Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008022.1 Kokia drynarioides strain JFW-HI SEQ_122676, 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: 16118
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:1522 original size:24 final size:25

Alignment explanation


    Indices: 1494--1545  Score: 88
    Period size: 24  Copynumber: 2.1  Consensus size: 25

       1484 TGTAAAACCC

                                     
       1494 ATCACCAGAGCATCAAATTGAAC-T
          1 ATCACCAGAGCATCAAATTGAACGT

                  *                  
       1518 ATCACCGGAGCATCAAATTGAACGT
          1 ATCACCAGAGCATCAAATTGAACGT

               
       1543 ATC
          1 ATC

       1546 CCAATTCCAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  24   22  0.85
  25    4  0.15

ACGTcount: A:0.38, C:0.25, G:0.15, T:0.21


Consensus pattern (25 bp):   
ATCACCAGAGCATCAAATTGAACGT

Found at i:2762 original size:19 final size:20

Alignment explanation


    Indices: 2728--2766  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       2718 GCTGTTTTTA

                                 
       2728 TTTTTAAAATAGTAAATTAAT
          1 TTTTTAAAATA-TAAATTAAT

                               
       2749 TTTTTAAAAT-TAAATTAA
          1 TTTTTAAAATATAAATTAA

       2767 AAAATAAATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  19    8  0.44
  21   10  0.56

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (20 bp):   
TTTTTAAAATATAAATTAAT

Found at i:5827 original size:59 final size:59

Alignment explanation


    Indices: 5735--5904  Score: 211
    Period size: 58  Copynumber: 2.9  Consensus size: 59

       5725 TTGGGGCTTG

                               *       *                * *       *     
       5735 AACTTGGCAATTATTTTCATATTGGGGTGTGAACTTGTTTTTGTTCGAA-TTAGGCCCTA
          1 AACTTGGCAATTATTTTCACATTGGGGCGTGAACTT-TTTTTGTCCCAAGTTAGACCCTA

                        *   *           *      *                      *
       5794 AACTTGGCAATTGTTTCCACATTGGGGCCTGAACTCTTTTTG-CCCAAGTTAGACCCTG
          1 AACTTGGCAATTATTTTCACATTGGGGCGTGAACTTTTTTTGTCCCAAGTTAGACCCTA

                                                                  
       5852 AACTTGGCAATTATTTTCACATTGGGGCGTGAACTTTTATTTGT-CCAAGTTAG
          1 AACTTGGCAATTATTTTCACATTGGGGCGTGAACTTTT-TTTGTCCCAAGTTAG

       5905 TCCTTGATAT


Statistics
Matches: 94,  Mismatches: 14, Indels: 6
        0.82            0.12        0.05

Matches are distributed among these distances:
  57    3  0.03
  58   48  0.51
  59   43  0.46

ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38


Consensus pattern (59 bp):   
AACTTGGCAATTATTTTCACATTGGGGCGTGAACTTTTTTTGTCCCAAGTTAGACCCTA

Found at i:5966 original size:31 final size:31

Alignment explanation


    Indices: 5931--6001  Score: 79
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       5921 GAAAACCCTA

                     **     *   *        * 
       5931 AAGTTCAAGTTCCAACGTGGGAACAATTGTC
          1 AAGTTCAAGCCCCAACATGGAAACAATTGCC

                   *       *               
       5962 AAGTTCAGGCCCCAATATGGAAACAATTGCC
          1 AAGTTCAAGCCCCAACATGGAAACAATTGCC

                     
       5993 AAGTTCAAG
          1 AAGTTCAAG

       6002 GACTAACTTG


Statistics
Matches: 32,  Mismatches: 8, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23


Consensus pattern (31 bp):   
AAGTTCAAGCCCCAACATGGAAACAATTGCC

Found at i:9912 original size:46 final size:47

Alignment explanation


    Indices: 9838--9934  Score: 151
    Period size: 46  Copynumber: 2.1  Consensus size: 47

       9828 TTAATTTCAA

                                         *                 
       9838 CAAACATCCTTAAAAAAATATTGTAGAATCTAAATCGATCCAAACTT
          1 CAAACATCCTTAAAAAAATATTGTAGAATATAAATCGATCCAAACTT

                 *         *                   *           
       9885 CAAACGTCCTT-AAAGAATATTGTAGAATATAAATTGATCCAAACTT
          1 CAAACATCCTTAAAAAAATATTGTAGAATATAAATCGATCCAAACTT

                
       9931 CAAA
          1 CAAA

       9935 AAAGTTATTA


Statistics
Matches: 46,  Mismatches: 4, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  46   36  0.78
  47   10  0.22

ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28


Consensus pattern (47 bp):   
CAAACATCCTTAAAAAAATATTGTAGAATATAAATCGATCCAAACTT
Done.