Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000178.1 Kokia drynarioides strain JFW-HI SEQ_110852, 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: 3853
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33


Found at i:1673 original size:144 final size:142

Alignment explanation


    Indices: 1525--1802  Score: 321
    Period size: 144  Copynumber: 1.9  Consensus size: 142

       1515 GGTTATAACC

                                *         *                                  
       1525 AAGGAACA-AAATTTCCAAATTGGTCAATTGGA-AAAG-AGTAATGGGTATTGAACCAACAAGTC
          1 AAGGAACAGAAA-TTCCAAACTGGTCAA-TAGACAAAGCAG-AA-GGG-ATTGAACCAACAAGTC

                  *              *       *                                   
       1587 TATTGTTGGAGAGA-TACAAATAAATCAATTTTCTCAAATATCCAATTTCTAATGGGATAGATCC
         61 TATTGTCGGAGAGACT-CAAACAAATCAAATTTCTCAAATATCCAATTTCTAATGGGATAGATCC

                              
       1651 ACTGATTTGGTTCCCTCG
        125 ACTGATTTGGTTCCCTCG

                 *    *   ** *      *                         *        *     
       1669 AAGGATCAGAGATTGGAGACTGGTTAATAGACCCAAAGCAGAAGGGATTGGACCAACAATTCTAT
          1 AAGGAACAGAAATTCCAAACTGGTCAATAGA--CAAAGCAGAAGGGATTGAACCAACAAGTCTAT

                                *                                         *  
       1734 TGTCGGAGAGACTCAAACAAGTCAAATTTCTCAAATATCCAATTTCTAATGGGATAGATCCATTG
         64 TGTCGGAGAGACTCAAACAAATCAAATTTCTCAAATATCCAATTTCTAATGGGATAGATCCACTG

                
       1799 ATTT
        129 ATTT

       1803 TGTTTATCCC


Statistics
Matches: 113,  Mismatches: 15, Indels: 12
        0.81            0.11        0.09

Matches are distributed among these distances:
 143    3  0.03
 144   96  0.85
 145    6  0.05
 146    6  0.05
 147    2  0.02

ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28


Consensus pattern (142 bp):   
AAGGAACAGAAATTCCAAACTGGTCAATAGACAAAGCAGAAGGGATTGAACCAACAAGTCTATTG
TCGGAGAGACTCAAACAAATCAAATTTCTCAAATATCCAATTTCTAATGGGATAGATCCACTGAT
TTGGTTCCCTCG

Found at i:1837 original size:144 final size:145

Alignment explanation


    Indices: 1571--1874  Score: 436
    Period size: 144  Copynumber: 2.1  Consensus size: 145

       1561 AGTAATGGGT

                *        *        *             *       *                    
       1571 ATTGAACCAACAAGTCTATTGTTGGAGAGATACAAATAAATCAATTTTCTCAAATATCCAATTTC
          1 ATTGGACCAACAATTCTATTGTCGGAGAGATACAAACAAATCAAATTTCTCAAATATCCAATTTC

                                                                             
       1636 TAATGGGATAGATCCACTGATTTGGTTCCCTCGAAGGATCAGAGATTGGAGACTGGTTAATAGAC
         66 TAATGGGATAGATCCACTGATTTGGTTCCCTCGAAGGATCAGAGATTGGAGACTGGTTAATAGAC

                  *        
       1701 CCAAAGCAGAAGGG-
        131 CCAAAGAAGAAGGGA

                                                    *                        
       1715 ATTGGACCAACAATTCTATTGTCGGAGAGACT-CAAACAAGTCAAATTTCTCAAATATCCAATTT
          1 ATTGGACCAACAATTCTATTGTCGGAGAGA-TACAAACAAATCAAATTTCTCAAATATCCAATTT

                             *        *   *                        *        *
       1779 CTAATGGGATAGATCCATTGATTTTGTTTATCC-C-AAGGATCAGAGATTGGAGATTGGTTAATT
         65 CTAATGGGATAGATCCACTGA-TTTGGTT-CCCTCGAAGGATCAGAGATTGGAGACTGGTTAATA

             *                
       1842 GGCCCAAAGAAGAAGGGA
        128 GACCCAAAGAAGAAGGGA

                           
       1860 ATTGGACCAACAATT
          1 ATTGGACCAACAATT

       1875 TCACATCGAC


Statistics
Matches: 143,  Mismatches: 13, Indels: 7
        0.88            0.08        0.04

Matches are distributed among these distances:
 144  118  0.83
 145   23  0.16
 146    2  0.01

ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28


Consensus pattern (145 bp):   
ATTGGACCAACAATTCTATTGTCGGAGAGATACAAACAAATCAAATTTCTCAAATATCCAATTTC
TAATGGGATAGATCCACTGATTTGGTTCCCTCGAAGGATCAGAGATTGGAGACTGGTTAATAGAC
CCAAAGAAGAAGGGA

Done.