Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003570.1 Kokia drynarioides strain JFW-HI SEQ_116436, 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: 5875
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31


Found at i:771 original size:52 final size:52

Alignment explanation


    Indices: 705--807  Score: 134
    Period size: 52  Copynumber: 2.0  Consensus size: 52

        695 GATGGGTCGA

                *                  * *    *                     
        705 AGGTTCCTTGAGTTTAAGTAGGTTCGAGGATACTTGAGTTTGAGCTGGTTGG
          1 AGGTCCCTTGAGTTTAAGTAGGTCCAAGGACACTTGAGTTTGAGCTGGTTGG

                           *   *           *            *      
        757 AGGTCCCTTGAGTTTGAGTGGGTCCAAGGACCCTTGAGTTTGAGTTGGTTG
          1 AGGTCCCTTGAGTTTAAGTAGGTCCAAGGACACTTGAGTTTGAGCTGGTTG

        808 AAGGACCATG


Statistics
Matches: 43,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  52   43  1.00

ACGTcount: A:0.17, C:0.13, G:0.35, T:0.35


Consensus pattern (52 bp):   
AGGTCCCTTGAGTTTAAGTAGGTCCAAGGACACTTGAGTTTGAGCTGGTTGG

Found at i:811 original size:26 final size:26

Alignment explanation


    Indices: 710--814  Score: 104
    Period size: 26  Copynumber: 4.0  Consensus size: 26

        700 GTCGAAGGTT

                      *   *           *
        710 CCTTGAGTTTAAGTAGGTTCG-AGGAT
          1 CCTTGAGTTTGAGTTGGTT-GAAGGAC

            *            *      *   * 
        736 ACTTGAGTTTGAGCTGGTTGGAGGTC
          1 CCTTGAGTTTGAGTTGGTTGAAGGAC

                          *   **      
        762 CCTTGAGTTTGAGTGGGTCCAAGGAC
          1 CCTTGAGTTTGAGTTGGTTGAAGGAC

                                      
        788 CCTTGAGTTTGAGTTGGTTGAAGGAC
          1 CCTTGAGTTTGAGTTGGTTGAAGGAC

             
        814 C
          1 C

        815 ATGAGCAGAT


Statistics
Matches: 62,  Mismatches: 16, Indels: 2
        0.77            0.20        0.03

Matches are distributed among these distances:
  25    1  0.02
  26   61  0.98

ACGTcount: A:0.19, C:0.14, G:0.34, T:0.32


Consensus pattern (26 bp):   
CCTTGAGTTTGAGTTGGTTGAAGGAC

Found at i:1876 original size:3 final size:3

Alignment explanation


    Indices: 1868--1910  Score: 86
    Period size: 3  Copynumber: 14.3  Consensus size: 3

       1858 CCTAAAATTT

                                                                     
       1868 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A

       1911 ATACAATATT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   40  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Done.