Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001619.1 Kokia drynarioides strain JFW-HI SEQ_113253, 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: 8325
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35


Found at i:1567 original size:15 final size:15

Alignment explanation


    Indices: 1547--1590  Score: 52
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       1537 TAACTATCCT

                          *
       1547 AACAATCACATTCCC
          1 AACAATCACATTCCA

                  * *      
       1562 AACAATTATATTCCA
          1 AACAATCACATTCCA

              *           
       1577 AAGAATCACATTCC
          1 AACAATCACATTCC

       1591 GTTAAAATCA


Statistics
Matches: 23,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.43, C:0.30, G:0.02, T:0.25


Consensus pattern (15 bp):   
AACAATCACATTCCA

Found at i:2265 original size:31 final size:31

Alignment explanation


    Indices: 2215--2275  Score: 88
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       2205 AATAGCCTAG

                *                 *        
       2215 TGACTTAAATAAAATCTTTCGACTAATTCAA
          1 TGACCTAAATAAAATCTTTCGAATAATTCAA

                                           
       2246 TGACCTAAATGAAAA-CTTTCGAATAATTCA
          1 TGACCTAAAT-AAAATCTTTCGAATAATTCA

       2276 GTGATTATTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  31   23  0.85
  32    4  0.15

ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33


Consensus pattern (31 bp):   
TGACCTAAATAAAATCTTTCGAATAATTCAA

Found at i:4075 original size:15 final size:15

Alignment explanation


    Indices: 4041--4075  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       4031 AGTATCATGT

                           
       4041 TTATTATTATTAATA
          1 TTATTATTATTAATA

            *             *
       4056 CTATTATTATTAATG
          1 TTATTATTATTAATA

                 
       4071 TTATT
          1 TTATT

       4076 TATTGTAATA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60


Consensus pattern (15 bp):   
TTATTATTATTAATA

Found at i:4755 original size:17 final size:17

Alignment explanation


    Indices: 4743--4810  Score: 73
    Period size: 17  Copynumber: 3.9  Consensus size: 17

       4733 TTTTAAATTC

                             
       4743 AAATTAAAGTTAAACTT
          1 AAATTAAAGTTAAACTT

              *     *        
       4760 AATTTAAATTTAAACTT
          1 AAATTAAAGTTAAACTT

                **             
       4777 AAAAGGAAAGTTTAAACTT
          1 -AAATTAAAG-TTAAACTT

                    *      
       4796 AAATTAAATTTAAAC
          1 AAATTAAAGTTAAAC

       4811 CCAAAACAAA


Statistics
Matches: 40,  Mismatches: 9, Indels: 4
        0.75            0.17        0.08

Matches are distributed among these distances:
  17   21  0.52
  18   11  0.28
  19    8  0.20

ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35


Consensus pattern (17 bp):   
AAATTAAAGTTAAACTT

Found at i:4769 original size:35 final size:37

Alignment explanation


    Indices: 4723--4810  Score: 112
    Period size: 36  Copynumber: 2.5  Consensus size: 37

       4713 AGACATTTAA

                                *   **           
       4723 TTAATTTAAATTTTAAA-TTCAAATTAAAG-TTAAAC
          1 TTAATTTAAATTTTAAACTTAAAAGGAAAGTTTAAAC

                                                 
       4758 TTAATTTAAA-TTTAAACTTAAAAGGAAAGTTTAAAC
          1 TTAATTTAAATTTTAAACTTAAAAGGAAAGTTTAAAC

                *             
       4794 TTAAATTAAA-TTTAAAC
          1 TTAATTTAAATTTTAAAC

       4811 CCAAAACAAA


Statistics
Matches: 47,  Mismatches: 4, Indels: 3
        0.87            0.07        0.06

Matches are distributed among these distances:
  34    6  0.13
  35   19  0.40
  36   22  0.47

ACGTcount: A:0.50, C:0.06, G:0.05, T:0.40


Consensus pattern (37 bp):   
TTAATTTAAATTTTAAACTTAAAAGGAAAGTTTAAAC
Done.