Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010827.1 Kokia drynarioides strain JFW-HI SEQ_125794, 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: 1993
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.33

Warning! 127 characters in sequence are not A, C, G, or T


Found at i:34 original size:17 final size:18

Alignment explanation


    Indices: 1--80  Score: 128
    Period size: 17  Copynumber: 4.6  Consensus size: 18

                              
          1 TAAATTTAAATTTTAAAA
          1 TAAATTTAAATTTTAAAA

                              
         19 TAAATTTAAA-TTTAAAA
          1 TAAATTTAAATTTTAAAA

                          *   
         36 TAAATTTAAATTTTTAAA
          1 TAAATTTAAATTTTAAAA

            *                 
         54 CAAATTT-AATTTTAAAA
          1 TAAATTTAAATTTTAAAA

                      
         71 TAAATTTAAA
          1 TAAATTTAAA

         81 GGGATTATGG


Statistics
Matches: 56,  Mismatches: 4, Indels: 4
        0.88            0.06        0.06

Matches are distributed among these distances:
  17   32  0.57
  18   24  0.43

ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44


Consensus pattern (18 bp):   
TAAATTTAAATTTTAAAA

Found at i:47 original size:35 final size:35

Alignment explanation


    Indices: 1--80  Score: 133
    Period size: 35  Copynumber: 2.3  Consensus size: 35

                              *                
          1 TAAATTTAAATTTTAAAATAAATTTAAATTTAAAA
          1 TAAATTTAAATTTTAAAACAAATTTAAATTTAAAA

                          *            *       
         36 TAAATTTAAATTTTTAAACAAATTTAATTTTAAAA
          1 TAAATTTAAATTTTAAAACAAATTTAAATTTAAAA

                      
         71 TAAATTTAAA
          1 TAAATTTAAA

         81 GGGATTATGG


Statistics
Matches: 42,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  35   42  1.00

ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44


Consensus pattern (35 bp):   
TAAATTTAAATTTTAAAACAAATTTAAATTTAAAA

Found at i:80 original size:6 final size:6

Alignment explanation


    Indices: 1--48  Score: 55
    Period size: 6  Copynumber: 8.2  Consensus size: 6

                                *                    *              
          1 TAAATT TAAATTT TAAA-A TAAATT TAAATT TAAA-A TAAATT TAAATT
          1 TAAATT TAAA-TT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT

             
         48 T
          1 T

         49 TTAAACAAAT


Statistics
Matches: 35,  Mismatches: 4, Indels: 6
        0.78            0.09        0.13

Matches are distributed among these distances:
   5    8  0.23
   6   21  0.60
   7    6  0.17

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (6 bp):   
TAAATT

Found at i:734 original size:37 final size:37

Alignment explanation


    Indices: 648--737  Score: 128
    Period size: 37  Copynumber: 2.4  Consensus size: 37

        638 CTGCTTCTTT

                        *        *      *        
        648 GTATCTCATCAGAAAGACGAATTTGGTTTACTTCTCC
          1 GTATCTCATCAGGAAGACGAACTTGGTTCACTTCTCC

                                                 
        685 GTATCTCATCAGGAAGACGAACTTGGTTCACTTC-CC
          1 GTATCTCATCAGGAAGACGAACTTGGTTCACTTCTCC

                   *         
        721 AGTATCTTATCAGGAAG
          1 -GTATCTCATCAGGAAG

        738 CTAACCATTT


Statistics
Matches: 48,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  36    2  0.04
  37   46  0.96

ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31


Consensus pattern (37 bp):   
GTATCTCATCAGGAAGACGAACTTGGTTCACTTCTCC

Found at i:1696 original size:27 final size:27

Alignment explanation


    Indices: 1666--1726  Score: 77
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       1656 CCAAGAATTC

                            *          
       1666 TATTAAAAAGAGGATCGAAGGAAACAA
          1 TATTAAAAAGAGGATCAAAGGAAACAA

                   **    *             
       1693 TATTAAAGGGAGGGTCAAAGGAAACAA
          1 TATTAAAAAGAGGATCAAAGGAAACAA

                   
       1720 TCATTAA
          1 T-ATTAA

       1727 TTGAAAATTG


Statistics
Matches: 29,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  27   24  0.83
  28    5  0.17

ACGTcount: A:0.51, C:0.08, G:0.23, T:0.18


Consensus pattern (27 bp):   
TATTAAAAAGAGGATCAAAGGAAACAA
Done.