Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011248.1 Kokia drynarioides strain JFW-HI SEQ_126226, 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: 27598
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32

Warning! 52 characters in sequence are not A, C, G, or T


Found at i:9743 original size:16 final size:16

Alignment explanation


    Indices: 9722--9754  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       9712 CAAACATTCA

                            
       9722 TTTTTATTTTATATTT
          1 TTTTTATTTTATATTT

                      *     
       9738 TTTTTATTTTTTATTT
          1 TTTTTATTTTATATTT

             
       9754 T
          1 T

       9755 ATGCTTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85


Consensus pattern (16 bp):   
TTTTTATTTTATATTT

Found at i:11516 original size:19 final size:20

Alignment explanation


    Indices: 11489--11539  Score: 59
    Period size: 21  Copynumber: 2.5  Consensus size: 20

      11479 TGGAGCTGCA

                *               
      11489 GTATAGATACTGAT-AAAAG
          1 GTATCGATACTGATGAAAAG

                        **       
      11508 GTATCGATACTTTTTGAAAAG
          1 GTATCGATAC-TGATGAAAAG

                       
      11529 GTATCGATACT
          1 GTATCGATACT

      11540 TTTTCTCCTT


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  19    9  0.33
  20    3  0.11
  21   15  0.56

ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33


Consensus pattern (20 bp):   
GTATCGATACTGATGAAAAG

Found at i:11529 original size:21 final size:21

Alignment explanation


    Indices: 11503--11543  Score: 82
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      11493 AGATACTGAT

                                 
      11503 AAAAGGTATCGATACTTTTTG
          1 AAAAGGTATCGATACTTTTTG

                                
      11524 AAAAGGTATCGATACTTTTT
          1 AAAAGGTATCGATACTTTTT

      11544 CTCCTTGTTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39


Consensus pattern (21 bp):   
AAAAGGTATCGATACTTTTTG

Found at i:11902 original size:33 final size:33

Alignment explanation


    Indices: 11864--11927  Score: 78
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      11854 AATACATTGC

                 *                  *   *     
      11864 TCCCCTTA-ATAAAAGA-CATTTTGAATTTAAGT
          1 TCCCCCTATATAAAA-ATCATTTTCAATATAAGT

                                            
      11896 TCCCCCTATATAAAAATCATTTTCAATATAAG
          1 TCCCCCTATATAAAAATCATTTTCAATATAAG

      11928 GCATAAAGAT


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  32    8  0.30
  33   19  0.70

ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36


Consensus pattern (33 bp):   
TCCCCCTATATAAAAATCATTTTCAATATAAGT

Found at i:16544 original size:17 final size:17

Alignment explanation


    Indices: 16512--16555  Score: 52
    Period size: 17  Copynumber: 2.5  Consensus size: 17

      16502 ATTAAATTAC

                       *      
      16512 AATGACAAATGGAAATGA
          1 AATGAC-AATGCAAATGA

                            *
      16530 AATGACAATGCAAATGT
          1 AATGACAATGCAAATGA

             *       
      16547 AGTGACAAT
          1 AATGACAAT

      16556 TAAAATGTAA


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

Matches are distributed among these distances:
  17   17  0.74
  18    6  0.26

ACGTcount: A:0.50, C:0.09, G:0.20, T:0.20


Consensus pattern (17 bp):   
AATGACAATGCAAATGA

Found at i:16580 original size:34 final size:34

Alignment explanation


    Indices: 16524--16589  Score: 80
    Period size: 34  Copynumber: 1.9  Consensus size: 34

      16514 TGACAAATGG

                       *                       
      16524 AAATGAAATGACAATGCAAATGT-AGTGACAATTA
          1 AAATGAAATGAAAATGCAAATGTGA-TGACAATTA

                 *          **              
      16558 AAATGTAATGAAAATGGGAATGTGATGACAAT
          1 AAATGAAATGAAAATGCAAATGTGATGACAAT

      16590 GCTAACTAGC


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  34   26  0.96
  35    1  0.04

ACGTcount: A:0.48, C:0.06, G:0.21, T:0.24


Consensus pattern (34 bp):   
AAATGAAATGAAAATGCAAATGTGATGACAATTA

Found at i:25991 original size:21 final size:21

Alignment explanation


    Indices: 25965--26023  Score: 82
    Period size: 21  Copynumber: 2.8  Consensus size: 21

      25955 GATACCTAAT

                                 
      25965 AAAAGGTATTGATACTTTTTA
          1 AAAAGGTATTGATACTTTTTA

                     *   *      *
      25986 AAAAGGTATCGATGCTTTTTG
          1 AAAAGGTATTGATACTTTTTA

                    *        
      26007 AAAAGGTACTGATACTT
          1 AAAAGGTATTGATACTT

      26024 GTCATTTTTT


Statistics
Matches: 32,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   32  1.00

ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37


Consensus pattern (21 bp):   
AAAAGGTATTGATACTTTTTA
Done.