Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003820.1 Kokia drynarioides strain JFW-HI SEQ_116816, 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: 34948
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33

Warning! 180 characters in sequence are not A, C, G, or T


Found at i:1309 original size:31 final size:31

Alignment explanation


    Indices: 1273--1333  Score: 95
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       1263 AATAGCCCAA

                         * *     *         
       1273 TGACTTAAATAAAGATTTTCGGATAGTTCAG
          1 TGACTTAAATAAAAACTTTCGAATAGTTCAG

                                          
       1304 TGACTTAAATAAAAACTTTCGAATAGTTCA
          1 TGACTTAAATAAAAACTTTCGAATAGTTCA

       1334 ATAATAATTT


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34


Consensus pattern (31 bp):   
TGACTTAAATAAAAACTTTCGAATAGTTCAG

Found at i:3169 original size:3 final size:3

Alignment explanation


    Indices: 3161--3256  Score: 102
    Period size: 3  Copynumber: 32.0  Consensus size: 3

       3151 CTAAAAGAAG

                                    *     *     **              *   *   *  
       3161 TAT TAT TAT TAT TAT TAT CAT TAC TAT CGT TAT TAT TAT CAT CAT CAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

            *   *   *                                                      
       3209 CAT CAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

       3257 CGACTTGTTT


Statistics
Matches: 83,  Mismatches: 10, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   3   83  1.00

ACGTcount: A:0.32, C:0.09, G:0.01, T:0.57


Consensus pattern (3 bp):   
TAT

Found at i:27571 original size:55 final size:55

Alignment explanation


    Indices: 27462--27577  Score: 135
    Period size: 55  Copynumber: 2.1  Consensus size: 55

      27452 ATTATGTAAT

                            *   *   **   *        *       *        
      27462 AATCAATTTAAATATATAAATAATTTATTTAAAAAAAATAATATTTCGACATGAC
          1 AATCAATTTAAATATAAAAACAATCGATTCAAAAAAAACAATATTTAGACATGAC

                                              *                     
      27517 AATCAATTTAAATATAAAAACAATCGATTCAAAAGAAACAATATTCTAGA-ATGAC
          1 AATCAATTTAAATATAAAAACAATCGATTCAAAAAAAACAATATT-TAGACATGAC

            *     
      27572 GATCAA
          1 AATCAA

      27578 CTCAATCCAA


Statistics
Matches: 51,  Mismatches: 9, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  55   48  0.94
  56    3  0.06

ACGTcount: A:0.53, C:0.10, G:0.06, T:0.30


Consensus pattern (55 bp):   
AATCAATTTAAATATAAAAACAATCGATTCAAAAAAAACAATATTTAGACATGAC

Found at i:30240 original size:12 final size:13

Alignment explanation


    Indices: 30223--30252  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

      30213 TAAATTGTAA

                         
      30223 AAATTATATTC-T
          1 AAATTATATTCTT

                         
      30235 AAATTATATTCTT
          1 AAATTATATTCTT

                 
      30248 AAATT
          1 AAATT

      30253 TTAAATATTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   11  0.65
  13    6  0.35

ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50


Consensus pattern (13 bp):   
AAATTATATTCTT

Found at i:30487 original size:26 final size:24

Alignment explanation


    Indices: 30437--30488  Score: 68
    Period size: 26  Copynumber: 2.1  Consensus size: 24

      30427 TTAATTTTCA

                               **   
      30437 ATCAATTTATTTTTTCAACTGTTT
          1 ATCAATTTATTTTTTCAACAATTT

                                      
      30461 ATCAATTTGATTTTTTTCAACAATTT
          1 ATCAATTT-A-TTTTTTCAACAATTT

              
      30487 AT
          1 AT

      30489 TTACAACGCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  24    8  0.33
  25    1  0.04
  26   15  0.62

ACGTcount: A:0.29, C:0.12, G:0.04, T:0.56


Consensus pattern (24 bp):   
ATCAATTTATTTTTTCAACAATTT

Found at i:30619 original size:3 final size:3

Alignment explanation


    Indices: 30611--30643  Score: 66
    Period size: 3  Copynumber: 11.0  Consensus size: 3

      30601 ACAAGGCCTG

                                                       
      30611 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
          1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT

      30644 ACGTATCCCT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   30  1.00

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


Consensus pattern (3 bp):   
CAT

Done.