Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005842.1 Kokia drynarioides strain JFW-HI SEQ_120138, 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: 15012
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34


Found at i:1471 original size:28 final size:28

Alignment explanation


    Indices: 1438--1504  Score: 82
    Period size: 28  Copynumber: 2.4  Consensus size: 28

       1428 TTTTGACATT

                          *              
       1438 GTGATGACGTGAATGGGAACGA-TACGAC
          1 GTGATGACGTGAATAGGAAC-ATTACGAC

                    * *                 
       1466 GTGATGACATAAATAGGAACATTACGAC
          1 GTGATGACGTGAATAGGAACATTACGAC

                *      
       1494 GTGACGACGTG
          1 GTGATGACGTG

       1505 TTCCTCACAT


Statistics
Matches: 32,  Mismatches: 6, Indels: 2
        0.80            0.15        0.05

Matches are distributed among these distances:
  27    1  0.03
  28   31  0.97

ACGTcount: A:0.34, C:0.15, G:0.31, T:0.19


Consensus pattern (28 bp):   
GTGATGACGTGAATAGGAACATTACGAC

Found at i:2176 original size:24 final size:24

Alignment explanation


    Indices: 2144--2208  Score: 130
    Period size: 24  Copynumber: 2.7  Consensus size: 24

       2134 GGGGTCACGC

                                    
       2144 GACAATAATATCAAATAGTGACGT
          1 GACAATAATATCAAATAGTGACGT

                                    
       2168 GACAATAATATCAAATAGTGACGT
          1 GACAATAATATCAAATAGTGACGT

                             
       2192 GACAATAATATCAAATA
          1 GACAATAATATCAAATA

       2209 ATACATACAA


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   41  1.00

ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25


Consensus pattern (24 bp):   
GACAATAATATCAAATAGTGACGT

Found at i:4329 original size:2 final size:2

Alignment explanation


    Indices: 4322--4346  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       4312 TAAAAATTTG

                                                 
       4322 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

       4347 AAGAGAGAGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:4530 original size:7 final size:7

Alignment explanation


    Indices: 4503--4547  Score: 54
    Period size: 7  Copynumber: 6.4  Consensus size: 7

       4493 AGTGAACCTT

                *  
       4503 AACAATC
          1 AACATTC

                  *
       4510 AACATTT
          1 AACATTC

              *    
       4517 AATATTC
          1 AACATTC

                   
       4524 AACATTC
          1 AACATTC

                   
       4531 AACATTC
          1 AACATTC

                 * 
       4538 AACATAC
          1 AACATTC

               
       4545 AAC
          1 AAC

       4548 GTACAACCGC


Statistics
Matches: 32,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
   7   32  1.00

ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27


Consensus pattern (7 bp):   
AACATTC

Found at i:6313 original size:38 final size:38

Alignment explanation


    Indices: 6271--6346  Score: 134
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       6261 GATTAAATCA

                                                  
       6271 GATTTTTATATTTTTACAAGGTCAAAATACAATTTTAT
          1 GATTTTTATATTTTTACAAGGTCAAAATACAATTTTAT

                             *           *        
       6309 GATTTTTATATTTTTACGAGGTCAAAATATAATTTTAT
          1 GATTTTTATATTTTTACAAGGTCAAAATACAATTTTAT

       6347 CTTTACCAAT


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  38   36  1.00

ACGTcount: A:0.36, C:0.07, G:0.09, T:0.49


Consensus pattern (38 bp):   
GATTTTTATATTTTTACAAGGTCAAAATACAATTTTAT

Found at i:11935 original size:23 final size:21

Alignment explanation


    Indices: 11909--11973  Score: 58
    Period size: 22  Copynumber: 2.9  Consensus size: 21

      11899 ATTGATTGAC

                                   
      11909 TTAATAAATTTAAAATATATATT
          1 TTAATAAATTT-AAATATAT-TT

                  *               
      11932 TTAATTTAATTTAAATATATTT
          1 TTAA-TAAATTTAAATATATTT

            *     *   *         
      11954 ATAATATATGATAAATATAT
          1 TTAATAAAT-TTAAATATAT

      11974 AACGCATTAT


Statistics
Matches: 35,  Mismatches: 5, Indels: 5
        0.78            0.11        0.11

Matches are distributed among these distances:
  21    3  0.09
  22   14  0.40
  23   12  0.34
  24    6  0.17

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (21 bp):   
TTAATAAATTTAAATATATTT
Done.