Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009205.1 Kokia drynarioides strain JFW-HI SEQ_123910, 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: 8311
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35


Found at i:2572 original size:2 final size:2

Alignment explanation


    Indices: 2565--2602  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       2555 AAATTAAAGT

                                                                    
       2565 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2603 AACTATAATC


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:4580 original size:16 final size:17

Alignment explanation


    Indices: 4547--4583  Score: 51
    Period size: 16  Copynumber: 2.3  Consensus size: 17

       4537 TATCACTACT

                       *     
       4547 AATT-TAAAATTTTATA
          1 AATTATAAAATGTTATA

                             
       4563 AATTATAAAATGTT-TA
          1 AATTATAAAATGTTATA

                 
       4579 AATTA
          1 AATTA

       4584 AAATTTTATT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  16   11  0.58
  17    8  0.42

ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46


Consensus pattern (17 bp):   
AATTATAAAATGTTATA

Found at i:5429 original size:12 final size:12

Alignment explanation


    Indices: 5388--5430  Score: 50
    Period size: 12  Copynumber: 3.6  Consensus size: 12

       5378 GCAGCAAAAT

                       *
       5388 AACAAAAATAAA
          1 AACAAAAATAAC

                    * * 
       5400 AACAAAAACAGC
          1 AACAAAAATAAC

                        
       5412 AACAAAAATAAC
          1 AACAAAAATAAC

             *     
       5424 ATCAAAA
          1 AACAAAA

       5431 CAGTAAAAAA


Statistics
Matches: 25,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  12   25  1.00

ACGTcount: A:0.74, C:0.16, G:0.02, T:0.07


Consensus pattern (12 bp):   
AACAAAAATAAC

Found at i:5430 original size:23 final size:23

Alignment explanation


    Indices: 5388--5489  Score: 116
    Period size: 23  Copynumber: 4.4  Consensus size: 23

       5378 GCAGCAAAAT

                       * *          
       5388 AACAAAAATAAAAACAAAAACAGC
          1 AACAAAAATAACATC-AAAACAGC

                                  *
       5412 AACAAAAATAACATCAAAACAGT
          1 AACAAAAATAACATCAAAACAGC

              *       *           *
       5435 AAAAAAAATAGCATCAAAACAGT
          1 AACAAAAATAACATCAAAACAGC

                    *              
       5458 AA-AAAAACAACATCAAAACAGC
          1 AACAAAAATAACATCAAAACAGC

               *      
       5480 AACCAAAATA
          1 AACAAAAATA

       5490 GTAAAAAAAC


Statistics
Matches: 67,  Mismatches: 10, Indels: 3
        0.84            0.12        0.04

Matches are distributed among these distances:
  22   19  0.28
  23   35  0.52
  24   13  0.19

ACGTcount: A:0.69, C:0.18, G:0.05, T:0.09


Consensus pattern (23 bp):   
AACAAAAATAACATCAAAACAGC

Found at i:5488 original size:45 final size:46

Alignment explanation


    Indices: 5404--5514  Score: 127
    Period size: 45  Copynumber: 2.5  Consensus size: 46

       5394 AATAAAAACA

                            *             *               
       5404 AAAACAGCAACAAAAATAACATCAAAACAGTAAAAAAAATAGCATC
          1 AAAACAGCAACAAAAACAACATCAAAACAGCAAAAAAAATAGCATC

                   *                         **       * **
       5450 AAAACAGTAA-AAAAACAACATCAAAACAGCAACCAAAATAGTAAA
          1 AAAACAGCAACAAAAACAACATCAAAACAGCAAAAAAAATAGCATC

                       *         
       5495 AAAACAGC-ACTAAAACAACA
          1 AAAACAGCAACAAAAACAACA

       5515 ATATAAAATT


Statistics
Matches: 54,  Mismatches: 10, Indels: 3
        0.81            0.15        0.04

Matches are distributed among these distances:
  44    1  0.02
  45   44  0.81
  46    9  0.17

ACGTcount: A:0.66, C:0.19, G:0.06, T:0.09


Consensus pattern (46 bp):   
AAAACAGCAACAAAAACAACATCAAAACAGCAAAAAAAATAGCATC
Done.