Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004277.1 Kokia drynarioides strain JFW-HI SEQ_117567, 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: 3179
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29


Found at i:1705 original size:23 final size:23

Alignment explanation


    Indices: 1677--1757  Score: 135
    Period size: 23  Copynumber: 3.5  Consensus size: 23

       1667 CGTCCATCCT

                    *              
       1677 TGCTGACTAGACCTTCTAGAAGC
          1 TGCTGACTGGACCTTCTAGAAGC

                  *                
       1700 TGCTGATTGGACCTTCTAGAAGC
          1 TGCTGACTGGACCTTCTAGAAGC

                  *                
       1723 TGCTGATTGGACCTTCTAGAAGC
          1 TGCTGACTGGACCTTCTAGAAGC

                        
       1746 TGCTGACTGGAC
          1 TGCTGACTGGAC

       1758 ACCACGTCAG


Statistics
Matches: 55,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   55  1.00

ACGTcount: A:0.22, C:0.23, G:0.26, T:0.28


Consensus pattern (23 bp):   
TGCTGACTGGACCTTCTAGAAGC

Found at i:2512 original size:10 final size:9

Alignment explanation


    Indices: 2489--2529  Score: 55
    Period size: 10  Copynumber: 4.2  Consensus size: 9

       2479 TAAGCAACCA

                     
       2489 TTTTTTCTT
          1 TTTTTTCTT

                       
       2498 CTTTTTCTCTT
          1 -TTTTT-TCTT

                     
       2509 TTTTTTCTT
          1 TTTTTTCTT

                      
       2518 TTATTTTCTT
          1 TT-TTTTCTT

              
       2528 TT
          1 TT

       2530 CGAACCTTCT


Statistics
Matches: 29,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   9    6  0.21
  10   19  0.66
  11    4  0.14

ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83


Consensus pattern (9 bp):   
TTTTTTCTT

Found at i:2566 original size:14 final size:15

Alignment explanation


    Indices: 2541--2576  Score: 51
    Period size: 15  Copynumber: 2.6  Consensus size: 15

       2531 GAACCTTCTG

                           
       2541 CTTTTTTT--CTGTT
          1 CTTTTTTTCACTGTT

                           
       2554 -TTTTTTTCACTGTT
          1 CTTTTTTTCACTGTT

                     
       2568 CTTTTTTTC
          1 CTTTTTTTC

       2577 TTCTTTATTG


Statistics
Matches: 20,  Mismatches: 0, Indels: 4
        0.83            0.00        0.17

Matches are distributed among these distances:
  12    7  0.35
  14    5  0.25
  15    8  0.40

ACGTcount: A:0.03, C:0.17, G:0.06, T:0.75


Consensus pattern (15 bp):   
CTTTTTTTCACTGTT

Found at i:2590 original size:14 final size:14

Alignment explanation


    Indices: 2573--2599  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       2563 CTGTTCTTTT

                          
       2573 TTTCTTCTTTATTG
          1 TTTCTTCTTTATTG

                         
       2587 TTTCTTCTTTATT
          1 TTTCTTCTTTATT

       2600 CGAACTCCTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.07, C:0.15, G:0.04, T:0.74


Consensus pattern (14 bp):   
TTTCTTCTTTATTG
Done.