Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013001.1 Kokia drynarioides strain JFW-HI SEQ_128019, 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: 15936
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32


Found at i:5825 original size:15 final size:14

Alignment explanation


    Indices: 5800--5834  Score: 52
    Period size: 15  Copynumber: 2.4  Consensus size: 14

       5790 TTTACATTTT

                  *       
       5800 ATTTTATTTGTTTC
          1 ATTTTACTTGTTTC

                           
       5814 ACTTTTACTTGTTTC
          1 A-TTTTACTTGTTTC

                  
       5829 ATTTTA
          1 ATTTTA

       5835 AAATTCTATG


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  14    6  0.32
  15   13  0.68

ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66


Consensus pattern (14 bp):   
ATTTTACTTGTTTC

Found at i:7312 original size:16 final size:16

Alignment explanation


    Indices: 7291--7324  Score: 68
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       7281 TATACAAAAT

                            
       7291 CACTTGACTTTTGAAC
          1 CACTTGACTTTTGAAC

                            
       7307 CACTTGACTTTTGAAC
          1 CACTTGACTTTTGAAC

              
       7323 CA
          1 CA

       7325 AATCACTTAT


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

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.26, C:0.26, G:0.12, T:0.35


Consensus pattern (16 bp):   
CACTTGACTTTTGAAC

Found at i:7331 original size:21 final size:20

Alignment explanation


    Indices: 7287--7332  Score: 55
    Period size: 16  Copynumber: 2.5  Consensus size: 20

       7277 TGCGTATACA

                                
       7287 AAATCACTTGACTTTTGAAC
          1 AAATCACTTGACTTTTGAAC

                                 
       7307 ----CACTTGACTTTTGAACC
          1 AAATCACTTGACTTTTGAA-C

                     
       7324 AAATCACTT
          1 AAATCACTT

       7333 ATTCTAACTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 9
        0.70            0.00        0.30

Matches are distributed among these distances:
  16   15  0.71
  17    1  0.05
  21    5  0.24

ACGTcount: A:0.33, C:0.24, G:0.09, T:0.35


Consensus pattern (20 bp):   
AAATCACTTGACTTTTGAAC

Found at i:7705 original size:18 final size:18

Alignment explanation


    Indices: 7682--7726  Score: 58
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       7672 TCACTTGAAA

                               
       7682 AAAGAAAATGAGAAA-AAG
          1 AAAGAAAATGA-AAAGAAG

                    *         
       7700 AAAGAAAAAGAAAAGAAG
          1 AAAGAAAATGAAAAGAAG

                      
       7718 AAA-AAAATG
          1 AAAGAAAATG

       7727 TTTGTTATAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  17    8  0.33
  18   16  0.67

ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04


Consensus pattern (18 bp):   
AAAGAAAATGAAAAGAAG

Found at i:13879 original size:21 final size:21

Alignment explanation


    Indices: 13827--13880  Score: 58
    Period size: 21  Copynumber: 2.6  Consensus size: 21

      13817 TGGATTTTTA

                  *              
      13827 GTATCGGTAGAAGCATGCATT
          1 GTATCGATAGAAGCATGCATT

              *                    
      13848 GTTTC-AGTAGAAGTCAT-CATT
          1 GTATCGA-TAGAAG-CATGCATT

                        
      13869 GTATCGATAGAA
          1 GTATCGATAGAA

      13881 CCATCACCAC


Statistics
Matches: 27,  Mismatches: 3, Indels: 6
        0.75            0.08        0.17

Matches are distributed among these distances:
  21   23  0.85
  22    4  0.15

ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31


Consensus pattern (21 bp):   
GTATCGATAGAAGCATGCATT
Done.