Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014219.1 Kokia drynarioides strain JFW-HI SEQ_129252, 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: 16515
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33


Found at i:3432 original size:17 final size:16

Alignment explanation


    Indices: 3395--3433  Score: 51
    Period size: 16  Copynumber: 2.3  Consensus size: 16

       3385 TGATCTAGGA

                            *
       3395 AAAATTTAAAAGAAAAT
          1 AAAA-TTAAAAGAAAAG

                             
       3412 AAAATTAAAAGAAATAG
          1 AAAATTAAAAGAAA-AG

                 
       3429 AAAAT
          1 AAAAT

       3434 AGAGGTGTTG


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  16   10  0.50
  17   10  0.50

ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21


Consensus pattern (16 bp):   
AAAATTAAAAGAAAAG

Found at i:6741 original size:42 final size:43

Alignment explanation


    Indices: 6640--6813  Score: 188
    Period size: 43  Copynumber: 4.1  Consensus size: 43

       6630 TTAATATTAA

                     *         *   *                   
       6640 CGGCGTTTGAGGGAAAAGCATCGCTAAAGACCATGTTCTTTAG
          1 CGGCGTTTGTGGGAAAAGCGTCGTTAAAGACCATGTTCTTTAG

               *    *        *            *            
       6683 CGGAGTTTATGGGAAAAACGTCGTTAAAGATCATGTT-TTTAG
          1 CGGCGTTTGTGGGAAAAGCGTCGTTAAAGACCATGTTCTTTAG

                 *     *        *  *          *  *     
       6725 CGGCGGTTGTGAGAAAAGCGCCGCTAAAGACCATATTTTTTAG
          1 CGGCGTTTGTGGGAAAAGCGTCGTTAAAGACCATGTTCTTTAG

             *            *               *        *   
       6768 CAGCGTTTGTGGGAGAAGCGTCGTTAAAGATCATGTTCTATAG
          1 CGGCGTTTGTGGGAAAAGCGTCGTTAAAGACCATGTTCTTTAG

               
       6811 CGG
          1 CGG

       6814 TTTTTTTCGC


Statistics
Matches: 103,  Mismatches: 27, Indels: 2
        0.78            0.20        0.02

Matches are distributed among these distances:
  42   33  0.32
  43   70  0.68

ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28


Consensus pattern (43 bp):   
CGGCGTTTGTGGGAAAAGCGTCGTTAAAGACCATGTTCTTTAG

Found at i:6790 original size:85 final size:86

Alignment explanation


    Indices: 6652--6813  Score: 227
    Period size: 85  Copynumber: 1.9  Consensus size: 86

       6642 GCGTTTGAGG

                    *             *         *                                
       6652 GAAAAGCATCGCTAAAGACCATGTTCTTTAGCGGAGTTTATGGGAAAAACGTCGTTAAAGATCAT
          1 GAAAAGCACCGCTAAAGACCATATTCTTTAGCAGAGTTTATGGGAAAAACGTCGTTAAAGATCAT

                 *               
       6717 GTT-TTTAGCGGCGGTTGTGA
         66 GTTCTATAGCGGCGGTTGTGA

                   *                 *        *    *     *  *                
       6737 GAAAAGCGCCGCTAAAGACCATATTTTTTAGCAGCGTTTGTGGGAGAAGCGTCGTTAAAGATCAT
          1 GAAAAGCACCGCTAAAGACCATATTCTTTAGCAGAGTTTATGGGAAAAACGTCGTTAAAGATCAT

                        
       6802 GTTCTATAGCGG
         66 GTTCTATAGCGG

       6814 TTTTTTTCGC


Statistics
Matches: 66,  Mismatches: 10, Indels: 1
        0.86            0.13        0.01

Matches are distributed among these distances:
  85   59  0.89
  86    7  0.11

ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28


Consensus pattern (86 bp):   
GAAAAGCACCGCTAAAGACCATATTCTTTAGCAGAGTTTATGGGAAAAACGTCGTTAAAGATCAT
GTTCTATAGCGGCGGTTGTGA

Found at i:6974 original size:23 final size:24

Alignment explanation


    Indices: 6948--6993  Score: 58
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       6938 TGTCTCCATT

                                    
       6948 TAAG-ACTTCCAAAAACACTATAG
          1 TAAGTACTTCCAAAAACACTATAG

                 **        *       
       6971 TAAGTTGTTCCAAAAGCACTATA
          1 TAAGTACTTCCAAAAACACTATA

       6994 TTTGGGTATT


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  23    4  0.21
  24   15  0.79

ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26


Consensus pattern (24 bp):   
TAAGTACTTCCAAAAACACTATAG

Found at i:15367 original size:16 final size:15

Alignment explanation


    Indices: 15337--15371  Score: 52
    Period size: 16  Copynumber: 2.3  Consensus size: 15

      15327 ATATACTACT

                    *      
      15337 GTTGAATTTTTTAGA
          1 GTTGAATTCTTTAGA

                            
      15352 GTTGATATTCTTTAGA
          1 GTTGA-ATTCTTTAGA

                
      15368 GTTG
          1 GTTG

      15372 GATAATTACA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  15    5  0.28
  16   13  0.72

ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51


Consensus pattern (15 bp):   
GTTGAATTCTTTAGA
Done.