Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008414.1 Kokia drynarioides strain JFW-HI SEQ_123085, 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: 7385
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35


Found at i:498 original size:21 final size:21

Alignment explanation


    Indices: 448--498  Score: 57
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        438 GGAGTTTTTA

                     *      *    
        448 GTATCGGTAGAAGCATGACTT
          1 GTATCGGTAAAAGCATCACTT

              * *        *       
        469 GTTTTGGTAAAAGTATCACTT
          1 GTATCGGTAAAAGCATCACTT

                     
        490 GTATCGGTA
          1 GTATCGGTA

        499 GAACCATCCC


Statistics
Matches: 23,  Mismatches: 7, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35


Consensus pattern (21 bp):   
GTATCGGTAAAAGCATCACTT

Found at i:3103 original size:15 final size:15

Alignment explanation


    Indices: 3078--3120  Score: 50
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       3068 TATTAAAAAT

                            
       3078 ATAATTTTATATTTGA
          1 ATAA-TTTATATTTGA

                         **
       3094 ATAATTTATATTTTT
          1 ATAATTTATATTTGA

                   *    
       3109 ATAATTTTTATT
          1 ATAATTTATATT

       3121 AAATTAATTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  15   20  0.83
  16    4  0.17

ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63


Consensus pattern (15 bp):   
ATAATTTATATTTGA

Found at i:3871 original size:23 final size:22

Alignment explanation


    Indices: 3789--3871  Score: 91
    Period size: 22  Copynumber: 3.8  Consensus size: 22

       3779 ATTATATTGT

                       *          
       3789 TGTTTTGG-TGCT-TTTTTTAC
          1 TGTTTTGGTTGTTGTTTTTTAC

                       *        * 
       3809 TGTTTTGGTTGGTGTTTTTTGC
          1 TGTTTTGGTTGTTGTTTTTTAC

                                    
       3831 TGTTTTGG-TGTTGTTTTTTTAAC
          1 TGTTTTGGTTGTTG-TTTTTT-AC

                      *       
       3854 TGTTTTGGTTTTTGTTTT
          1 TGTTTTGGTTGTTGTTTT

       3872 GGTGTTTTTT


Statistics
Matches: 53,  Mismatches: 5, Indels: 7
        0.82            0.08        0.11

Matches are distributed among these distances:
  20    8  0.15
  21    7  0.13
  22   21  0.40
  23   13  0.25
  24    4  0.08

ACGTcount: A:0.04, C:0.05, G:0.24, T:0.67


Consensus pattern (22 bp):   
TGTTTTGGTTGTTGTTTTTTAC

Found at i:4254 original size:41 final size:41

Alignment explanation


    Indices: 4197--4317  Score: 215
    Period size: 41  Copynumber: 3.0  Consensus size: 41

       4187 TGACTTCTAA

                      *                              
       4197 ATTCGGGTCGGGTTTGGACAAAATTTTAGACCCATTTTTCG
          1 ATTCGGGTCGAGTTTGGACAAAATTTTAGACCCATTTTTCG

                                                     
       4238 ATTCGGGTCGAGTTTGGACAAAATTTTAGACCCATTTTTCG
          1 ATTCGGGTCGAGTTTGGACAAAATTTTAGACCCATTTTTCG

               * *                                 
       4279 ATTTGTGTCGAGTTTGGACAAAATTTTAGACCCATTTTT
          1 ATTCGGGTCGAGTTTGGACAAAATTTTAGACCCATTTTT

       4318 AAGGAAAACT


Statistics
Matches: 77,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  41   77  1.00

ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39


Consensus pattern (41 bp):   
ATTCGGGTCGAGTTTGGACAAAATTTTAGACCCATTTTTCG

Found at i:5557 original size:27 final size:28

Alignment explanation


    Indices: 5510--5580  Score: 72
    Period size: 27  Copynumber: 2.6  Consensus size: 28

       5500 CGGGCCAAAC

                       * *  *    *      
       5510 ACAAAATAATGATATTTCGAGTCAGA-T
          1 ACAAAATAATGCTCTTCCGAGCCAGAGT

               *                        
       5537 ACAGAATAATGCTCTTCCGAGCCAGAGT
          1 ACAAAATAATGCTCTTCCGAGCCAGAGT

            *       *       
       5565 TCAAAATATTGCTCTT
          1 ACAAAATAATGCTCTT

       5581 TTGAGCCAAA


Statistics
Matches: 35,  Mismatches: 8, Indels: 1
        0.80            0.18        0.02

Matches are distributed among these distances:
  27   21  0.60
  28   14  0.40

ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30


Consensus pattern (28 bp):   
ACAAAATAATGCTCTTCCGAGCCAGAGT

Found at i:5649 original size:27 final size:27

Alignment explanation


    Indices: 5524--5671  Score: 109
    Period size: 27  Copynumber: 5.4  Consensus size: 27

       5514 AATAATGATA

                   *    * *      *     
       5524 TTTCGAGTCAGATACAGAATAATGCTC
          1 TTTCGAGCCAGAAATAGAATATTGCTC

              *         **   *          
       5551 TTCCGAGCCAGAGTTCAAAATATTGCTC
          1 TTTCGAGCCAGAAAT-AGAATATTGCTC

               *      *                 
       5579 TTTTGAGCCAAAAACT-GAATATTGCTC
          1 TTTCGAGCCAGAAA-TAGAATATTGCTC

               **   *   *          *   
       5606 TTTTAAGCTAGATATAGAATATTTCTC
          1 TTTCGAGCCAGAAATAGAATATTGCTC

                              **  *    
       5633 TTTCGAGCCAGAAATAGAGCATCGCTC
          1 TTTCGAGCCAGAAATAGAATATTGCTC

                        
       5660 TTTCGAGCCAGA
          1 TTTCGAGCCAGA

       5672 CTTATTGAAT


Statistics
Matches: 92,  Mismatches: 26, Indels: 6
        0.74            0.21        0.05

Matches are distributed among these distances:
  26    1  0.01
  27   71  0.77
  28   19  0.21
  29    1  0.01

ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Consensus pattern (27 bp):   
TTTCGAGCCAGAAATAGAATATTGCTC
Done.