Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006765.1 Kokia drynarioides strain JFW-HI SEQ_121363, 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: 2777
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37


Found at i:132 original size:59 final size:60

Alignment explanation


    Indices: 53--169  Score: 139
    Period size: 59  Copynumber: 2.0  Consensus size: 60

         43 TAAAAATGTG

                   *   *   *       *              *   *                  
         53 ATTTTTAGAAAGTTTGGGGGTCACAATCA-AAGTTTTGGAAAGTTCGAG-GTCAAAATATA
          1 ATTTTTAAAAAATTTAGGGGTCAAAAT-ATAAGTTTTGAAAAATTCGAGTGTCAAAATATA

                                           *                    *     
        112 ATTTTTAAAAAATTTAGGGGTCAAAATATAATTTTTGAAAAATTCGAGTGTCGAAATA
          1 ATTTTTAAAAAATTTAGGGGTCAAAATATAAGTTTTGAAAAATTCGAGTGTCAAAATA

        170 GAAGTTCTGG


Statistics
Matches: 48,  Mismatches: 8, Indels: 3
        0.81            0.14        0.05

Matches are distributed among these distances:
  58    1  0.02
  59   39  0.81
  60    8  0.17

ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34


Consensus pattern (60 bp):   
ATTTTTAAAAAATTTAGGGGTCAAAATATAAGTTTTGAAAAATTCGAGTGTCAAAATATA

Found at i:169 original size:30 final size:29

Alignment explanation


    Indices: 85--169  Score: 98
    Period size: 30  Copynumber: 2.9  Consensus size: 29

         75 ACAATCAAAG

                 *   *                   
         85 TTTTGGAAAGTTCGAGGTCAAAATATAAT
          1 TTTTGAAAAATTCGAGGTCAAAATATAAT

                *        * *              
        114 TTTTAAAAAATTTAGGGGTCAAAATATAAT
          1 TTTTGAAAAA-TTCGAGGTCAAAATATAAT

                                *     
        144 TTTTGAAAAATTCGAGTGTCGAAATA
          1 TTTTGAAAAATTCGAG-GTCAAAATA

        170 GAAGTTCTGG


Statistics
Matches: 45,  Mismatches: 9, Indels: 3
        0.79            0.16        0.05

Matches are distributed among these distances:
  29   11  0.24
  30   34  0.76

ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35


Consensus pattern (29 bp):   
TTTTGAAAAATTCGAGGTCAAAATATAAT

Found at i:2581 original size:70 final size:71

Alignment explanation


    Indices: 2463--2606  Score: 227
    Period size: 70  Copynumber: 2.0  Consensus size: 71

       2453 ATCTTACATA

                                          *      *    *                      
       2463 AATACTTGTCAAACACATAAACCAATTTAAGTAACGTTATTAGTCCAAGATGAAAGTGGCAACTA
          1 AATACTTGTCAAACACATAAACCAATTTAACTAACGTCATTAATCCAAGATGAAAGTGGCAACTA

              *   
       2528 ATGTTG
         66 ATATTG

                              *         *                                    
       2534 AATA-TTGTCAAACACATGAACCAATTTGACTAACGTCATTAATCCAAGATGAAAGTGGCAACTA
          1 AATACTTGTCAAACACATAAACCAATTTAACTAACGTCATTAATCCAAGATGAAAGTGGCAACTA

                  
       2598 ATATTG
         66 ATATTG

               
       2604 AAT
          1 AAT

       2607 GAGAAGCCCA


Statistics
Matches: 67,  Mismatches: 6, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  70   63  0.94
  71    4  0.06

ACGTcount: A:0.42, C:0.16, G:0.15, T:0.28


Consensus pattern (71 bp):   
AATACTTGTCAAACACATAAACCAATTTAACTAACGTCATTAATCCAAGATGAAAGTGGCAACTA
ATATTG
Done.