Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012034.1 Kokia drynarioides strain JFW-HI SEQ_127032, 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: 20745
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:2114 original size:16 final size:16

Alignment explanation


    Indices: 2090--2123  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       2080 GCTCTGCTGA

                            
       2090 ATAGAGTCTTGAGTTT
          1 ATAGAGTCTTGAGTTT

                *           
       2106 ATAGGGTCTTGAGTTT
          1 ATAGAGTCTTGAGTTT

              
       2122 AT
          1 AT

       2124 GGCAGCTTTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44


Consensus pattern (16 bp):   
ATAGAGTCTTGAGTTT

Found at i:3611 original size:30 final size:30

Alignment explanation


    Indices: 3570--3772  Score: 187
    Period size: 30  Copynumber: 6.8  Consensus size: 30

       3560 AAAAATGAAA

                *         *          *     
       3570 TTTTAGAAAATTTGGGGGTC-AAATTTAAAT
          1 TTTTGGAAAATTTGAGGGTCAAAATAT-AAT

                         *                
       3600 TTTTGGAAAATTTAAGGGTCAAAATATAAT
          1 TTTTGGAAAATTTGAGGGTCAAAATATAAT

                 *      *                 
       3630 TTTTGAAAAATTAGAGGGTCAAAATATAAT
          1 TTTTGGAAAATTTGAGGGTCAAAATATAAT

                      *           *      * 
       3660 TTTTGGAAATTTTTG-GGGTCACAATATATT
          1 TTTTGGAAA-ATTTGAGGGTCAAAATATAAT

                *       *  *       *      
       3690 TTTTAGAAAATTCGAAGGTCAAACTATAAT
          1 TTTTGGAAAATTTGAGGGTCAAAATATAAT

                     *  *  * *            
       3720 TTTTGGAAAGTTCGAAGTTCAAAATATAAT
          1 TTTTGGAAAATTTGAGGGTCAAAATATAAT

                *    *              
       3750 TTTTTGAAAGTTTG-GGGATCAAA
          1 TTTTGGAAAATTTGAGGG-TCAAA

       3773 TTTTAAATAA


Statistics
Matches: 142,  Mismatches: 27, Indels: 8
        0.80            0.15        0.05

Matches are distributed among these distances:
  29    4  0.03
  30  130  0.92
  31    8  0.06

ACGTcount: A:0.38, C:0.05, G:0.18, T:0.38


Consensus pattern (30 bp):   
TTTTGGAAAATTTGAGGGTCAAAATATAAT

Found at i:3718 original size:90 final size:89

Alignment explanation


    Indices: 3599--3766  Score: 221
    Period size: 90  Copynumber: 1.9  Consensus size: 89

       3589 CAAATTTAAA

                 *       *                                *                  
       3599 TTTTTGGAAAATTTAAGGGTCAAAATATAATTTTTGAAAAATTAGAGGGTCAAAATATAATTTTT
          1 TTTTTAGAAAATTGAAGGGTCAAAATATAATTTTTGAAAAATTAGAAGGTCAAAATATAATTTTT

                  *                  
       3664 GGAAATTTTTGGGGTCACAATATAT
         66 GGAAA-GTTTGGGGTCACAATATAT

                                     *           *   *  *    *               
       3689 TTTTTAGAAAATTCGAA-GGTCAAACTATAATTTTTGGAAAGTTCGAAGTTCAAAATATAATTTT
          1 TTTTTAGAAAATT-GAAGGGTCAAAATATAATTTTTGAAAAATTAGAAGGTCAAAATATAATTTT

             *            
       3753 TTGAAAGTTTGGGG
         65 TGGAAAGTTTGGGG

       3767 ATCAAATTTT


Statistics
Matches: 67,  Mismatches: 10, Indels: 3
        0.84            0.12        0.04

Matches are distributed among these distances:
  89    7  0.10
  90   58  0.87
  91    2  0.03

ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39


Consensus pattern (89 bp):   
TTTTTAGAAAATTGAAGGGTCAAAATATAATTTTTGAAAAATTAGAAGGTCAAAATATAATTTTT
GGAAAGTTTGGGGTCACAATATAT

Found at i:9689 original size:17 final size:17

Alignment explanation


    Indices: 9667--9704  Score: 76
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       9657 CACAAAGAGT

                             
       9667 CTGTTTCTTTATATGGA
          1 CTGTTTCTTTATATGGA

                             
       9684 CTGTTTCTTTATATGGA
          1 CTGTTTCTTTATATGGA

                
       9701 CTGT
          1 CTGT

       9705 CCTACAGCAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53


Consensus pattern (17 bp):   
CTGTTTCTTTATATGGA

Found at i:18042 original size:6 final size:7

Alignment explanation


    Indices: 18013--18046  Score: 50
    Period size: 7  Copynumber: 4.7  Consensus size: 7

      18003 GAGTTCGAAT

                   
      18013 AAAGAAA
          1 AAAGAAA

                *   
      18020 ACAATAAA
          1 A-AAGAAA

                   
      18028 AAAGAAA
          1 AAAGAAA

                   
      18035 AAAGAAA
          1 AAAGAAA

                 
      18042 AAAGA
          1 AAAGA

      18047 GAGAAAATTG


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
   7   18  0.75
   8    6  0.25

ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03


Consensus pattern (7 bp):   
AAAGAAA

Found at i:18912 original size:23 final size:23

Alignment explanation


    Indices: 18882--18939  Score: 80
    Period size: 23  Copynumber: 2.5  Consensus size: 23

      18872 CTGACGTGAC

                             *     
      18882 ATCCAGTCAGCAGCTTCTAAAAG
          1 ATCCAGTCAGCAGCTTCCAAAAG

                       *           
      18905 ATCCAGTCAGCGGCTTCCAAAAG
          1 ATCCAGTCAGCAGCTTCCAAAAG

            *  *        
      18928 GTCTAGTCAGCA
          1 ATCCAGTCAGCA

      18940 AGGATGGACG


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   30  1.00

ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21


Consensus pattern (23 bp):   
ATCCAGTCAGCAGCTTCCAAAAG
Done.