Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014008.1 Kokia drynarioides strain JFW-HI SEQ_129039, 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: 14513
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.32

Warning! 373 characters in sequence are not A, C, G, or T


Found at i:5962 original size:24 final size:24

Alignment explanation


    Indices: 5909--5959  Score: 66
    Period size: 25  Copynumber: 2.1  Consensus size: 24

       5899 CGCAACAAAA

                             *   *  
       5909 TTTCTTCCTTCTCTCCTTCTTTTC
          1 TTTCTTCCTTCTCTCCTCCTTCTC

                       *             
       5933 TTTCTTCCTTTTTCTCCTCCTTCTC
          1 TTTCTTCC-TTCTCTCCTCCTTCTC

              
       5958 TT
          1 TT

       5960 CTTATTTCTC


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  24    8  0.35
  25   15  0.65

ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63


Consensus pattern (24 bp):   
TTTCTTCCTTCTCTCCTCCTTCTC

Found at i:5967 original size:21 final size:21

Alignment explanation


    Indices: 5935--5974  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       5925 TTCTTTTCTT

                                 
       5935 TCTTCCTTTTTCTCCTCCTTC
          1 TCTTCCTTTTTCTCCTCCTTC

                           *    
       5956 TCTT-CTTATTTCTCTTCCT
          1 TCTTCCTT-TTTCTCCTCCT

       5975 CAATATCCAC


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

Matches are distributed among these distances:
  20    3  0.18
  21   14  0.82

ACGTcount: A:0.03, C:0.38, G:0.00, T:0.60


Consensus pattern (21 bp):   
TCTTCCTTTTTCTCCTCCTTC

Found at i:7045 original size:140 final size:140

Alignment explanation


    Indices: 6790--7070  Score: 420
    Period size: 140  Copynumber: 2.0  Consensus size: 140

       6780 AATAATTGGT

                                          *        *    ** *                 
       6790 AATTAATAAAGTGGAACCAGACCTTGCTTTGCACGGTGAGGAATCGATGATGCATGGTATAGTTA
          1 AATTAATAAAGTGGAACCAGACCTTGCTTTACACGGTGAAGAATAAACGATGCATGGTATAGTTA

                       *                       *                             
       6855 TTGGGGTTGTTGCCTATCCAAATGGCACCATCAACTCATAAATCACTCATTAACATGTCAGCT-C
         66 TTGGGGTTGTTACCTATCCAAATGGCACCATCAACGCATAAATCACTCATTAACATGTCA-CTGC

                       
       6919 CCTCTTCAGTC
        130 CCTCTTCAGTC

                                                                             
       6930 AATTAATAAAGTGGAACCAGACCTTGCTTTACACGGTGAAGAATAAACGATGCATGGTATAGTTA
          1 AATTAATAAAGTGGAACCAGACCTTGCTTTACACGGTGAAGAATAAACGATGCATGGTATAGTTA

                              * *            *  *        *     *             
       6995 TTGGGGTTGTTACCTATCTAGATGGCACCATCAGCGGATAAATCAGTCATTGACATGTCACTGCC
         66 TTGGGGTTGTTACCTATCCAAATGGCACCATCAACGCATAAATCACTCATTAACATGTCACTGCC

                 *    
       7060 CTCTTTAGTC
        131 CTCTTCAGTC

             
       7070 A
          1 A

       7071 GTTGCTCTAG


Statistics
Matches: 126,  Mismatches: 14, Indels: 2
        0.89            0.10        0.01

Matches are distributed among these distances:
 139    2  0.02
 140  124  0.98

ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29


Consensus pattern (140 bp):   
AATTAATAAAGTGGAACCAGACCTTGCTTTACACGGTGAAGAATAAACGATGCATGGTATAGTTA
TTGGGGTTGTTACCTATCCAAATGGCACCATCAACGCATAAATCACTCATTAACATGTCACTGCC
CTCTTCAGTC

Found at i:14000 original size:23 final size:23

Alignment explanation


    Indices: 13948--14122  Score: 138
    Period size: 23  Copynumber: 7.4  Consensus size: 23

      13938 TATACGGAAC

                          *        
      13948 AAACAGAGAGCACATA-AGTGCT
          1 AAACAGAGAGCACACACAGTGCT

               *                      
      13970 GGGCAACAGAGAGCACACACAGTGCT
          1 ---AAACAGAGAGCACACACAGTGCT

                     **     *   *  
      13996 AAACAGAGAATACACAAAGTACT
          1 AAACAGAGAGCACACACAGTGCT

             **      *      *      
      14019 AGTCAGAGATCACACAAAGTGCT
          1 AAACAGAGAGCACACACAGTGCT

              *                 *  
      14042 AATCAGAGAGCACACACAGTACT
          1 AAACAGAGAGCACACACAGTGCT

                             *  *  *  
      14065 AATAACAGAGAGCACGAGA-TGTACT
          1 -A-AACAGAGAGCAC-ACACAGTGCT

                                   
      14090 AAACAGAGAGCACACACAGTGCT
          1 AAACAGAGAGCACACACAGTGCT

              *       
      14113 AATCAGAGAG
          1 AAACAGAGAG

      14123 TGCGCTAGTG


Statistics
Matches: 122,  Mismatches: 23, Indels: 12
        0.78            0.15        0.08

Matches are distributed among these distances:
  22    2  0.02
  23   80  0.66
  24    2  0.02
  25   30  0.25
  26    8  0.07

ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13


Consensus pattern (23 bp):   
AAACAGAGAGCACACACAGTGCT

Found at i:14072 original size:71 final size:69

Alignment explanation


    Indices: 13976--14122  Score: 181
    Period size: 71  Copynumber: 2.1  Consensus size: 69

      13966 TGCTGGGCAA

                             *                            **      *          
      13976 CAGAGAGCACACACAGTGCTAAACAGAGAATACAC-A-AAGTACTAGTCAGAGATCACACAAAGT
          1 CAGAGAGCACACACAGTACTAAACAGAG-A-ACACGAGAAGTACTAAACAGAGAGCACACAAAGT

                  
      14039 GCTAAT
         64 GCTAAT

                                           *       *                     *   
      14045 CAGAGAGCACACACAGTACTAATAACAGAGAGCACGAGATGTACTAAACAGAGAGCACACACAGT
          1 CAGAGAGCACACACAGTACT-A-AACAGAGAACACGAGAAGTACTAAACAGAGAGCACACAAAGT

                  
      14110 GCTAAT
         64 GCTAAT

                   
      14116 CAGAGAG
          1 CAGAGAG

      14123 TGCGCTAGTG


Statistics
Matches: 67,  Mismatches: 7, Indels: 6
        0.84            0.09        0.08

Matches are distributed among these distances:
  69   22  0.33
  70    3  0.04
  71   42  0.63

ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13


Consensus pattern (69 bp):   
CAGAGAGCACACACAGTACTAAACAGAGAACACGAGAAGTACTAAACAGAGAGCACACAAAGTGC
TAAT
Done.