Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006126.1 Kokia drynarioides strain JFW-HI SEQ_120646, 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: 5427
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:529 original size:80 final size:78

Alignment explanation


    Indices: 412--570  Score: 228
    Period size: 80  Copynumber: 2.0  Consensus size: 78

        402 CAACCAATAA

                       *          *                *    *       * *          
        412 ACACATTAAGGTTACATAAGTCTTCATTAAGGAGAAATGTCATGTCTTTTCATCTACATCAGATC
          1 ACACATTAAGGATACATAAGTCATCATTAAGGAGAAATGCCATGCCTTTTCAACCACATCAGATC

                         
        477 CTAATGAAGAGAC
         66 CTAATGAAGAGAC

                                                                             
        490 ACACATTAAGGATACAATAAGTCATCATTTAAGGAGAAATGCCATGCCTTTTCAACCACATCAGA
          1 ACACATTAAGGATAC-ATAAGTCATCA-TTAAGGAGAAATGCCATGCCTTTTCAACCACATCAGA

                *     *    
        555 TCCTTATGAATAGAC
         64 TCCTAATGAAGAGAC

             
        570 A
          1 A

        571 TGACTCATTG


Statistics
Matches: 71,  Mismatches: 8, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  78   14  0.20
  79   10  0.14
  80   47  0.66

ACGTcount: A:0.38, C:0.19, G:0.14, T:0.28


Consensus pattern (78 bp):   
ACACATTAAGGATACATAAGTCATCATTAAGGAGAAATGCCATGCCTTTTCAACCACATCAGATC
CTAATGAAGAGAC

Found at i:613 original size:80 final size:80

Alignment explanation


    Indices: 529--681  Score: 225
    Period size: 80  Copynumber: 1.9  Consensus size: 80

        519 TAAGGAGAAA

                                          *     *          *    *        *   
        529 TGCCATGCCTTTTCAACCACATCAGATCCTTATGAATAGACATGACTCATTGGCTTCCCTATAAG
          1 TGCCATGCCTTTTCAACCACATCAGATCCTAATGAAGAGACATGACTAATTGACTTCCCTACAAG

                           
        594 AGTTAAAAACAAAAT
         66 AGTTAAAAACAAAAT

                            **    *                                   *      
        609 TGCCATGCCTTTTCAATTACATTAGATCCTAATGAAGAGACATGACTAATTGACTTCCTTACAAG
          1 TGCCATGCCTTTTCAACCACATCAGATCCTAATGAAGAGACATGACTAATTGACTTCCCTACAAG

                    
        674 AGTTAAAA
         66 AGTTAAAA

        682 TGAAATTAAT


Statistics
Matches: 64,  Mismatches: 9, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  80   64  1.00

ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30


Consensus pattern (80 bp):   
TGCCATGCCTTTTCAACCACATCAGATCCTAATGAAGAGACATGACTAATTGACTTCCCTACAAG
AGTTAAAAACAAAAT

Found at i:1897 original size:18 final size:21

Alignment explanation


    Indices: 1857--1910  Score: 72
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       1847 TGGGAAGGTT

                                 
       1857 CTACCGATACAAGTATGACTA
          1 CTACCGATACAAGTATGACTA

                        *   *   *
       1878 CTACCGATACAATTATTACTT
          1 CTACCGATACAAGTATGACTA

                *       
       1899 CTACTGATACAA
          1 CTACCGATACAA

       1911 CAAACTCCAG


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   29  1.00

ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30


Consensus pattern (21 bp):   
CTACCGATACAAGTATGACTA
Done.