Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002437.1 Kokia drynarioides strain JFW-HI SEQ_114547, 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: 26262
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33


Found at i:442 original size:3 final size:3

Alignment explanation


    Indices: 434--482  Score: 62
    Period size: 3  Copynumber: 16.0  Consensus size: 3

        424 GGGCCCTAAA

                              *                       *      *          
        434 AAT AAT AAT AAT ATTT AAT AAT AAT AAT AAT AGT AAT GAT AAT AAT
          1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

               
        480 AAT
          1 AAT

        483 TTGGATCCTT


Statistics
Matches: 39,  Mismatches: 6, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
   3   37  0.95
   4    2  0.05

ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37


Consensus pattern (3 bp):   
AAT

Found at i:996 original size:42 final size:42

Alignment explanation


    Indices: 941--1148  Score: 273
    Period size: 42  Copynumber: 5.0  Consensus size: 42

        931 ACAATGAAAA

                *            *  *       *             
        941 AAAAATAAATGGACCTCTACGCTTGGGCTTCTAAATGCAATG
          1 AAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCAATG

                                                        
        983 AAAAGTAAATGGACCTCCACA-TCTGGG-CTCCTAAATGCAATG
          1 AAAAGTAAATGGACCTCCACACT-TGGGCCT-CTAAATGCAATG

                       * *           *                
       1025 AAAAGTAAATGAAACTCCACACTTGAGCCTCTAAATGCAATG
          1 AAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCAATG

                       *                              
       1067 AAAAGTAAATGAACCT-C-CACTTGGG-CTCTAAATGCAATG
          1 AAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCAATG

                                  * *                 
       1106 AAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATG
          1 AAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCAATG

             
       1148 A
          1 A

       1149 GTGCTTTCCT


Statistics
Matches: 147,  Mismatches: 12, Indels: 14
        0.85            0.07        0.08

Matches are distributed among these distances:
  39   29  0.20
  40    8  0.05
  41    9  0.06
  42   98  0.67
  43    3  0.02

ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22


Consensus pattern (42 bp):   
AAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCAATG

Found at i:3458 original size:19 final size:19

Alignment explanation


    Indices: 3436--3484  Score: 98
    Period size: 19  Copynumber: 2.6  Consensus size: 19

       3426 TCAAGATTCT

                               
       3436 TGAATCAAAGGATTTAGAA
          1 TGAATCAAAGGATTTAGAA

                               
       3455 TGAATCAAAGGATTTAGAA
          1 TGAATCAAAGGATTTAGAA

                       
       3474 TGAATCAAAGG
          1 TGAATCAAAGG

       3485 TAATCACTAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   30  1.00

ACGTcount: A:0.47, C:0.06, G:0.22, T:0.24


Consensus pattern (19 bp):   
TGAATCAAAGGATTTAGAA

Done.