Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010728.1 Kokia drynarioides strain JFW-HI SEQ_125681, 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: 6689
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:1875 original size:36 final size:35

Alignment explanation


    Indices: 1821--1918  Score: 115
    Period size: 36  Copynumber: 2.7  Consensus size: 35

       1811 TGGTAACAGG

                      *  *                   *  
       1821 CATGACCTTTGGGCCAACAGGGAGTAAAATGAATAT
          1 CATGA-CTTTTGGTCAACAGGGAGTAAAATGAACAT

                               *            *   
       1857 CATGACTTTTGAGTCAACAAGGAGTAAAATGAGCAT
          1 CATGACTTTTG-GTCAACAGGGAGTAAAATGAACAT

               *     *                
       1893 CATCACTTTAGGTCAACAGGGAGTAA
          1 CATGACTTTTGGTCAACAGGGAGTAA

       1919 GAATAACCTT


Statistics
Matches: 53,  Mismatches: 8, Indels: 3
        0.83            0.12        0.05

Matches are distributed among these distances:
  35   19  0.36
  36   34  0.64

ACGTcount: A:0.37, C:0.16, G:0.23, T:0.23


Consensus pattern (35 bp):   
CATGACTTTTGGTCAACAGGGAGTAAAATGAACAT

Found at i:1916 original size:35 final size:36

Alignment explanation


    Indices: 1835--1918  Score: 116
    Period size: 36  Copynumber: 2.4  Consensus size: 36

       1825 ACCTTTGGGC

                               *     *     *    
       1835 CAACAGGGAGTAAAATGAATATCATGACTTTTGAGT
          1 CAACAGGGAGTAAAATGAACATCATCACTTTAGAGT

                 *            *                 
       1871 CAACAAGGAGTAAAATGAGCATCATCACTTTAG-GT
          1 CAACAGGGAGTAAAATGAACATCATCACTTTAGAGT

                         
       1906 CAACAGGGAGTAA
          1 CAACAGGGAGTAA

       1919 GAATAACCTT


Statistics
Matches: 42,  Mismatches: 6, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  35   14  0.33
  36   28  0.67

ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23


Consensus pattern (36 bp):   
CAACAGGGAGTAAAATGAACATCATCACTTTAGAGT

Found at i:6605 original size:22 final size:21

Alignment explanation


    Indices: 6577--6618  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       6567 TTTCTTTTTC

                                   
       6577 CTTTTCT-TCTCTTCCTTCTTCT
          1 CTTTTCTCT-TCTTCC-TCTTCT

                                
       6599 CTTTTCTCTTCTTCCTCTTC
          1 CTTTTCTCTTCTTCCTCTTC

       6619 AACACCTACA


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  21    5  0.26
  22   13  0.68
  23    1  0.05

ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62


Consensus pattern (21 bp):   
CTTTTCTCTTCTTCCTCTTCT
Done.