Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005776.1 Kokia drynarioides strain JFW-HI SEQ_120043, 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: 13670
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:12359 original size:29 final size:29

Alignment explanation


    Indices: 12327--12485  Score: 155
    Period size: 28  Copynumber: 5.4  Consensus size: 29

      12317 TTTCGAAAGT

                *                        
      12327 TTCGAGGTAAAAAATGGGATTTTTGGAAG
          1 TTCGGGGTAAAAAATGGGATTTTTGGAAG

                              * *          
      12356 TTCGGGGGT--AAAATGGTAATTTTGGAAGG
          1 TTC-GGGGTAAAAAATGGGATTTTTGGAA-G

                    *       *       *    
      12385 TTCGGGGTCAAAAATGAGATTTTTTGAAG
          1 TTCGGGGTAAAAAATGGGATTTTTGGAAG

               *              * *          
      12414 TTTAGGGGT--AAAATGGTAATTTTGGAAGG
          1 -TTCGGGGTAAAAAATGGGATTTTTGGAA-G

                                          
      12443 TTCGGGGTAAAAAAATGGGATTTTTGGAAG
          1 TTCGGGGT-AAAAAATGGGATTTTTGGAAG

                         
      12473 TTCGGGGGTAAAA
          1 TTC-GGGGTAAAA

      12486 TAGTAATATT


Statistics
Matches: 105,  Mismatches: 15, Indels: 19
        0.76            0.11        0.14

Matches are distributed among these distances:
  28   42  0.40
  29    9  0.09
  30   33  0.31
  31   21  0.20

ACGTcount: A:0.31, C:0.04, G:0.33, T:0.31


Consensus pattern (29 bp):   
TTCGGGGTAAAAAATGGGATTTTTGGAAG

Found at i:12409 original size:59 final size:58

Alignment explanation


    Indices: 12299--12499  Score: 267
    Period size: 58  Copynumber: 3.4  Consensus size: 58

      12289 TTCGGATGCA

                  *    *    *      *   *    *                          
      12299 CGGGGGCAAAAGGGTAGTTTTCGAAAGTTTCGAGGTAAAAAATGGGATTTTTGGAAGTT
          1 CGGGGGTAAAATGGTAATTTT-GGAAGGTTCGGGGTAAAAAATGGGATTTTTGGAAGTT

                                               *       *       *      
      12358 CGGGGGTAAAATGGTAATTTTGGAAGGTTCGGGGTCAAAAATGAGATTTTTTGAAGTT
          1 CGGGGGTAAAATGGTAATTTTGGAAGGTTCGGGGTAAAAAATGGGATTTTTGGAAGTT

            **                                                         
      12416 TAGGGGTAAAATGGTAATTTTGGAAGGTTCGGGGTAAAAAAATGGGATTTTTGGAAGTT
          1 CGGGGGTAAAATGGTAATTTTGGAAGGTTCGGGGT-AAAAAATGGGATTTTTGGAAGTT

                        *            
      12475 CGGGGGTAAAATAGTAATATTTGGA
          1 CGGGGGTAAAATGGTAAT-TTTGGA

      12500 CAGTTTAGGG


Statistics
Matches: 123,  Mismatches: 17, Indels: 3
        0.86            0.12        0.02

Matches are distributed among these distances:
  58   64  0.52
  59   53  0.43
  60    6  0.05

ACGTcount: A:0.31, C:0.04, G:0.33, T:0.31


Consensus pattern (58 bp):   
CGGGGGTAAAATGGTAATTTTGGAAGGTTCGGGGTAAAAAATGGGATTTTTGGAAGTT

Found at i:12498 original size:29 final size:27

Alignment explanation


    Indices: 12347--12504  Score: 120
    Period size: 28  Copynumber: 5.4  Consensus size: 27

      12337 AAAATGGGAT

                                   *    
      12347 TTTTGGAAGTTCGGGGGTAAAATGGTAA
          1 TTTTGGAAGTTC-GGGGTAAAATAGTAA

                                          *
      12375 TTTTGGAAGGTTCGGGGTCAAAAATGAG-AT
          1 TTTTGGAA-GTTCGGGGT--AAAAT-AGTAA

                *       *          *    
      12405 TTTTTGAAGTTTAGGGGTAAAATGGTAA
          1 TTTTGGAAG-TTCGGGGTAAAATAGTAA

                                      * * *
      12433 TTTTGGAAGGTTCGGGGTAAAAAAATGGGAT
          1 TTTTGGAA-GTTCGGGGT---AAAATAGTAA

                                        
      12464 TTTTGGAAGTTCGGGGGTAAAATAGTAA
          1 TTTTGGAAGTTC-GGGGTAAAATAGTAA

                         
      12492 TATTTGGACAGTT
          1 T-TTTGGA-AGTT

      12505 TAGGGACCTC


Statistics
Matches: 104,  Mismatches: 13, Indels: 24
        0.74            0.09        0.17

Matches are distributed among these distances:
  27    1  0.01
  28   41  0.39
  29   12  0.12
  30   28  0.27
  31   22  0.21

ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34


Consensus pattern (27 bp):   
TTTTGGAAGTTCGGGGTAAAATAGTAA

Found at i:13570 original size:15 final size:15

Alignment explanation


    Indices: 13530--13571  Score: 66
    Period size: 15  Copynumber: 2.8  Consensus size: 15

      13520 TATTATTAAT

                      *    
      13530 ATTATTATTGATGTC
          1 ATTATTATTGTTGTC

                           
      13545 ATTATTATTGTTGTC
          1 ATTATTATTGTTGTC

                *       
      13560 ATTAATATTGTT
          1 ATTATTATTGTT

      13572 AATGATATTA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   25  1.00

ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57


Consensus pattern (15 bp):   
ATTATTATTGTTGTC
Done.