Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005006.1 Kokia drynarioides strain JFW-HI SEQ_118765, 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: 2328
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37


Found at i:1801 original size:31 final size:31

Alignment explanation


    Indices: 1763--1894  Score: 110
    Period size: 31  Copynumber: 4.3  Consensus size: 31

       1753 TTATTGGCCC

                      *                    
       1763 AATTTGGTACTTAAACTTGACACTTTTTCCT
          1 AATTTGGTACATAAACTTGACACTTTTTCCT

                        *               ** 
       1794 AATTTGGTACATGAACTTGACACTTTTTTTT
          1 AATTTGGTACATAAACTTGACACTTTTTCCT

                 *     *        ***    **    
       1825 AAGTTGGGTACTTAAACATTTTGA---GGTCC-
          1 AA-TTTGGTACATAAAC-TTGACACTTTTTCCT

                                 *         
       1854 AATTTGGTACATAAACTTGACTCTTTTTCCT
          1 AATTTGGTACATAAACTTGACACTTTTTCCT

                      
       1885 AATTTGGTAC
          1 AATTTGGTAC

       1895 CTAATCTTTT


Statistics
Matches: 73,  Mismatches: 22, Indels: 12
        0.68            0.21        0.11

Matches are distributed among these distances:
  27    2  0.03
  28   12  0.16
  29    2  0.03
  30    4  0.05
  31   39  0.53
  32   11  0.15
  33    3  0.04

ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43


Consensus pattern (31 bp):   
AATTTGGTACATAAACTTGACACTTTTTCCT

Found at i:1824 original size:91 final size:91

Alignment explanation


    Indices: 1716--1894  Score: 245
    Period size: 91  Copynumber: 2.0  Consensus size: 91

       1706 TTCATACTTC

                   *               *          **    *                  *     
       1716 AACTTGATACTTCTTTTTAA-TTTGGTACTT-AATTTTTTTATTGGCCCAATTTGGTACTTAAAC
          1 AACTTGACACTTCTTTTTAAGTTGGGTACTTAAACATTTTGA--GGCCCAATTTGGTACATAAAC

                                        
       1779 TTGACACTTTTTCCTAATTTGGTACATG
         64 TTGACACTTTTTCCTAATTTGGTACATG

                        *                               *                    
       1807 AACTTGACACTTTTTTTTAAGTTGGGTACTTAAACATTTTGAGGTCCAATTTGGTACATAAACTT
          1 AACTTGACACTTCTTTTTAAGTTGGGTACTTAAACATTTTGAGGCCCAATTTGGTACATAAACTT

               *                   
       1872 GACTCTTTTTCCTAATTTGGTAC
         66 GACACTTTTTCCTAATTTGGTAC

       1895 CTAATCTTTT


Statistics
Matches: 77,  Mismatches: 9, Indels: 4
        0.86            0.10        0.04

Matches are distributed among these distances:
  91   61  0.79
  92    9  0.12
  93    7  0.09

ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46


Consensus pattern (91 bp):   
AACTTGACACTTCTTTTTAAGTTGGGTACTTAAACATTTTGAGGCCCAATTTGGTACATAAACTT
GACACTTTTTCCTAATTTGGTACATG

Found at i:2144 original size:27 final size:27

Alignment explanation


    Indices: 2113--2179  Score: 93
    Period size: 27  Copynumber: 2.6  Consensus size: 27

       2103 GTTCAGGCAT

                                  *    
       2113 CAAATTGAATAAAAAAAAATTAGGTAC
          1 CAAATTGAATAAAAAAAAATTAAGTAC

                             **        
       2140 CAAATTGAATAAAAAAAGTTTAAGTAC
          1 CAAATTGAATAAAAAAAAATTAAGTAC

                           
       2167 CAAATT-AA-AAAAA
          1 CAAATTGAATAAAAA

       2180 GTGTCAAGTT


Statistics
Matches: 37,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  25    5  0.14
  26    2  0.05
  27   30  0.81

ACGTcount: A:0.61, C:0.07, G:0.09, T:0.22


Consensus pattern (27 bp):   
CAAATTGAATAAAAAAAAATTAAGTAC
Done.