Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008347.1 Kokia drynarioides strain JFW-HI SEQ_123014, 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: 5009
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Found at i:2812 original size:17 final size:17

Alignment explanation


    Indices: 2761--2817  Score: 60
    Period size: 17  Copynumber: 3.3  Consensus size: 17

       2751 CCCAATGAAC

                        *     
       2761 TTAAATTTATTTTTAAAT
          1 TTAAATTTA-TTATAAAT

                     ****    
       2779 TTAAATTTAGCCGAAAT
          1 TTAAATTTATTATAAAT

                             
       2796 TTAAATTTATTATAAAT
          1 TTAAATTTATTATAAAT

                 
       2813 TTAAA
          1 TTAAA

       2818 ATGTCCAAGG


Statistics
Matches: 31,  Mismatches: 8, Indels: 1
        0.77            0.20        0.03

Matches are distributed among these distances:
  17   22  0.71
  18    9  0.29

ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49


Consensus pattern (17 bp):   
TTAAATTTATTATAAAT

Found at i:3323 original size:200 final size:199

Alignment explanation


    Indices: 2980--3565  Score: 852
    Period size: 200  Copynumber: 2.9  Consensus size: 199

       2970 GCACGGTCAT

                                                                             
       2980 TCTCCCTGATGAGATACTGAGGAGAAGACCCAAACGAGGCTCAAAGCAAGCAAAATCTTCGAACC
          1 TCTCCCTGATGAGATACTGAGGAGAAGACCCAAACGAGGCTCAAAGCAAGC-AAATCTTCGAACC

                                         *  *                                
       3045 CCAGCTTCTTGATGAGACACTGAGAAGCGAGCTGAAGCAATAAATGGTTAGCTTCCTGATGAGAT
         65 CCAGCTTCTTGATGAGACACTGAGAAGCGGGCCGAAGCAATAAATGGTTAGCTTCCTGATGAGAT

              *                                                              
       3110 ACAGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACGATGATGG
        130 ACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACGATGATGG

                 
       3175 GACCA
        195 GACCA

                                   *           *                     *       
       3180 TCTCCCTGATGAGATACTGAGGATAAGACCCAAACAAGGCTCAAAGCAAGCAATATCATCGAACC
          1 TCTCCCTGATGAGATACTGAGGAGAAGACCCAAACGAGGCTCAAAGCAAGCAA-ATCTTCGAACC

                                                                   *         
       3245 CCAGCTTCTTGATGAGACACTGAGAAGCGGGCCGAAGCAATAAATGGTTAGCTTCTTGATGAGAT
         65 CCAGCTTCTTGATGAGACACTGAGAAGCGGGCCGAAGCAATAAATGGTTAGCTTCCTGATGAGAT

                                           *                    *            
       3310 ACGGAGAAGTGAACCAAATTCGTCTTCCTGACGAGATACAGAGAAGCGGATTAAAACGATGATGG
        130 ACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACGATGATGG

                 
       3375 GACCA
        195 GACCA

               *          *             *                 **            *    
       3380 TCTTCCTGATGAGACACTGAGGAGAAGATCCAAACGAGGCTCAAAGTGAGCCAAATCTTTTGAAC
          1 TCTCCCTGATGAGATACTGAGGAGAAGACCCAAACGAGGCTCAAAGCAAG-CAAATC-TTCGAAC

              *      **                 **  **       *           *           
       3445 CCTAGCTTCCCGATGAGACACTGAGAAGTAGGTGGAAGC--CAAATGGTTAGCCTCCTGATGAGA
         64 CCCAGCTTCTTGATGAGACACTGAGAAGCGGGCCGAAGCAATAAATGGTTAGCTTCCTGATGAGA

            * *  *     *                *               *             
       3508 GATGGGGAAGTAAACCAAATTCGTCTTCTTGATGAGATACAGAGGAGCGGATTGAAAC
        129 TACGGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC

       3566 AAGCGATGCG


Statistics
Matches: 347,  Mismatches: 36, Indels: 7
        0.89            0.09        0.02

Matches are distributed among these distances:
 199   73  0.21
 200  234  0.67
 201   40  0.12

ACGTcount: A:0.34, C:0.20, G:0.25, T:0.20


Consensus pattern (199 bp):   
TCTCCCTGATGAGATACTGAGGAGAAGACCCAAACGAGGCTCAAAGCAAGCAAATCTTCGAACCC
CAGCTTCTTGATGAGACACTGAGAAGCGGGCCGAAGCAATAAATGGTTAGCTTCCTGATGAGATA
CGGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACGATGATGGG
ACCA
Done.