Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002727.1 Kokia drynarioides strain JFW-HI SEQ_115030, 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: 3161
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37


Found at i:518 original size:22 final size:22

Alignment explanation


    Indices: 493--535  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        483 TCTCCTCTCG

                                  
        493 CTCAGATAAACTTAATTCTTCT
          1 CTCAGATAAACTTAATTCTTCT

                **        *      
        515 CTCATTTAAACTTATTTCTTC
          1 CTCAGATAAACTTAATTCTTC

        536 ATTTCTCCCA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.28, C:0.23, G:0.02, T:0.47


Consensus pattern (22 bp):   
CTCAGATAAACTTAATTCTTCT

Found at i:1857 original size:237 final size:237

Alignment explanation


    Indices: 1442--1916  Score: 914
    Period size: 237  Copynumber: 2.0  Consensus size: 237

       1432 CATCATTACT

                                                                             
       1442 TTTTCGCTGACATGGCAGTGCTAACAAAATTTTTCTTCCAATTTTTCTTTTCTTCTTATTCTTTT
          1 TTTTCGCTGACATGGCAGTGCTAACAAAATTTTTCTTCCAATTTTTCTTTTCTTCTTATTCTTTT

                                     *                                       
       1507 TCTTACCTAAATTTTTTCGATTCCAGAAAACCCAGATTTTGTTCGACAGAGAGTTATAACCAGTA
         66 TCTTACCTAAATTTTTTCGATTCCAAAAAACCCAGATTTTGTTCGACAGAGAGTTATAACCAGTA

                                                                             
       1572 AGGAGGTTATGGTCGTAGTCGATGGTGGTTTCATGGTGGATGAATTTTCTACTAAAAATTAGGGA
        131 AGGAGGTTATGGTCGTAGTCGATGGTGGTTTCATGGTGGATGAATTTTCTACTAAAAATTAGGGA

                                                      
       1637 AAGTGACAAAAAGAACATGGAGCAGAAAATGAATCTGTAAAA
        196 AAGTGACAAAAAGAACATGGAGCAGAAAATGAATCTGTAAAA

                                                                             
       1679 TTTTCGCTGACATGGCAGTGCTAACAAAATTTTTCTTCCAATTTTTCTTTTCTTCTTATTCTTTT
          1 TTTTCGCTGACATGGCAGTGCTAACAAAATTTTTCTTCCAATTTTTCTTTTCTTCTTATTCTTTT

                                                          *           *      
       1744 TCTTACCTAAATTTTTTCGATTCCAAAAAACCCAGATTTTGTTCGATAGAGAGTTATAGCCAGTA
         66 TCTTACCTAAATTTTTTCGATTCCAAAAAACCCAGATTTTGTTCGACAGAGAGTTATAACCAGTA

                                                                             
       1809 AGGAGGTTATGGTCGTAGTCGATGGTGGTTTCATGGTGGATGAATTTTCTACTAAAAATTAGGGA
        131 AGGAGGTTATGGTCGTAGTCGATGGTGGTTTCATGGTGGATGAATTTTCTACTAAAAATTAGGGA

                                  *                   
       1874 AAGTGACAAAAAGAACATGGAGTAGAAAATGAATCTGTAAAA
        196 AAGTGACAAAAAGAACATGGAGCAGAAAATGAATCTGTAAAA

             
       1916 T
          1 T

       1917 GGCAATGCTT


Statistics
Matches: 234,  Mismatches: 4, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 237  234  1.00

ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36


Consensus pattern (237 bp):   
TTTTCGCTGACATGGCAGTGCTAACAAAATTTTTCTTCCAATTTTTCTTTTCTTCTTATTCTTTT
TCTTACCTAAATTTTTTCGATTCCAAAAAACCCAGATTTTGTTCGACAGAGAGTTATAACCAGTA
AGGAGGTTATGGTCGTAGTCGATGGTGGTTTCATGGTGGATGAATTTTCTACTAAAAATTAGGGA
AAGTGACAAAAAGAACATGGAGCAGAAAATGAATCTGTAAAA

Found at i:2744 original size:21 final size:21

Alignment explanation


    Indices: 2718--2779  Score: 54
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       2708 TGCGGAGGCG

                                 
       2718 ATAAGGCAAGAAAAAGAAAAA
          1 ATAAGGCAAGAAAAAGAAAAA

                  *                * 
       2739 ATAAGGTAAGGAGAAGAAGGAAAGA
          1 ATAAGGCAA-GA-AA-AA-GAAAAA

                *            
       2764 A-AACGCAAGAAAAAGA
          1 ATAAGGCAAGAAAAAGA

       2780 GGCTACAAAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 9
        0.72            0.09        0.20

Matches are distributed among these distances:
  20    2  0.06
  21   10  0.30
  22    4  0.12
  23    4  0.12
  24    7  0.21
  25    6  0.18

ACGTcount: A:0.65, C:0.05, G:0.26, T:0.05


Consensus pattern (21 bp):   
ATAAGGCAAGAAAAAGAAAAA
Done.