Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012980.1 Kokia drynarioides strain JFW-HI SEQ_127998, 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: 7601
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35


Found at i:506 original size:6 final size:6

Alignment explanation


    Indices: 492--557  Score: 55
    Period size: 6  Copynumber: 11.2  Consensus size: 6

        482 TTTTAAATCC

                       *             *           **                 
        492 ATTTAA ATTTTA A-TTAA ATTTTA ATTTAA A-GCAA ATTTAA ATTTAAA
          1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA

             **                   
        539 AGATAA ATTTAA ATTTAA A
          1 ATTTAA ATTTAA ATTTAA A

        558 AATAAATTTG


Statistics
Matches: 45,  Mismatches: 12, Indels: 6
        0.71            0.19        0.10

Matches are distributed among these distances:
   5    7  0.16
   6   34  0.76
   7    4  0.09

ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44


Consensus pattern (6 bp):   
ATTTAA

Found at i:564 original size:18 final size:17

Alignment explanation


    Indices: 492--566  Score: 78
    Period size: 17  Copynumber: 4.2  Consensus size: 17

        482 TTTTAAATCC

                      *  *   
        492 ATTTAAATTTTAATTAA
          1 ATTTAAATTTAAAATAA

                *        **  
        509 ATTTTAATTTAAAGCAA
          1 ATTTAAATTTAAAATAA

                               
        526 ATTTAAATTTAAAAGATAA
          1 ATTTAAATTT-AAA-ATAA

                              
        545 ATTTAAATTTAAAAATAA
          1 ATTTAAATTT-AAAATAA

                
        563 ATTT
          1 ATTT

        567 GAATCAATTT


Statistics
Matches: 49,  Mismatches: 7, Indels: 3
        0.83            0.12        0.05

Matches are distributed among these distances:
  17   22  0.45
  18   11  0.22
  19   16  0.33

ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44


Consensus pattern (17 bp):   
ATTTAAATTTAAAATAA

Found at i:1289 original size:206 final size:206

Alignment explanation


    Indices: 1034--1519  Score: 706
    Period size: 206  Copynumber: 2.3  Consensus size: 206

       1024 GTATCAAGAT

                             **                  *    *                     *
       1034 GCTAATCCGTTTTTATTATTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGG
          1 GCTAA-CC-TTTTTATTGCTTCGACCTGCTTCTCAGTATCTCGTCAGGAAGCTGGGGTTCGAAGA

                                                     *                       
       1099 TTTGCTCACACCGAGCGCGGGCTTGACTTGGTCTTCTTCTCGGTATCTCATCAAGAAGATGA-CT
         64 TTTGCTCACACCGAGCGCGGGCTTGACTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGATC-

              *   *          *                                            *  
       1163 GCGTCGTTTGTTTCAATTCGCGTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTTAG
        128 GCATCGCTTGTTTCAATCCGCGTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAG

                         *
       1228 TATCTCATCAGGAG
        193 TATCTCATCAGGAA

                                                             *    *  *       
       1242 GCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTATCTCGTCAGGAAGTTGGGATTTGAAGATT
          1 GCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTATCTCGTCAGGAAGCTGGGGTTCGAAGATT

                    *      *   *    *                          *             
       1307 TGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCA
         66 TGCTCACACCGAGCGCGGGCTTGACTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGATCGCA

             *                *                                              
       1372 TTGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTAT
        131 TCGCTTGTTTCAATCCGCGTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTAT

                       
       1437 CTCATCAGGAA
        196 CTCATCAGGAA

            *                    *      *                                    
       1448 ACTAA-CTGTTTTATTGCTTCAACCTGCCTCTCAGTATCTCGTCAGGAAGCTGGGGTTCGAAGAT
          1 GCTAACCT-TTTTATTGCTTCGACCTGCTTCTCAGTATCTCGTCAGGAAGCTGGGGTTCGAAGAT

                    
       1512 TTGCTCAC
         65 TTGCTCAC

       1520 TTTGAGCCTC


Statistics
Matches: 249,  Mismatches: 27, Indels: 6
        0.88            0.10        0.02

Matches are distributed among these distances:
 205    2  0.01
 206  239  0.96
 207    3  0.01
 208    5  0.02

ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35


Consensus pattern (206 bp):   
GCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTATCTCGTCAGGAAGCTGGGGTTCGAAGATT
TGCTCACACCGAGCGCGGGCTTGACTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGATCGCA
TCGCTTGTTTCAATCCGCGTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTAT
CTCATCAGGAA
Done.