Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000048.1 Kokia drynarioides strain JFW-HI SEQ_93543, 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: 8215
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:4594 original size:3 final size:3

Alignment explanation


    Indices: 4586--4617  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       4576 TTTAAATTAT

                                                      
       4586 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT

       4618 ATTATTATTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTC

Found at i:5485 original size:17 final size:18

Alignment explanation


    Indices: 5447--5486  Score: 66
    Period size: 17  Copynumber: 2.3  Consensus size: 18

       5437 AAAAAAATAT

                              
       5447 TAAATATTAAATTAAGAA
          1 TAAATATTAAATTAAGAA

                              
       5465 -AAATATTAAATTAA-AA
          1 TAAATATTAAATTAAGAA

                  
       5481 TAAATA
          1 TAAATA

       5487 AATAAAAACC


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    2  0.10
  17   19  0.90

ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33


Consensus pattern (18 bp):   
TAAATATTAAATTAAGAA

Found at i:6065 original size:9 final size:9

Alignment explanation


    Indices: 6053--6128  Score: 55
    Period size: 9  Copynumber: 8.1  Consensus size: 9

       6043 AATTATTAAA

                     
       6053 AAAAATTAT
          1 AAAAATTAT

                  * *
       6062 AAAAATCAC
          1 AAAAATTAT

                      
       6071 AAATAA-TAT
          1 AAA-AATTAT

                  *   
       6080 AAAATAATAT
          1 AAAA-ATTAT

            *         
       6090 TAAAATTGAT
          1 AAAAATT-AT

                 *    
       6100 ATAAACTTAT
          1 A-AAAATTAT

                     
       6110 AAAAATTAT
          1 AAAAATTAT

                 *   
       6119 AAAAAATAT
          1 AAAAATTAT

             
       6128 A
          1 A

       6129 TTAAATACTA


Statistics
Matches: 52,  Mismatches: 10, Indels: 10
        0.72            0.14        0.14

Matches are distributed among these distances:
   8    1  0.02
   9   33  0.63
  10   13  0.25
  11    5  0.10

ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30


Consensus pattern (9 bp):   
AAAAATTAT

Found at i:6095 original size:11 final size:10

Alignment explanation


    Indices: 6071--6143  Score: 51
    Period size: 10  Copynumber: 7.3  Consensus size: 10

       6061 TAAAAATCAC

                      
       6071 AAATAATATA
          1 AAATAATATA

                       
       6081 AAATAATATTA
          1 AAATAATA-TA

                 *     
       6092 AAATTGATATA
          1 AAA-TAATATA

              * *     
       6103 AACTTATA-A
          1 AAATAATATA

                *   * 
       6112 AAATTATAAA
          1 AAATAATATA

                     *
       6122 AAAT-ATATT
          1 AAATAATATA

                 *    
       6131 AAATACTATA
          1 AAATAATATA

               
       6141 AAA
          1 AAA

       6144 ATTTATTTAA


Statistics
Matches: 51,  Mismatches: 8, Indels: 8
        0.76            0.12        0.12

Matches are distributed among these distances:
   9   15  0.29
  10   23  0.45
  11    9  0.18
  12    4  0.08

ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33


Consensus pattern (10 bp):   
AAATAATATA
Done.