Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008240.1 Kokia drynarioides strain JFW-HI SEQ_122904, 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, 985

Length: 1642
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32


Found at i:315 original size:3 final size:3

Alignment explanation


    Indices: 307--351  Score: 54
    Period size: 3  Copynumber: 15.0  Consensus size: 3

        297 TTAAATGAAT

                                 *    *  **                            
        307 TAA TAA TAA TAA TAA TTA TAT TTT TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

        352 ACCGAAAGGC


Statistics
Matches: 36,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   3   36  1.00

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (3 bp):   
TAA

Found at i:1523 original size:29 final size:30

Alignment explanation


    Indices: 1490--1620  Score: 162
    Period size: 29  Copynumber: 4.5  Consensus size: 30

       1480 AAACTATTCG

                                          
       1490 AAAATTCCATTTTTACCCTC-AAACTTCCA
          1 AAAATTCCATTTTTACCCTCAAAACTTCCA

                            *    *         
       1519 AAAA-TCCTATTTTTAACCTCGAAACTTCCA
          1 AAAATTCC-ATTTTTACCCTCAAAACTTCCA

                         *                
       1549 AAAATTCCATTTTAACCC-CAAAACTTCCA
          1 AAAATTCCATTTTTACCCTCAAAACTTCCA

                  *             **        
       1578 AAAATTTCATTTTTACCC-CCGAACTTCCA
          1 AAAATTCCATTTTTACCCTCAAAACTTCCA

                 *        
       1607 AAAATCCCATTTTT
          1 AAAATTCCATTTTT

       1621 GATCTTGAAA


Statistics
Matches: 89,  Mismatches: 10, Indels: 6
        0.85            0.10        0.06

Matches are distributed among these distances:
  28    3  0.03
  29   62  0.70
  30   21  0.24
  31    3  0.03

ACGTcount: A:0.36, C:0.29, G:0.02, T:0.34


Consensus pattern (30 bp):   
AAAATTCCATTTTTACCCTCAAAACTTCCA

Found at i:1546 original size:30 final size:29

Alignment explanation


    Indices: 1490--1641  Score: 148
    Period size: 29  Copynumber: 5.2  Consensus size: 29

       1480 AAACTATTCG

                *          *             
       1490 AAAATTCCATTTTTACCCTC-AAACTTCC
          1 AAAAATCCATTTTTAACCTCGAAACTTCC

                                          
       1518 AAAAATCCTATTTTTAACCTCGAAACTTCC
          1 AAAAATCC-ATTTTTAACCTCGAAACTTCC

                               * *        
       1548 AAAAATTCCA-TTTTAACCCCAAAACTTCC
          1 AAAAA-TCCATTTTTAACCTCGAAACTTCC

                   *        *  *          
       1577 AAAAATTTCATTTTTACCCCCG-AACTTCC
          1 AAAAA-TCCATTTTTAACCTCGAAACTTCC

                           * *  *       * 
       1606 AAAAATCCCATTTTTGATCTTGAAACTTTC
          1 AAAAAT-CCATTTTTAACCTCGAAACTTCC

                  
       1636 AAAAAT
          1 AAAAAT

       1642 T


Statistics
Matches: 104,  Mismatches: 14, Indels: 10
        0.81            0.11        0.08

Matches are distributed among these distances:
  28    8  0.08
  29   58  0.56
  30   35  0.34
  31    3  0.03

ACGTcount: A:0.37, C:0.27, G:0.03, T:0.34


Consensus pattern (29 bp):   
AAAAATCCATTTTTAACCTCGAAACTTCC

Found at i:1582 original size:59 final size:58

Alignment explanation


    Indices: 1490--1619  Score: 174
    Period size: 59  Copynumber: 2.2  Consensus size: 58

       1480 AAACTATTCG

                         *                                  *           
       1490 AAAATTCCATTTTTACCCTCAAACTTCCAAAAATC-CTATTTTTAACCTCGAAACTTCCA
          1 AAAATTCCATTTTAACCCTCAAACTTCCAAAAATCTC-ATTTTTAACCCCG-AACTTCCA

                                               *         *             
       1549 AAAATTCCATTTTAACCC-CAAAACTTCCAAAAATTTCATTTTTACCCCCGAACTTCCA
          1 AAAATTCCATTTTAACCCTC-AAACTTCCAAAAATCTCATTTTTAACCCCGAACTTCCA

                 *       
       1607 AAAATCCCATTTT
          1 AAAATTCCATTTT

       1620 TGATCTTGAA


Statistics
Matches: 64,  Mismatches: 5, Indels: 5
        0.86            0.07        0.07

Matches are distributed among these distances:
  58   21  0.33
  59   42  0.66
  60    1  0.02

ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33


Consensus pattern (58 bp):   
AAAATTCCATTTTAACCCTCAAACTTCCAAAAATCTCATTTTTAACCCCGAACTTCCA

Done.