Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010230.1 Kokia drynarioides strain JFW-HI SEQ_125060, 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, 936

Length: 1561
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.32

Warning! 94 characters in sequence are not A, C, G, or T


Found at i:1422 original size:4 final size:4

Alignment explanation


    Indices: 1400--1485  Score: 59
    Period size: 4  Copynumber: 21.2  Consensus size: 4

       1390 AACACATTAC

                 *     *                     *   *                     * 
       1400 CTTT ATTT CCTT C-TT CTTT CTTT CCTCT CCTT C-TT CTTT CTTT CCTCT
          1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT -CTTT

             *      *                           *          
       1448 CCTT CTTC CTTT CTTT CTTT CTTT CCTTT ATTT CTTT C
          1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT C

       1486 CCGTTTATTT


Statistics
Matches: 63,  Mismatches: 14, Indels: 10
        0.72            0.16        0.11

Matches are distributed among these distances:
   3    6  0.10
   4   47  0.75
   5   10  0.16

ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64


Consensus pattern (4 bp):   
CTTT

Found at i:1468 original size:25 final size:20

Alignment explanation


    Indices: 1407--1464  Score: 107
    Period size: 20  Copynumber: 2.9  Consensus size: 20

       1397 TACCTTTATT

                                
       1407 TCCTTCTTCTTTCTTTCCTC
          1 TCCTTCTTCTTTCTTTCCTC

                                
       1427 TCCTTCTTCTTTCTTTCCTC
          1 TCCTTCTTCTTTCTTTCCTC

                              
       1447 TCCTTCTTCCTTTCTTTC
          1 TCCTTCTT-CTTTCTTTC

       1465 TTTCTTTCCT


Statistics
Matches: 37,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  20   28  0.76
  21    9  0.24

ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60


Consensus pattern (20 bp):   
TCCTTCTTCTTTCTTTCCTC

Found at i:1473 original size:17 final size:17

Alignment explanation


    Indices: 1400--1485  Score: 74
    Period size: 17  Copynumber: 5.3  Consensus size: 17

       1390 AACACATTAC

                *            
       1400 CTTTATTTCC-TTC-TT
          1 CTTTCTTTCCTTTCTTT

                       *  *  
       1415 CTTTCTTTCCTCTCCTT
          1 CTTTCTTTCCTTTCTTT

                            * 
       1432 C-TTCTTT-CTTTCCTCT
          1 CTTTCTTTCCTTT-CTTT

             *               
       1448 CCTTC-TTCCTTTCTTT
          1 CTTTCTTTCCTTTCTTT

                         *   
       1464 CTTTCTTTCCTTTATTT
          1 CTTTCTTTCCTTTCTTT

                 
       1481 CTTTC
          1 CTTTC

       1486 CCGTTTATTT


Statistics
Matches: 57,  Mismatches: 8, Indels: 10
        0.76            0.11        0.13

Matches are distributed among these distances:
  15   12  0.21
  16   20  0.35
  17   25  0.44

ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64


Consensus pattern (17 bp):   
CTTTCTTTCCTTTCTTT
Done.