Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004468.1 Kokia drynarioides strain JFW-HI SEQ_117885, 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: 14061
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36


Found at i:4815 original size:15 final size:15

Alignment explanation


    Indices: 4780--4818  Score: 62
    Period size: 14  Copynumber: 2.7  Consensus size: 15

       4770 TCCCCAAATG

                           
       4780 TCAAATATTTCTACC
          1 TCAAATATTTCTACC

                      *    
       4795 TC-AATATTTTTACC
          1 TCAAATATTTCTACC

                      
       4809 TCAAATATTT
          1 TCAAATATTT

       4819 AGAGACACTG


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  14   13  0.59
  15    9  0.41

ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46


Consensus pattern (15 bp):   
TCAAATATTTCTACC

Found at i:10205 original size:29 final size:29

Alignment explanation


    Indices: 10164--10258  Score: 118
    Period size: 34  Copynumber: 3.1  Consensus size: 29

      10154 TGTTCAACTT

                                          
      10164 TTGATCATTTAACCTTCCATCTTCCTTAAC
          1 TTGATC-TTTAACCTTCCATCTTCCTTAAC

                                              
      10194 TTGATCTTTAACCTTCCATCTTCCTTAACCTCCC
          1 TTGATCTTTAACCTTCCATCTTCCTTAA-----C

              *            *             
      10228 TTAATCTTTAACCTTTCATCTTCCTTAAC
          1 TTGATCTTTAACCTTCCATCTTCCTTAAC

              
      10257 TT
          1 TT

      10259 TTCATATTCT


Statistics
Matches: 58,  Mismatches: 2, Indels: 11
        0.82            0.03        0.15

Matches are distributed among these distances:
  29   25  0.43
  30    6  0.10
  34   27  0.47

ACGTcount: A:0.21, C:0.32, G:0.02, T:0.45


Consensus pattern (29 bp):   
TTGATCTTTAACCTTCCATCTTCCTTAAC

Found at i:10223 original size:17 final size:17

Alignment explanation


    Indices: 10172--10256  Score: 72
    Period size: 17  Copynumber: 5.3  Consensus size: 17

      10162 TTTTGATCAT

                             
      10172 TTAACCTTCCATCTTCC
          1 TTAACCTTCCATCTTCC

                     *       
      10189 TTAA-CTT-GATC-T--
          1 TTAACCTTCCATCTTCC

                             
      10201 TTAACCTTCCATCTTCC
          1 TTAACCTTCCATCTTCC

                   *  * **  *
      10218 TTAACCTCCCTTAATCT
          1 TTAACCTTCCATCTTCC

                    *        
      10235 TTAACCTTTCATCTTCC
          1 TTAACCTTCCATCTTCC

                 
      10252 TTAAC
          1 TTAAC

      10257 TTTTCATATT


Statistics
Matches: 50,  Mismatches: 13, Indels: 10
        0.68            0.18        0.14

Matches are distributed among these distances:
  12    4  0.08
  13    3  0.06
  14    4  0.08
  15    4  0.08
  16    3  0.06
  17   32  0.64

ACGTcount: A:0.21, C:0.34, G:0.01, T:0.44


Consensus pattern (17 bp):   
TTAACCTTCCATCTTCC

Found at i:11530 original size:9 final size:9

Alignment explanation


    Indices: 11487--11522  Score: 54
    Period size: 9  Copynumber: 3.8  Consensus size: 9

      11477 TTATTATATT

                     
      11487 ATATTTTAA
          1 ATATTTTAA

                       
      11496 ACTATTTATAA
          1 A-TATTT-TAA

                     
      11507 ATATTTTAA
          1 ATATTTTAA

                   
      11516 ATATTTT
          1 ATATTTT

      11523 GAAAATTTAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
   9   11  0.44
  10   10  0.40
  11    4  0.16

ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56


Consensus pattern (9 bp):   
ATATTTTAA
Done.