Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009232.1 Kokia drynarioides strain JFW-HI SEQ_123937, 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: 16344
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35


Found at i:3213 original size:16 final size:16

Alignment explanation


    Indices: 3192--3224  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       3182 ATAATCACAT

                            
       3192 CTTTTAACAATAAACA
          1 CTTTTAACAATAAACA

                            
       3208 CTTTTAACAATAAACA
          1 CTTTTAACAATAAACA

             
       3224 C
          1 C

       3225 GATTCATTGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30


Consensus pattern (16 bp):   
CTTTTAACAATAAACA

Found at i:4325 original size:35 final size:36

Alignment explanation


    Indices: 4276--4352  Score: 138
    Period size: 35  Copynumber: 2.2  Consensus size: 36

       4266 TTTTTAAACT

                                                
       4276 AATGAAAATCAACTCTAAAATTGTCAACAAC-AAAA
          1 AATGAAAATCAACTCTAAAATTGTCAACAACAAAAA

                     *                          
       4311 AATGAAAATGAACTCTAAAATTGTCAACAACAAAAA
          1 AATGAAAATCAACTCTAAAATTGTCAACAACAAAAA

                  
       4347 AATGAA
          1 AATGAA

       4353 CTCTAAAATT


Statistics
Matches: 40,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  35   30  0.75
  36   10  0.25

ACGTcount: A:0.58, C:0.14, G:0.08, T:0.19


Consensus pattern (36 bp):   
AATGAAAATCAACTCTAAAATTGTCAACAACAAAAA

Found at i:4350 original size:30 final size:32

Alignment explanation


    Indices: 4279--4362  Score: 118
    Period size: 35  Copynumber: 2.6  Consensus size: 32

       4269 TTAAACTAAT

                  *                           
       4279 GAAAATCAACTCTAAAATTGTCAACAACAAAAAA
          1 GAAAATGAACTCTAAAATTGTCAACAAC--AAAA

                                             
       4313 TGAAAATGAACTCTAAAATTGTCAACAAC-AAA
          1 -GAAAATGAACTCTAAAATTGTCAACAACAAAA

                               
       4345 -AAAATGAACTCTAAAATT
          1 GAAAATGAACTCTAAAATT

       4363 ATTTAACATT


Statistics
Matches: 48,  Mismatches: 1, Indels: 5
        0.89            0.02        0.09

Matches are distributed among these distances:
  30   18  0.38
  32    3  0.06
  35   27  0.56

ACGTcount: A:0.56, C:0.15, G:0.07, T:0.21


Consensus pattern (32 bp):   
GAAAATGAACTCTAAAATTGTCAACAACAAAA

Found at i:10996 original size:20 final size:21

Alignment explanation


    Indices: 10960--11009  Score: 52
    Period size: 20  Copynumber: 2.4  Consensus size: 21

      10950 ATTAGCATGG

                             *    
      10960 TTTATATTAAGTGTAAATA-GA
          1 TTTA-ATTAAGTGTAAAAATGA

                                  
      10981 TTTAATTAAGAT-TAAAAATGA
          1 TTTAATTAAG-TGTAAAAATGA

                     
      11002 -TTAATTAA
          1 TTTAATTAA

      11010 AGCTTAATGA


Statistics
Matches: 26,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  20   19  0.73
  21    7  0.27

ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42


Consensus pattern (21 bp):   
TTTAATTAAGTGTAAAAATGA

Found at i:15676 original size:16 final size:17

Alignment explanation


    Indices: 15636--15688  Score: 58
    Period size: 16  Copynumber: 3.2  Consensus size: 17

      15626 AATTAAAACA

                              
      15636 TTTAGAATTATATTTAA-
          1 TTTAGAATTA-ATTTAAT

                             
      15653 -TTAGAATTAATTTAAT
          1 TTTAGAATTAATTTAAT

                     *        
      15669 TTTA-AATTCATGTTAAT
          1 TTTAGAATTAAT-TTAAT

               
      15686 TTT
          1 TTT

      15689 TTTGGTTTTT


Statistics
Matches: 32,  Mismatches: 1, Indels: 6
        0.82            0.03        0.15

Matches are distributed among these distances:
  15    6  0.19
  16   15  0.47
  17   11  0.34

ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55


Consensus pattern (17 bp):   
TTTAGAATTAATTTAAT

Found at i:16104 original size:88 final size:88

Alignment explanation


    Indices: 15942--16115  Score: 206
    Period size: 88  Copynumber: 2.0  Consensus size: 88

      15932 TCTTGAATTG

                                                                *            
      15942 GATTTATTTTATTTTTAGCCCTAAGATTTAGATTTTAGGGTTTAACAGATTTTATTAAATATTAG
          1 GATTTATTTTATTTTTAGCCCTAAGATTTAGATTTTAGGGTTTAACAGATTTAATTAAATATTAG

              *       *            
      16007 TTCGAAATTTTGGTTATGGATCA
         66 TTAGAAATTTGGGTTATGGATCA

                                  * *     **      **     * *         *  *    
      16030 GATTTATTTTATTTTTAGCCCTGATATTTATTTTTTAGTTTTTAATATATTTAATTATATTTTAA
          1 GATTTATTTTATTTTTAGCCCTAAGATTTAGATTTTAGGGTTTAACAGATTTAATTAAATATT-A

            *                     
      16095 TTTAG-AATTTGGGTTATGGAT
         65 GTTAGAAATTTGGGTTATGGAT

      16116 ATTCATTGCA


Statistics
Matches: 71,  Mismatches: 14, Indels: 2
        0.82            0.16        0.02

Matches are distributed among these distances:
  88   67  0.94
  89    4  0.06

ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53


Consensus pattern (88 bp):   
GATTTATTTTATTTTTAGCCCTAAGATTTAGATTTTAGGGTTTAACAGATTTAATTAAATATTAG
TTAGAAATTTGGGTTATGGATCA
Done.