Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012857.1 Kokia drynarioides strain JFW-HI SEQ_127871, 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: 8189
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34


Found at i:537 original size:26 final size:27

Alignment explanation


    Indices: 498--550  Score: 74
    Period size: 25  Copynumber: 2.0  Consensus size: 27

        488 TTCTCGGATA

                                         
        498 AAAAAATTGCAAATTTTTTTGGT-TTGGT
          1 AAAAAATT-CAAA-TTTTTTGGTGTTGGT

                                      
        526 AAAAAATT-AAATTTTTTGGTGTTGG
          1 AAAAAATTCAAATTTTTTGGTGTTGG

        551 CCATGTAATG


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  25    9  0.38
  26    7  0.29
  28    8  0.33

ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45


Consensus pattern (27 bp):   
AAAAAATTCAAATTTTTTGGTGTTGGT

Found at i:4678 original size:86 final size:86

Alignment explanation


    Indices: 4461--4845  Score: 589
    Period size: 86  Copynumber: 4.5  Consensus size: 86

       4451 AATTTAACAT

                          **                     *         *      *          
       4461 TATTTAAATAAAAAAGATTATTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAAT
          1 TATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT

                        *       * 
       4526 ACATTATTTATCAAATTTT-CA
         66 ACATTATTTAT-TAATTTTATA

                       *                    *         *       *              
       4547 TATTTAAAGTACAAATTA-T-TT-TTATATTATAATTTTTATTAAATAATTTGTTGATTTGACAA
          1 TATTTAAA-TAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAA

            *                     
       4609 CACATTATTTATTAATTTTATA
         65 TACATTATTTATTAATTTTATA

                                                                             
       4631 TATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
          1 TATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT

                         *       
       4696 ACATTATTTATTAGTTTTATA
         66 ACATTATTTATTAATTTTATA

                          *                                                  
       4717 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
          1 TATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT

                                 
       4782 ACATTATTTATTAATTTTATA
         66 ACATTATTTATTAATTTTATA

                                     *                 
       4803 TATTTAAATAAAAATTATTATTATTTTATTACAATTTTTATCA
          1 TATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCA

       4846 TATTTTAAAT


Statistics
Matches: 272,  Mismatches: 22, Indels: 10
        0.89            0.07        0.03

Matches are distributed among these distances:
  83   14  0.05
  84   56  0.21
  85    4  0.01
  86  192  0.71
  87    6  0.02

ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50


Consensus pattern (86 bp):   
TATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
ACATTATTTATTAATTTTATA

Found at i:5151 original size:17 final size:18

Alignment explanation


    Indices: 5129--5166  Score: 69
    Period size: 17  Copynumber: 2.2  Consensus size: 18

       5119 ATGGATGTTC

                              
       5129 AACCTTTCATCTTCTT-T
          1 AACCTTTCATCTTCTTGT

                              
       5146 AACCTTTCATCTTCTTGT
          1 AACCTTTCATCTTCTTGT

               
       5164 AAC
          1 AAC

       5167 TACTTTTTTC


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17   16  0.80
  18    4  0.20

ACGTcount: A:0.21, C:0.29, G:0.03, T:0.47


Consensus pattern (18 bp):   
AACCTTTCATCTTCTTGT

Found at i:7824 original size:17 final size:17

Alignment explanation


    Indices: 7804--7845  Score: 57
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       7794 CTCCCTTGAC

                          *  
       7804 CTTTAACCTTCCATTTT
          1 CTTTAACCTTCCATATT

                      *      
       7821 CTTTAACCTTTCATATT
          1 CTTTAACCTTCCATATT

                    
       7838 CTTGTAAC
          1 CTT-TAAC

       7846 TACTTTTCCT


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

Matches are distributed among these distances:
  17   18  0.82
  18    4  0.18

ACGTcount: A:0.21, C:0.26, G:0.02, T:0.50


Consensus pattern (17 bp):   
CTTTAACCTTCCATATT
Done.