Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007219.1 Kokia drynarioides strain JFW-HI SEQ_121834, 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: 12185
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34


Found at i:2737 original size:20 final size:19

Alignment explanation


    Indices: 2710--2749  Score: 55
    Period size: 20  Copynumber: 2.1  Consensus size: 19

       2700 CAACGAGTTC

                                
       2710 ACAAAAAA-CACAAGAAAAA
          1 ACAAAAAACCA-AAGAAAAA

                                
       2729 ACAAGAAAACCAAAGAAAAA
          1 ACAA-AAAACCAAAGAAAAA

             
       2749 A
          1 A

       2750 TCGTGTCAAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  19    4  0.21
  20   13  0.68
  21    2  0.11

ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00


Consensus pattern (19 bp):   
ACAAAAAACCAAAGAAAAA

Found at i:6810 original size:87 final size:89

Alignment explanation


    Indices: 6672--6845  Score: 289
    Period size: 87  Copynumber: 2.0  Consensus size: 89

       6662 TAATGAGTTA

                                *     *              *          *            
       6672 TCTTATTAAGTGGGAGGTTTCAAATGTAGAAAAAGATTTGCGGCAGTGCATCTTTTTCTGTTATT
          1 TCTTATTAAGTGGGAGGTTTAAAATGCAGAAAAAGATTTGCAGCAGTGCATCATTTTCTGTTATT

                                    
       6737 CGATCAAC-AAAGAGAATGAGAAC
         66 CGATCAACAAAAGAGAATGAGAAC

                                                                             
       6760 TCTTATTAAGTGGGAGG-TTAAAATGCAGAAAAAGATTTGCAGCAGTGCATCATTTTCTGTTATT
          1 TCTTATTAAGTGGGAGGTTTAAAATGCAGAAAAAGATTTGCAGCAGTGCATCATTTTCTGTTATT

                 *                
       6824 CGATCGACAAAAGAGAATGAGA
         66 CGATCAACAAAAGAGAATGAGA

       6846 CGATGCAGGG


Statistics
Matches: 80,  Mismatches: 5, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
  87   50  0.62
  88   30  0.38

ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30


Consensus pattern (89 bp):   
TCTTATTAAGTGGGAGGTTTAAAATGCAGAAAAAGATTTGCAGCAGTGCATCATTTTCTGTTATT
CGATCAACAAAAGAGAATGAGAAC

Found at i:7732 original size:3 final size:3

Alignment explanation


    Indices: 7724--7781  Score: 66
    Period size: 3  Copynumber: 20.0  Consensus size: 3

       7714 CTGGCTTGTG

                                 *                   *      *              
       7724 GAA GAA GAA GAA GAA GTA GAA G-A GAA GAA GGA GAA AAA GAA GAA GAA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA

            *              
       7771 AAA G-A GAA GAA
          1 GAA GAA GAA GAA

       7782 ATGGAGATAC


Statistics
Matches: 45,  Mismatches: 8, Indels: 4
        0.79            0.14        0.07

Matches are distributed among these distances:
   2    4  0.09
   3   41  0.91

ACGTcount: A:0.66, C:0.00, G:0.33, T:0.02


Consensus pattern (3 bp):   
GAA

Found at i:7764 original size:20 final size:20

Alignment explanation


    Indices: 7726--7766  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       7716 GGCTTGTGGA

                         **     
       7726 AGAAGAAGAAGAAGTAGAAG
          1 AGAAGAAGAAGAAAAAGAAG

                    *           
       7746 AGAAGAAGGAGAAAAAGAAG
          1 AGAAGAAGAAGAAAAAGAAG

             
       7766 A
          1 A

       7767 AGAAAAAGAG


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

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.63, C:0.00, G:0.34, T:0.02


Consensus pattern (20 bp):   
AGAAGAAGAAGAAAAAGAAG

Found at i:7768 original size:29 final size:29

Alignment explanation


    Indices: 7726--7781  Score: 85
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       7716 GGCTTGTGGA

                *         * *            
       7726 AGAAGAAGAAGAAGTAGAAGAGAAGAAGG
          1 AGAAAAAGAAGAAGAAAAAGAGAAGAAGG

                                       
       7755 AGAAAAAGAAGAAGAAAAAGAGAAGAA
          1 AGAAAAAGAAGAAGAAAAAGAGAAGAA

       7782 ATGGAGATAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  29   24  1.00

ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02


Consensus pattern (29 bp):   
AGAAAAAGAAGAAGAAAAAGAGAAGAAGG
Done.