Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002719.1 Kokia drynarioides strain JFW-HI SEQ_115014, 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: 11194
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:8529 original size:16 final size:16

Alignment explanation


    Indices: 8480--8534  Score: 56
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       8470 TTTGCCTAAA

                            
       8480 AAGTACTTCCTCCATG
          1 AAGTACTTCCTCCATG

               *       *        
       8496 AAGAACAATAGACCTCCATG
          1 AAGTAC--T--TCCTCCATG

                            
       8516 AAGTACTTCCTCCATG
          1 AAGTACTTCCTCCATG

               
       8532 AAG
          1 AAG

       8535 AAGCTATTCA


Statistics
Matches: 31,  Mismatches: 4, Indels: 8
        0.72            0.09        0.19

Matches are distributed among these distances:
  16   16  0.52
  18    2  0.06
  20   13  0.42

ACGTcount: A:0.35, C:0.27, G:0.15, T:0.24


Consensus pattern (16 bp):   
AAGTACTTCCTCCATG

Found at i:8598 original size:21 final size:21

Alignment explanation


    Indices: 8574--8613  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       8564 GCTACCTTCA

                                  
       8574 CAAGAAACAATGAA-ATCAATT
          1 CAAGAAACAAT-AACATCAATT

                  *            
       8595 CAAGAAGCAATAACATCAA
          1 CAAGAAACAATAACATCAA

       8614 ATTTACCTGC


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    2  0.12
  21   15  0.88

ACGTcount: A:0.57, C:0.17, G:0.10, T:0.15


Consensus pattern (21 bp):   
CAAGAAACAATAACATCAATT

Found at i:10888 original size:30 final size:30

Alignment explanation


    Indices: 10852--10911  Score: 93
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      10842 AAATCGCAGA

                         *                
      10852 AAAAACGCCGCTATAGAACATGGTCTTTAG
          1 AAAAACGCCGCTAAAGAACATGGTCTTTAG

                   *  *                   
      10882 AAAAACGTCGTTAAAGAACATGGTCTTTAG
          1 AAAAACGCCGCTAAAGAACATGGTCTTTAG

      10912 CGGCACTTAT


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25


Consensus pattern (30 bp):   
AAAAACGCCGCTAAAGAACATGGTCTTTAG

Found at i:10947 original size:43 final size:43

Alignment explanation


    Indices: 10893--11059  Score: 200
    Period size: 43  Copynumber: 3.9  Consensus size: 43

      10883 AAAACGTCGT

                                                        
      10893 TAAAGAACATGGTCTTTAGCGGC-ACTTATCCCACAAACGCCAC
          1 TAAAGAACATGGTCTTTAGCGGCGACTT-TCCCACAAACGCCAC

                  *                 *                * 
      10936 TAAAGACCATGGTCTTTAGCGGCGCCTTTCCCACAAACGCCGC
          1 TAAAGAACATGGTCTTTAGCGGCGACTTTCCCACAAACGCCAC

                                  *                       
      10979 TAAAGAACATGAG-CTTTAGC-TCTG-CTTTTCCCACAAACGCCAC
          1 TAAAGAACATG-GTCTTTAGCGGC-GAC-TTTCCCACAAACGCCAC

                                 *         *       
      11022 TAAAGAACATGGTCTTTAGCGACG-CTTTTCTCACAAAC
          1 TAAAGAACATGGTCTTTAGCGGCGAC-TTTCCCACAAAC

      11060 ACCATTAATA


Statistics
Matches: 110,  Mismatches: 8, Indels: 12
        0.85            0.06        0.09

Matches are distributed among these distances:
  42    3  0.03
  43  102  0.93
  44    5  0.05

ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24


Consensus pattern (43 bp):   
TAAAGAACATGGTCTTTAGCGGCGACTTTCCCACAAACGCCAC
Done.