Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007950.1 Kokia drynarioides strain JFW-HI SEQ_122598, 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: 37541
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:49 original size:2 final size:2

Alignment explanation


    Indices: 1--33  Score: 50
    Period size: 2  Copynumber: 17.0  Consensus size: 2

                                 *                            
          1 TA TA TA TA TA TA TA CA TA TA TA TA TA -A TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         34 ATAAACTCAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   1    1  0.04
   2   27  0.96

ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45


Consensus pattern (2 bp):   
TA

Found at i:5485 original size:17 final size:18

Alignment explanation


    Indices: 5465--5509  Score: 51
    Period size: 17  Copynumber: 2.7  Consensus size: 18

       5455 TGAAGATTGA

                              
       5465 TTAATATTTTAAAT-AAT
          1 TTAATATTTTAAATAAAT

                      **      
       5482 TTAAT-TTTTTTATAAAT
          1 TTAATATTTTAAATAAAT

                        
       5499 TT-ATATTTTAA
          1 TTAATATTTTAA

       5510 GTGTACAACC


Statistics
Matches: 22,  Mismatches: 4, Indels: 4
        0.73            0.13        0.13

Matches are distributed among these distances:
  16    8  0.36
  17   14  0.64

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


Consensus pattern (18 bp):   
TTAATATTTTAAATAAAT

Found at i:23506 original size:32 final size:29

Alignment explanation


    Indices: 23470--23541  Score: 90
    Period size: 32  Copynumber: 2.3  Consensus size: 29

      23460 TCCATTCATA

                           *                
      23470 TTATTTTTTTTAATTTTTTAAAAATATTTATT
          1 TTATTTTTTTTAA-TATTTAAAAA-ATTTA-T

                                          
      23502 TTATTTTATTTTAATATTTAAAAAATTTAT
          1 TTATTTT-TTTTAATATTTAAAAAATTTAT

            *         
      23532 ATATTTTTTT
          1 TTATTTTTTT

      23542 ATTTATTGAA


Statistics
Matches: 37,  Mismatches: 2, Indels: 5
        0.84            0.05        0.11

Matches are distributed among these distances:
  29    3  0.08
  30    7  0.19
  31    5  0.14
  32   16  0.43
  33    6  0.16

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (29 bp):   
TTATTTTTTTTAATATTTAAAAAATTTAT

Found at i:23526 original size:33 final size:34

Alignment explanation


    Indices: 23470--23545  Score: 97
    Period size: 33  Copynumber: 2.3  Consensus size: 34

      23460 TCCATTCATA

                           *   *               
      23470 TTATTTT-TTTTAATTTTTTAAAAATATT-TAT-T
          1 TTATTTTATTTTAATATTTAAAAAAT-TTATATAT

                                              
      23502 TTATTTTATTTTAATATTTAAAAAATTTATATAT
          1 TTATTTTATTTTAATATTTAAAAAATTTATATAT

                       
      23536 TT-TTTTATTT
          1 TTATTTTATTT

      23546 ATTGAAATTA


Statistics
Matches: 39,  Mismatches: 2, Indels: 5
        0.85            0.04        0.11

Matches are distributed among these distances:
  32    9  0.23
  33   27  0.69
  34    3  0.08

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (34 bp):   
TTATTTTATTTTAATATTTAAAAAATTTATATAT

Found at i:25388 original size:31 final size:29

Alignment explanation


    Indices: 25320--25394  Score: 80
    Period size: 31  Copynumber: 2.5  Consensus size: 29

      25310 TATTAAATTA

                                         
      25320 AAATTTCATATATAAAAACACATAAAATC
          1 AAATTTCATATATAAAAACACATAAAATC

             *                 *      *  *  
      25349 -GATGTTCATATATAACATTACACATGAACTC
          1 AAAT-TTCATATATAA-A-AACACATAAAATC

                           
      25380 AAATTTCATATATAA
          1 AAATTTCATATATAA

      25395 TTTTGATATT


Statistics
Matches: 37,  Mismatches: 5, Indels: 6
        0.77            0.10        0.12

Matches are distributed among these distances:
  28    2  0.05
  29   11  0.30
  30    1  0.03
  31   21  0.57
  32    2  0.05

ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32


Consensus pattern (29 bp):   
AAATTTCATATATAAAAACACATAAAATC
Done.