Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000056.1 Kokia drynarioides strain JFW-HI SEQ_110591, 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: 9332
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:3273 original size:38 final size:36

Alignment explanation


    Indices: 3231--3338  Score: 111
    Period size: 38  Copynumber: 3.0  Consensus size: 36

       3221 TTAAAAACAA

                                                  
       3231 AATTAAATTTTATATTAATATTAATATTAAATAAATAT
          1 AATTAAATTTTATATTAATA-TAATA-TAAATAAATAT

                 *    *                         
       3269 AATTATA-TTGATA-T-A-ATAATA-AAATAAATAT
          1 AATTAAATTTTATATTAATATAATATAAATAAATAT

                                                   
       3300 AATT-AATATTTATATTAATATAATAATAAAATAAATAT
          1 AATTAAAT-TTTATATTAATATAAT-AT-AAATAAATAT

             
       3338 A
          1 A

       3339 TGAGGGGAGG


Statistics
Matches: 58,  Mismatches: 4, Indels: 16
        0.74            0.05        0.21

Matches are distributed among these distances:
  30    1  0.02
  31   14  0.24
  32    5  0.09
  33    6  0.10
  34    2  0.03
  35    6  0.10
  36    2  0.03
  37    5  0.09
  38   17  0.29

ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43


Consensus pattern (36 bp):   
AATTAAATTTTATATTAATATAATATAAATAAATAT

Found at i:3299 original size:17 final size:17

Alignment explanation


    Indices: 3279--3338  Score: 66
    Period size: 17  Copynumber: 3.3  Consensus size: 17

       3269 AATTATATTG

                             
       3279 ATATAATAATAAAATAA
          1 ATATAATAATAAAATAA

                            *  * 
       3296 ATATAATTAATATTTATATTA
          1 ATATAA-TAATA---AAATAA

                             
       3317 ATATAATAATAAAATAA
          1 ATATAATAATAAAATAA

                 
       3334 ATATA
          1 ATATA

       3339 TGAGGGGAGG


Statistics
Matches: 35,  Mismatches: 4, Indels: 8
        0.74            0.09        0.17

Matches are distributed among these distances:
  17   15  0.43
  18    5  0.14
  20    5  0.14
  21   10  0.29

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (17 bp):   
ATATAATAATAAAATAA

Found at i:4783 original size:23 final size:23

Alignment explanation


    Indices: 4736--4784  Score: 64
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       4726 TATGTTCTAA

                      *         *  
       4736 AACATGTTTGTTTAATGTTAGTG
          1 AACATGTTTGATTAATGTTAATG

                                    
       4759 AACATGTTTGATTAA-GTTAAATG
          1 AACATGTTTGATTAATGTT-AATG

               
       4782 AAC
          1 AAC

       4785 TTTTTCGTGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  22    3  0.13
  23   20  0.87

ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41


Consensus pattern (23 bp):   
AACATGTTTGATTAATGTTAATG

Found at i:9294 original size:20 final size:21

Alignment explanation


    Indices: 9255--9297  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       9245 TAAATACAAA

                     *   *       
       9255 AATTATATATTTTTATTATAT
          1 AATTATATAATTTAATTATAT

                                 
       9276 AATTA-ATAATTTAATTATAT
          1 AATTATATAATTTAATTATAT

              
       9296 AA
          1 AA

       9298 AAGAAGGAAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   15  0.75
  21    5  0.25

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (21 bp):   
AATTATATAATTTAATTATAT
Done.