Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008960.1 Kokia drynarioides strain JFW-HI SEQ_123656, 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: 19446
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:5065 original size:17 final size:18

Alignment explanation


    Indices: 5033--5069  Score: 58
    Period size: 17  Copynumber: 2.1  Consensus size: 18

       5023 GTTTATTGTG

                     *        
       5033 TTTAATTGCTTGTTTATA
          1 TTTAATTGCATGTTTATA

                              
       5051 TTTAATT-CATGTTTATA
          1 TTTAATTGCATGTTTATA

              
       5068 TT
          1 TT

       5070 GTTATTGGCC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17   11  0.61
  18    7  0.39

ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62


Consensus pattern (18 bp):   
TTTAATTGCATGTTTATA

Found at i:6269 original size:40 final size:40

Alignment explanation


    Indices: 6177--6269  Score: 107
    Period size: 40  Copynumber: 2.3  Consensus size: 40

       6167 CCTTTTCGAT

                               ** *      *          
       6177 CTTTTCATTTATTATCCTTTTTTATAATTTCCTTGTCAAC
          1 CTTTTCATTTATTATCCTTCCTGATAATTACCTTGTCAAC

                   *                           *     
       6217 CTTTTCAGTTATTATCCTTCCTGATAA-TACCATTTTCAAC
          1 CTTTTCATTTATTATCCTTCCTGATAATTACC-TTGTCAAC

                 *       
       6257 CTTTTTATTTATT
          1 CTTTTCATTTATT

       6270 CAGAAATATT


Statistics
Matches: 44,  Mismatches: 8, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  39    3  0.07
  40   41  0.93

ACGTcount: A:0.22, C:0.20, G:0.03, T:0.55


Consensus pattern (40 bp):   
CTTTTCATTTATTATCCTTCCTGATAATTACCTTGTCAAC

Found at i:7596 original size:19 final size:18

Alignment explanation


    Indices: 7547--7598  Score: 50
    Period size: 19  Copynumber: 2.7  Consensus size: 18

       7537 CTATTGTGTT

                         *     
       7547 TTTTTTCCTTTTTTCTCTC
          1 TTTTTT-CTTTTTCCTCTC

                 *          *  
       7566 TTTTTCCATTTTTCCTTTC
          1 TTTTTTC-TTTTTCCTCTC

                          
       7585 GTTTTTTCTTTTTC
          1 -TTTTTTCTTTTTC

       7599 TTTGTTAGGC


Statistics
Matches: 27,  Mismatches: 4, Indels: 4
        0.77            0.11        0.11

Matches are distributed among these distances:
  18    1  0.04
  19   20  0.74
  20    6  0.22

ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73


Consensus pattern (18 bp):   
TTTTTTCTTTTTCCTCTC

Found at i:19275 original size:2 final size:2

Alignment explanation


    Indices: 19268--19294  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      19258 TTGTCATTAG

                                                    
      19268 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

      19295 TAAAAGAAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.