Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003518.1 Kokia drynarioides strain JFW-HI SEQ_116358, 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, 714

Length: 1190
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35


Found at i:85 original size:16 final size:17

Alignment explanation


    Indices: 50--92  Score: 52
    Period size: 16  Copynumber: 2.6  Consensus size: 17

         40 AACTATGAAA

                          *  
         50 ACAAATAAAATGCAGGG
          1 ACAAATAAAATGCAAGG

                           * 
         67 ACAAA-AAAATGCAATG
          1 ACAAATAAAATGCAAGG

                *     
         83 ACAATTAAAA
          1 ACAAATAAAA

         93 GAAATGCATA


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  16   13  0.59
  17    9  0.41

ACGTcount: A:0.60, C:0.12, G:0.14, T:0.14


Consensus pattern (17 bp):   
ACAAATAAAATGCAAGG

Found at i:511 original size:18 final size:18

Alignment explanation


    Indices: 488--541  Score: 76
    Period size: 18  Copynumber: 3.1  Consensus size: 18

        478 GGCAACATAT

                              
        488 TCTTCTTTTTCTTCCTTC
          1 TCTTCTTTTTCTTCCTTC

                              
        506 TCTTCTTTTTCTT-CTTC
          1 TCTTCTTTTTCTTCCTTC

             *                 
        523 TTTTCTTTCTTC-TCCTTC
          1 TCTTCTTT-TTCTTCCTTC

             
        541 T
          1 T

        542 TCCTTAATAC


Statistics
Matches: 33,  Mismatches: 1, Indels: 4
        0.87            0.03        0.11

Matches are distributed among these distances:
  17   12  0.36
  18   21  0.64

ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69


Consensus pattern (18 bp):   
TCTTCTTTTTCTTCCTTC

Found at i:512 original size:3 final size:3

Alignment explanation


    Indices: 487--543  Score: 55
    Period size: 3  Copynumber: 19.0  Consensus size: 3

        477 AGGCAACATA

                      *                        *                         
        487 TTC TTC TTT TTC TTCC TTC -TC TTC TTT TTC TTC TTC TT- TTC TTTC
          1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC

                 *         
        532 TTC TCC TTC TTC
          1 TTC TTC TTC TTC

        544 CTTAATACCC


Statistics
Matches: 44,  Mismatches: 6, Indels: 8
        0.76            0.10        0.14

Matches are distributed among these distances:
   2    4  0.09
   3   34  0.77
   4    6  0.14

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTC

Found at i:520 original size:21 final size:22

Alignment explanation


    Indices: 487--546  Score: 63
    Period size: 21  Copynumber: 2.8  Consensus size: 22

        477 AGGCAACATA

                                   
        487 TTCTTCTTT-TTCTTCCTTCTC-
          1 TTCTT-TTTCTTCTTCCTTCTCT

                              *   
        508 TTCTTTTTCTTCTT-CTTTTCT
          1 TTCTTTTTCTTCTTCCTTCTCT

                 * *          
        529 TTCTTCTCCTTCTTCCTT
          1 TTCTTTTTCTTCTTCCTT

        547 AATACCCATA


Statistics
Matches: 33,  Mismatches: 3, Indels: 5
        0.80            0.07        0.12

Matches are distributed among these distances:
  20    8  0.24
  21   22  0.67
  22    3  0.09

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (22 bp):   
TTCTTTTTCTTCTTCCTTCTCT

Done.