Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002239.1 Kokia drynarioides strain JFW-HI SEQ_114241, 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: 22106
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30


Found at i:7230 original size:38 final size:37

Alignment explanation


    Indices: 7187--7260  Score: 105
    Period size: 38  Copynumber: 2.0  Consensus size: 37

       7177 TGCACCCAAG

                  *                                
       7187 ACTATCGCTGCATAAA-TATTCTTCAAATTGCATCCAGA
          1 ACTATCACTGCA-AAAGTATTCTTC-AATTGCATCCAGA

                   *                            
       7225 ACTATCATTGCAAAAGTATTCTTCAATTGCATCCAG
          1 ACTATCACTGCAAAAGTATTCTTCAATTGCATCCAG

       7261 GAATGTCATT


Statistics
Matches: 33,  Mismatches: 2, Indels: 3
        0.87            0.05        0.08

Matches are distributed among these distances:
  37   15  0.45
  38   18  0.55

ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32


Consensus pattern (37 bp):   
ACTATCACTGCAAAAGTATTCTTCAATTGCATCCAGA

Found at i:7270 original size:37 final size:38

Alignment explanation


    Indices: 7195--7274  Score: 112
    Period size: 37  Copynumber: 2.1  Consensus size: 38

       7185 AGACTATCGC

                                                  
       7195 TGCATAAATATTCTTCAAATTGCATCCAGAACTATCAT
          1 TGCATAAATATTCTTCAAATTGCATCCAGAACTATCAT

                                               *    
       7233 TGCA-AAAGTATTCTTC-AATTGCATCCAGGAA-TGTCAT
          1 TGCATAAA-TATTCTTCAAATTGCATCCA-GAACTATCAT

                 
       7270 TGCAT
          1 TGCAT

       7275 GAACATGTCC


Statistics
Matches: 38,  Mismatches: 1, Indels: 6
        0.84            0.02        0.13

Matches are distributed among these distances:
  37   23  0.61
  38   15  0.39

ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34


Consensus pattern (38 bp):   
TGCATAAATATTCTTCAAATTGCATCCAGAACTATCAT

Found at i:8012 original size:16 final size:16

Alignment explanation


    Indices: 7991--8021  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       7981 TTGTGGATCC

                            
       7991 CATTTTACCTTTATTA
          1 CATTTTACCTTTATTA

                   *       
       8007 CATTTTATCTTTATT
          1 CATTTTACCTTTATT

       8022 TTCACATTAT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61


Consensus pattern (16 bp):   
CATTTTACCTTTATTA

Found at i:10287 original size:17 final size:17

Alignment explanation


    Indices: 10265--10304  Score: 71
    Period size: 17  Copynumber: 2.4  Consensus size: 17

      10255 TTGCAGTATA

                  *          
      10265 ATTGTCCCTACATTTTT
          1 ATTGTCACTACATTTTT

                             
      10282 ATTGTCACTACATTTTT
          1 ATTGTCACTACATTTTT

                  
      10299 ATTGTC
          1 ATTGTC

      10305 GCTGCATCTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  17   22  1.00

ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53


Consensus pattern (17 bp):   
ATTGTCACTACATTTTT

Found at i:11404 original size:37 final size:37

Alignment explanation


    Indices: 11363--11434  Score: 117
    Period size: 37  Copynumber: 1.9  Consensus size: 37

      11353 TAATGTCACT

                  *      * *                     
      11363 GCATGAGCACTTCTATATTGCACCCAAAACTGTCGTC
          1 GCATGAACACTTCCAGATTGCACCCAAAACTGTCGTC

                                               
      11400 GCATGAACACTTCCAGATTGCACCCAAAACTGTCG
          1 GCATGAACACTTCCAGATTGCACCCAAAACTGTCG

      11435 CCACAGGAAT


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  37   32  1.00

ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24


Consensus pattern (37 bp):   
GCATGAACACTTCCAGATTGCACCCAAAACTGTCGTC

Found at i:11551 original size:37 final size:38

Alignment explanation


    Indices: 11465--11552  Score: 117
    Period size: 38  Copynumber: 2.3  Consensus size: 38

      11455 TACAGCCAAG

                                            *     
      11465 ACTGTCGCTGCATAAATATTCTTCAAATTGCATCCAGA
          1 ACTGTCGCTGCATAAATATTCTTCAAATTGCACCCAGA

               *  *        *                       
      11503 ACTATCACTGCATAAGTATTCTTC-AATTGCACCCAGGA
          1 ACTGTCGCTGCATAAATATTCTTCAAATTGCACCCA-GA

                         
      11541 A-TGTCGCTGCAT
          1 ACTGTCGCTGCAT

      11553 GAACATGTCT


Statistics
Matches: 43,  Mismatches: 6, Indels: 3
        0.83            0.12        0.06

Matches are distributed among these distances:
  37   19  0.44
  38   24  0.56

ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31


Consensus pattern (38 bp):   
ACTGTCGCTGCATAAATATTCTTCAAATTGCACCCAGA

Found at i:11594 original size:26 final size:26

Alignment explanation


    Indices: 11542--11595  Score: 72
    Period size: 26  Copynumber: 2.1  Consensus size: 26

      11532 CACCCAGGAA

                                * *   
      11542 TGTCGCTGCATGAACATGTCTAGAAT
          1 TGTCGCTGCATGAACATGTCCAAAAT

                        *  *          
      11568 TGTCGCTGCATGTACGTGTCCAAAAT
          1 TGTCGCTGCATGAACATGTCCAAAAT

              
      11594 TG
          1 TG

      11596 AGCCTAAAAT


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31


Consensus pattern (26 bp):   
TGTCGCTGCATGAACATGTCCAAAAT
Done.