Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006923.1 Kokia drynarioides strain JFW-HI SEQ_121526, 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: 3009
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33


Found at i:1592 original size:19 final size:19

Alignment explanation


    Indices: 1555--1590  Score: 56
    Period size: 18  Copynumber: 1.9  Consensus size: 19

       1545 AGTTCGGCCC

                               
       1555 ATTTGGGCTTTAGGTTTTA
          1 ATTTGGGCTTTAGGTTTTA

                       *      
       1574 ATTTGGG-TTTGGGTTTT
          1 ATTTGGGCTTTAGGTTTT

       1591 TAGGGTAATT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    9  0.56
  19    7  0.44

ACGTcount: A:0.11, C:0.03, G:0.31, T:0.56


Consensus pattern (19 bp):   
ATTTGGGCTTTAGGTTTTA

Found at i:1777 original size:28 final size:28

Alignment explanation


    Indices: 1746--1834  Score: 69
    Period size: 28  Copynumber: 3.1  Consensus size: 28

       1736 ATATATATAA

                                        
       1746 GTTTAGTGGAAGTAAGGTTCTATATTTG
          1 GTTTAGTGGAAGTAAGGTTCTATATTTG

                       *     *  *           *
       1774 GTTTTA-T--ATGTTAATG-ACTATATATATAA
          1 G-TTTAGTGGAAG-TAAGGTTCTATAT-T-T-G

                                        
       1803 GTTTAGTGGAAGTAAGGTTCTATATTTG
          1 GTTTAGTGGAAGTAAGGTTCTATATTTG

                
       1831 GTTT
          1 GTTT

       1835 TATATGTTAA


Statistics
Matches: 44,  Mismatches: 8, Indels: 18
        0.63            0.11        0.26

Matches are distributed among these distances:
  26    8  0.18
  27    5  0.11
  28   11  0.25
  29    7  0.16
  30    5  0.11
  31    8  0.18

ACGTcount: A:0.28, C:0.03, G:0.22, T:0.46


Consensus pattern (28 bp):   
GTTTAGTGGAAGTAAGGTTCTATATTTG

Found at i:1779 original size:29 final size:29

Alignment explanation


    Indices: 1747--1836  Score: 73
    Period size: 29  Copynumber: 3.1  Consensus size: 29

       1737 TATATATAAG

                                         
       1747 TTTAGTGGAAGTAAGGTTCTATATTTGGT
          1 TTTAGTGGAAGTAAGGTTCTATATTTGGT

                     *     *  *           *  
       1776 TTTA-T--ATGTTAATG-ACTATATATATAAG-
          1 TTTAGTGGAAG-TAAGGTTCTATAT-T-T-GGT

                                         
       1804 TTTAGTGGAAGTAAGGTTCTATATTTGGT
          1 TTTAGTGGAAGTAAGGTTCTATATTTGGT

                
       1833 TTTA
          1 TTTA

       1837 TATGTTAATG


Statistics
Matches: 44,  Mismatches: 8, Indels: 18
        0.63            0.11        0.26

Matches are distributed among these distances:
  26    8  0.18
  27    5  0.11
  28    7  0.16
  29   11  0.25
  30    5  0.11
  31    8  0.18

ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47


Consensus pattern (29 bp):   
TTTAGTGGAAGTAAGGTTCTATATTTGGT

Found at i:1821 original size:57 final size:57

Alignment explanation


    Indices: 1735--1849  Score: 230
    Period size: 57  Copynumber: 2.0  Consensus size: 57

       1725 CCTACTATAG

                                                                     
       1735 TATATATATAAGTTTAGTGGAAGTAAGGTTCTATATTTGGTTTTATATGTTAATGAC
          1 TATATATATAAGTTTAGTGGAAGTAAGGTTCTATATTTGGTTTTATATGTTAATGAC

                                                                     
       1792 TATATATATAAGTTTAGTGGAAGTAAGGTTCTATATTTGGTTTTATATGTTAATGAC
          1 TATATATATAAGTTTAGTGGAAGTAAGGTTCTATATTTGGTTTTATATGTTAATGAC

             
       1849 T
          1 T

       1850 TAATGCTTGT


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  57   58  1.00

ACGTcount: A:0.31, C:0.03, G:0.19, T:0.46


Consensus pattern (57 bp):   
TATATATATAAGTTTAGTGGAAGTAAGGTTCTATATTTGGTTTTATATGTTAATGAC
Done.