Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006433.1 Kokia drynarioides strain JFW-HI SEQ_121015, 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: 9597
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36


Found at i:2476 original size:23 final size:23

Alignment explanation


    Indices: 2425--2486  Score: 56
    Period size: 23  Copynumber: 2.7  Consensus size: 23

       2415 GAGATATCGA

                                * *
       2425 AATTAAATTATAATTTTTATCAT
          1 AATTAAATTATAATTTTTATAAG

                      *             
       2448 AA-TAAATATGTAATTTTTA-AAG
          1 AATTAAAT-TATAATTTTTATAAG

                    * *      
       2470 AATTAAATCAAAATTTT
          1 AATTAAATTATAATTTT

       2487 ATCATTTTTA


Statistics
Matches: 31,  Mismatches: 6, Indels: 5
        0.74            0.14        0.12

Matches are distributed among these distances:
  22   14  0.45
  23   17  0.55

ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45


Consensus pattern (23 bp):   
AATTAAATTATAATTTTTATAAG

Found at i:3500 original size:17 final size:17

Alignment explanation


    Indices: 3478--3534  Score: 64
    Period size: 17  Copynumber: 3.3  Consensus size: 17

       3468 CTTTCATCTT

                             
       3478 TTAACTTTCCATCTTCC
          1 TTAACTTTCCATCTTCC

                               
       3495 TTAACTTTCC-T-TTGACC
          1 TTAACTTTCCATCTT--CC

                  *           
       3512 TTTAACCTTCCATCTTCC
          1 -TTAACTTTCCATCTTCC

                 
       3530 TTAAC
          1 TTAAC

       3535 CTCCCTTAAT


Statistics
Matches: 34,  Mismatches: 1, Indels: 10
        0.76            0.02        0.22

Matches are distributed among these distances:
  15    2  0.06
  16    1  0.03
  17   17  0.50
  18   11  0.32
  19    1  0.03
  20    2  0.06

ACGTcount: A:0.19, C:0.33, G:0.02, T:0.46


Consensus pattern (17 bp):   
TTAACTTTCCATCTTCC

Found at i:3535 original size:17 final size:17

Alignment explanation


    Indices: 3465--3536  Score: 62
    Period size: 17  Copynumber: 4.3  Consensus size: 17

       3455 ATGGATGTTC

                  *          
       3465 AACCTTTCATCTT--TT
          1 AACCTTCCATCTTCCTT

               *             
       3480 AACTTTCCATCTTCCTT
          1 AACCTTCCATCTTCCTT

               *                
       3497 AACTTTCC-T-TTGACCTTT
          1 AACCTTCCATCTT--CC-TT

                             
       3515 AACCTTCCATCTTCCTT
          1 AACCTTCCATCTTCCTT

                 
       3532 AACCT
          1 AACCT

       3537 CCCTTAATCT


Statistics
Matches: 47,  Mismatches: 3, Indels: 12
        0.76            0.05        0.19

Matches are distributed among these distances:
  15   13  0.28
  16    1  0.02
  17   19  0.40
  18   11  0.23
  19    1  0.02
  20    2  0.04

ACGTcount: A:0.19, C:0.33, G:0.01, T:0.46


Consensus pattern (17 bp):   
AACCTTCCATCTTCCTT

Found at i:3562 original size:34 final size:35

Alignment explanation


    Indices: 3477--3554  Score: 104
    Period size: 35  Copynumber: 2.3  Consensus size: 35

       3467 CCTTTCATCT

                  *                 *   *  *   
       3477 TTTAACTTTCCATCTTCCTTAACTTTCCTTTGACC
          1 TTTAACCTTCCATCTTCCTTAACTCTCCCTTAACC

                                             * 
       3512 TTTAACCTTCCATCTTCCTTAAC-CTCCCTTAATC
          1 TTTAACCTTCCATCTTCCTTAACTCTCCCTTAACC

                     
       3546 TTTAACCTT
          1 TTTAACCTT

       3555 TTATCTTCTT


Statistics
Matches: 38,  Mismatches: 5, Indels: 1
        0.86            0.11        0.02

Matches are distributed among these distances:
  34   16  0.42
  35   22  0.58

ACGTcount: A:0.19, C:0.33, G:0.01, T:0.46


Consensus pattern (35 bp):   
TTTAACCTTCCATCTTCCTTAACTCTCCCTTAACC

Found at i:8614 original size:34 final size:34

Alignment explanation


    Indices: 8576--8668  Score: 150
    Period size: 34  Copynumber: 2.7  Consensus size: 34

       8566 CCTTTCATCT

                     *                 *      
       8576 TTTAACCTTACATCTTCCTTAACTTCCTTTAACC
          1 TTTAACCTTCCATCTTCCTTAACTTCCCTTAACC

                                   *        * 
       8610 TTTAACCTTCCATCTTCCTTAACCTCCCTTAATC
          1 TTTAACCTTCCATCTTCCTTAACTTCCCTTAACC

                                     
       8644 TTTAACCTTCCATCTTCCTTAACTT
          1 TTTAACCTTCCATCTTCCTTAACTT

       8669 TTCATATTCT


Statistics
Matches: 54,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  34   54  1.00

ACGTcount: A:0.22, C:0.34, G:0.00, T:0.44


Consensus pattern (34 bp):   
TTTAACCTTCCATCTTCCTTAACTTCCCTTAACC

Found at i:8631 original size:17 final size:17

Alignment explanation


    Indices: 8564--8666  Score: 81
    Period size: 17  Copynumber: 6.2  Consensus size: 17

       8554 ATGGATGTTC

                  *          
       8564 AACCTTTCATCTT--TT
          1 AACCTTCCATCTTCCTT

                  *          
       8579 AACCTTACATCTTCCTT
          1 AACCTTCCATCTTCCTT

                                
       8596 AA-CTTCC-T-TTAACCTTT
          1 AACCTTCCATCTT--CC-TT

                             
       8613 AACCTTCCATCTTCCTT
          1 AACCTTCCATCTTCCTT

                 *  * **  *  
       8630 AACCTCCCTTAATCTTT
          1 AACCTTCCATCTTCCTT

                             
       8647 AACCTTCCATCTTCCTT
          1 AACCTTCCATCTTCCTT

               
       8664 AAC
          1 AAC

       8667 TTTTCATATT


Statistics
Matches: 68,  Mismatches: 12, Indels: 14
        0.72            0.13        0.15

Matches are distributed among these distances:
  14    2  0.03
  15   13  0.19
  16    6  0.09
  17   37  0.54
  18    7  0.10
  19    1  0.01
  20    2  0.03

ACGTcount: A:0.22, C:0.35, G:0.00, T:0.43


Consensus pattern (17 bp):   
AACCTTCCATCTTCCTT
Done.