Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005941.1 Kokia drynarioides strain JFW-HI SEQ_120327, 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: 5802
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36

Warning! 4 characters in sequence are not A, C, G, or T


Found at i:244 original size:4 final size:4

Alignment explanation


    Indices: 237--279  Score: 61
    Period size: 4  Copynumber: 10.8  Consensus size: 4

        227 TTCTTCCTTC

                                             *                    
        237 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
          1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC

        280 CTTCATTTTT


Statistics
Matches: 35,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   3    3  0.09
   4   29  0.83
   5    3  0.09

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (4 bp):   
TTCT

Found at i:276 original size:11 final size:11

Alignment explanation


    Indices: 234--290  Score: 60
    Period size: 11  Copynumber: 4.9  Consensus size: 11

        224 TCCTTCTTCC

                 *     
        234 TTCTTCTTTCT
          1 TTCTTTTTTCT

                         
        245 TTCTTTCTTTCTT
          1 TTCTTT-TTTC-T

                        
        258 TCTCTTTTTTCT
          1 T-TCTTTTTTCT

                      *
        270 TTCTTTTTTCC
          1 TTCTTTTTTCT

               *      
        281 TTCATTTTTC
          1 TTCTTTTTTC

        291 GTTGGTCCCC


Statistics
Matches: 40,  Mismatches: 3, Indels: 6
        0.82            0.06        0.12

Matches are distributed among these distances:
  11   23  0.57
  12    6  0.15
  13    6  0.15
  14    5  0.12

ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74


Consensus pattern (11 bp):   
TTCTTTTTTCT

Found at i:3613 original size:2 final size:2

Alignment explanation


    Indices: 3606--3631  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       3596 ACGACATTAG

                                                  
       3606 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       3632 TAAGAATCGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:3865 original size:62 final size:62

Alignment explanation


    Indices: 3781--3907  Score: 200
    Period size: 62  Copynumber: 2.0  Consensus size: 62

       3771 TTTTTAATAG

                                        *         *                       
       3781 AATAAAAATATAAGTTCACATATTAAAAGAAACATTACTTTCATTTTTCTAATTTTACTGTA
          1 AATAAAAATATAAGTTCACATATTAAAAAAAACATTACCTTCATTTTTCTAATTTTACTGTA

                         *                   *  *           *             
       3843 AATAAAAATATAATTTCACATATTAAAAAAAACCTTGCCTTCATTTTTTTAATTTTACTGTA
          1 AATAAAAATATAAGTTCACATATTAAAAAAAACATTACCTTCATTTTTCTAATTTTACTGTA

               
       3905 AAT
          1 AAT

       3908 CAAGGTAAAT


Statistics
Matches: 59,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  62   59  1.00

ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41


Consensus pattern (62 bp):   
AATAAAAATATAAGTTCACATATTAAAAAAAACATTACCTTCATTTTTCTAATTTTACTGTA
Done.