA
Done.