Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006228.1 Kokia drynarioides strain JFW-HI SEQ_120799, 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: 21756
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32


Found at i:2204 original size:59 final size:58

Alignment explanation


    Indices: 1999--2220  Score: 344
    Period size: 59  Copynumber: 3.9  Consensus size: 58

       1989 ATACATTGAT

                                                      *                
       1999 GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATGATTTAATAAAATAGAA
          1 GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATA-AA

                  *                        *                          
       2058 GTTATTCTGAATA-TTTTGTACACATTA-TTATATATTGTATCATTTAATAAAAT--A
          1 GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAAA

               *                                                       
       2112 GTTCTTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAAAA
          1 GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAAT-AAA

                    *              *                          
       2171 GTTATTTTCAATATTTTTGTACATATTATTTTTATATTGTATCATTTAAT
          1 GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAAT

       2221 TGAGAACCCA


Statistics
Matches: 149,  Mismatches: 9, Indels: 10
        0.89            0.05        0.06

Matches are distributed among these distances:
  54   12  0.08
  55   14  0.09
  56   25  0.17
  57   24  0.16
  58   14  0.09
  59   60  0.40

ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52


Consensus pattern (58 bp):   
GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAAA

Found at i:2254 original size:113 final size:113

Alignment explanation


    Indices: 2021--2247  Score: 253
    Period size: 113  Copynumber: 2.0  Consensus size: 113

       2011 ATTTTTGTAC

                                *             *          *                   
       2021 ACATTATTTTTATATTGTATGATTTAATAAAATAGAAGTTATTCTGAATATTTTGTACACATTAT
          1 ACATTATTTTTATATTGTATCATTTAATAAAATAAAAGTTATTCTCAATATTTTGTACACATTAT

                                       ** **  *    **    * *
       2086 TATATATTGTATCATTTAATAAAATAGTTCTTTTGAATATTTTTGTAC
         66 TATATATTGTATCATTTAATAAAATAGCCCAATTCAATAAGTTTGAAA

                                                       *                *    
       2134 ACATTATTTTTATATTGTATCATTTAATAAAATAAAAGTTATTTTCAATATTTTTGTACATATTA
          1 ACATTATTTTTATATTGTATCATTTAATAAAATAAAAGTTATTCTCAATA-TTTTGTACACATTA

               *                   * *                         
       2199 TTTTTATATTGTATCATTTAATTGAGA-A-CCCAATTCAA-AAGTTTGAAA
         65 -TTATATATTGTATCATTTAA-TAAAATAGCCCAATTCAATAAGTTTGAAA

             
       2247 A
          1 A

       2248 TTTTATTATT


Statistics
Matches: 94,  Mismatches: 17, Indels: 6
        0.80            0.15        0.05

Matches are distributed among these distances:
 113   53  0.56
 114   18  0.19
 115   20  0.21
 116    3  0.03

ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48


Consensus pattern (113 bp):   
ACATTATTTTTATATTGTATCATTTAATAAAATAAAAGTTATTCTCAATATTTTGTACACATTAT
TATATATTGTATCATTTAATAAAATAGCCCAATTCAATAAGTTTGAAA

Found at i:8849 original size:15 final size:15

Alignment explanation


    Indices: 8817--8845  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       8807 CTACATGACA

                           
       8817 CTTCTTCTTCCTCCT
          1 CTTCTTCTTCCTCCT

                           
       8832 CTTCTTC-TCCTCCT
          1 CTTCTTCTTCCTCCT

       8846 TCTTTCGCTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    7  0.50
  15    7  0.50

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


Consensus pattern (15 bp):   
CTTCTTCTTCCTCCT

Found at i:9165 original size:15 final size:15

Alignment explanation


    Indices: 9147--9178  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       9137 TATCTTTTTT

                    *      
       9147 CTCAACATTTTCTTC
          1 CTCAACATCTTCTTC

                           
       9162 CTCAACATCTTCTTC
          1 CTCAACATCTTCTTC

              
       9177 CT
          1 CT

       9179 TCTTGTTCAC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.19, C:0.38, G:0.00, T:0.44


Consensus pattern (15 bp):   
CTCAACATCTTCTTC
Done.