Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004930.1 Kokia drynarioides strain JFW-HI SEQ_118633, 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: 4366
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34


Found at i:356 original size:18 final size:19

Alignment explanation


    Indices: 322--357  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

        312 ATTTACTAAA

                               
        322 TTGACCTTAATTAAAACCT
          1 TTGACCTTAATTAAAACCT

                    *         
        341 TTGACCTTCA-TAAAACC
          1 TTGACCTTAATTAAAACC

        358 AAAGCCCTTA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33


Consensus pattern (19 bp):   
TTGACCTTAATTAAAACCT

Found at i:1009 original size:37 final size:37

Alignment explanation


    Indices: 963--1067  Score: 129
    Period size: 37  Copynumber: 2.8  Consensus size: 37

        953 TCTGTATAGT

                *           *                **  
        963 AATATCAAACAATTTCACATATCAATCAATTTAGTAC
          1 AATAACAAACAATTTCGCATATCAATCAATTTAACAC

               *       *                        *
       1000 AATGACAAACATTTTCGCATATCAATCAATTTAACAT
          1 AATAACAAACAATTTCGCATATCAATCAATTTAACAC

                           *   *           
       1037 AATAACAAACAATTTTGCACATCAATCAATT
          1 AATAACAAACAATTTCGCATATCAATCAATT

       1068 CAATACGGTA


Statistics
Matches: 57,  Mismatches: 11, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  37   57  1.00

ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31


Consensus pattern (37 bp):   
AATAACAAACAATTTCGCATATCAATCAATTTAACAC

Found at i:2721 original size:32 final size:33

Alignment explanation


    Indices: 2665--2735  Score: 92
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       2655 ATAAGAAAAA

                                             
       2665 TAAATTCTATTAGGATTTGGAAA-GGAGTAATT
          1 TAAATTCTATTAGGATTTGGAAAGGGAGTAATT

             *                  *       *     
       2697 TGAATTCTAGTTAGGATTT-TAAAGGGATTAATT
          1 TAAATTCTA-TTAGGATTTGGAAAGGGAGTAATT

                  
       2730 TAAATT
          1 TAAATT

       2736 TCAAATTAAG


Statistics
Matches: 33,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  32   11  0.33
  33   22  0.67

ACGTcount: A:0.37, C:0.03, G:0.20, T:0.41


Consensus pattern (33 bp):   
TAAATTCTATTAGGATTTGGAAAGGGAGTAATT

Done.