Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004232.1 Kokia drynarioides strain JFW-HI SEQ_117493, 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: 1815
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31


Found at i:1192 original size:14 final size:14

Alignment explanation


    Indices: 1167--1210  Score: 56
    Period size: 14  Copynumber: 3.2  Consensus size: 14

       1157 GCCTTTTAAC

                 *        
       1167 TTTACGATTTAAGG
          1 TTTACAATTTAAGG

                           
       1181 TTT-CAAATTTAAGG
          1 TTTAC-AATTTAAGG

                          
       1195 TTTACAATTT-AGG
          1 TTTACAATTTAAGG

               
       1208 TTT
          1 TTT

       1211 TAGGGTTTAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  13    7  0.26
  14   19  0.70
  15    1  0.04

ACGTcount: A:0.30, C:0.07, G:0.16, T:0.48


Consensus pattern (14 bp):   
TTTACAATTTAAGG

Found at i:1464 original size:21 final size:21

Alignment explanation


    Indices: 1440--1481  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1430 TAGGGTCCAT

                    *    *       
       1440 TTGCCCCGTAGGAGTAGAGTA
          1 TTGCCCCGGAGGAATAGAGTA

                  *              
       1461 TTGCCCGGGAGGAATAGAGTA
          1 TTGCCCCGGAGGAATAGAGTA

       1482 AAGCGATGGC


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21


Consensus pattern (21 bp):   
TTGCCCCGGAGGAATAGAGTA

Found at i:1599 original size:44 final size:45

Alignment explanation


    Indices: 1488--1612  Score: 198
    Period size: 45  Copynumber: 2.8  Consensus size: 45

       1478 AGTAAAGCGA

                             *           **              
       1488 TGGCTCGTCAAACTGAGCCTGATATCCTTCCCTTGAGTATTGCGG
          1 TGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTGCGG

              *         *                                
       1533 TGACTCGTCAAATTGAGGCTGATATCCTTGGCTTGAGTATTGC-G
          1 TGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTGCGG

                                                
       1577 TGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGA
          1 TGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGA

       1613 TGAGCTATGC


Statistics
Matches: 73,  Mismatches: 7, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  44   35  0.48
  45   38  0.52

ACGTcount: A:0.19, C:0.22, G:0.26, T:0.32


Consensus pattern (45 bp):   
TGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTGCGG
Done.