Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009792.1 Kokia drynarioides strain JFW-HI SEQ_124513, 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: 9516
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:3819 original size:43 final size:43

Alignment explanation


    Indices: 3758--3860  Score: 181
    Period size: 43  Copynumber: 2.4  Consensus size: 43

       3748 ATATTAGTGA

                                                       
       3758 CGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTCTTTAACGG
          1 CGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTCTTTAACGG

                                                    *   
       3801 CGTTTGT-GGTAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGG
          1 CGTTTGTAGG-AAAAGCGCCGCTAAAGACCATGTTCTTTAACGG

                             
       3844 CGTTTGTAGGAAAAGCG
          1 CGTTTGTAGGAAAAGCG

       3861 TCGCGATTTT


Statistics
Matches: 57,  Mismatches: 1, Indels: 4
        0.92            0.02        0.06

Matches are distributed among these distances:
  42    2  0.04
  43   53  0.93
  44    2  0.04

ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26


Consensus pattern (43 bp):   
CGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTCTTTAACGG

Found at i:4567 original size:160 final size:160

Alignment explanation


    Indices: 4303--4617  Score: 560
    Period size: 160  Copynumber: 2.0  Consensus size: 160

       4293 TGACATCTCA

                        *                                             * *    
       4303 ATTGCCATGGAGTAGCTCGCTTGCACCAAGAATGTCTCATCAACTAGCCAAGGTGAGGGGGAAGT
          1 ATTGCCATGGAGCAGCTCGCTTGCACCAAGAATGTCTCATCAACTAGCCAAGGTGAGGCGAAAGT

                  *                                     *                    
       4368 GGAGAGTTGACACTTTTCACTACCCCTAAAGACCTAAATAGCTTTTATAGCTATGCTCCTAGGAA
         66 GGAGAGCTGACACTTTTCACTACCCCTAAAGACCTAAATAGCTTCTATAGCTATGCTCCTAGGAA

                                          
       4433 ACATTGAGAGTTTTCTTATTTGGCATCTTG
        131 ACATTGAGAGTTTTCTTATTTGGCATCTTG

                                     *                                       
       4463 ATTGCCATGGAGCAGCTCGCTTGCAGCAAGGAA-GTCTCATCAACTAGCCAAGGTGAGGCGAAAG
          1 ATTGCCATGGAGCAGCTCGCTTGCACCAA-GAATGTCTCATCAACTAGCCAAGGTGAGGCGAAAG

                                                                             
       4527 TGGAGAGCTGACACTTTTCACTACCCCTAAAGACCTAAATAGCTTCTATAGCTATGCTCCTAGGA
         65 TGGAGAGCTGACACTTTTCACTACCCCTAAAGACCTAAATAGCTTCTATAGCTATGCTCCTAGGA

                                      
       4592 AACATTGAGAGTTTTCTTATTTGGCA
        130 AACATTGAGAGTTTTCTTATTTGGCA

       4618 CTCCAAGGCC


Statistics
Matches: 148,  Mismatches: 6, Indels: 2
        0.95            0.04        0.01

Matches are distributed among these distances:
 160  145  0.98
 161    3  0.02

ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28


Consensus pattern (160 bp):   
ATTGCCATGGAGCAGCTCGCTTGCACCAAGAATGTCTCATCAACTAGCCAAGGTGAGGCGAAAGT
GGAGAGCTGACACTTTTCACTACCCCTAAAGACCTAAATAGCTTCTATAGCTATGCTCCTAGGAA
ACATTGAGAGTTTTCTTATTTGGCATCTTG
Done.