Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004222.1 Kokia drynarioides strain JFW-HI SEQ_117478, 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, 946

Length: 1577
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37


Found at i:255 original size:4 final size:4

Alignment explanation


    Indices: 246--331  Score: 77
    Period size: 4  Copynumber: 21.2  Consensus size: 4

        236 AACACATTAC

                                             *   *                       
        246 CTTT CTTT CTTT C-TT CTTT CTTT CCTCT CCTT C-TT CTTT CTTT CTTTT
          1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT C-TTT

             *      *         *  *                         
        294 CCTT CTTC CTTT CTTC CCTT CTTTT CTTT CTTT CTTT C
          1 CTTT CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT C

        332 CCGTTTATTT


Statistics
Matches: 66,  Mismatches: 11, Indels: 10
        0.76            0.13        0.11

Matches are distributed among these distances:
   3    6  0.09
   4   50  0.76
   5   10  0.15

ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66


Consensus pattern (4 bp):   
CTTT

Found at i:281 original size:20 final size:20

Alignment explanation


    Indices: 256--327  Score: 87
    Period size: 20  Copynumber: 3.7  Consensus size: 20

        246 CTTTCTTTCT

                                
        256 TTCTTCTTTCTTTCCTCTCC
          1 TTCTTCTTTCTTTCCTCTCC

                          * *   
        276 TTCTTCTTTCTTTCTTTTCC
          1 TTCTTCTTTCTTTCCTCTCC

                               * 
        296 TTCTTCCTTTC-TTCC-CTTC
          1 TTCTT-CTTTCTTTCCTCTCC

                          
        315 TT-TTCTTTCTTTC
          1 TTCTTCTTTCTTTC

        328 TTTCCCGTTT


Statistics
Matches: 45,  Mismatches: 5, Indels: 6
        0.80            0.09        0.11

Matches are distributed among these distances:
  17    5  0.11
  18    5  0.11
  19    4  0.09
  20   26  0.58
  21    5  0.11

ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65


Consensus pattern (20 bp):   
TTCTTCTTTCTTTCCTCTCC

Found at i:324 original size:17 final size:16

Alignment explanation


    Indices: 246--325  Score: 72
    Period size: 17  Copynumber: 4.7  Consensus size: 16

        236 AACACATTAC

                        *   
        246 CTTTCTTTCTT-TCTT
          1 CTTTCTTTCTTCCCTT

                                
        261 CTTTCTTTCCTCTCCTTCTT
          1 CTTTCTTT-CT-TCC--CTT

                        *    
        281 CTTTCTTTCTTTTCCTT
          1 CTTTCTTTC-TTCCCTT

               *            
        298 CTTCCTTTCTTCCCTT
          1 CTTTCTTTCTTCCCTT

                        
        314 CTTTTCTTTCTT
          1 C-TTTCTTTCTT

        326 TCTTTCCCGT


Statistics
Matches: 53,  Mismatches: 5, Indels: 12
        0.76            0.07        0.17

Matches are distributed among these distances:
  15    8  0.15
  16    9  0.17
  17   21  0.40
  19    3  0.06
  20   12  0.23

ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66


Consensus pattern (16 bp):   
CTTTCTTTCTTCCCTT

Found at i:1557 original size:2 final size:2

Alignment explanation


    Indices: 1550--1575  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1540 ACTTCATGAA

                                                  
       1550 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       1576 TT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.