Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011123.1 Kokia drynarioides strain JFW-HI SEQ_126096, 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: 16638
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:459 original size:258 final size:257

Alignment explanation


    Indices: 1--561  Score: 804
    Period size: 258  Copynumber: 2.2  Consensus size: 257

                                                                             
          1 ATAAGGTCCATATGGTACCAATTTACAACACCTGAAACAAATGTTAGGAAAGCTCATATTTTACA
          1 ATAAGGTCCATATGGTACCAATTTACAACACCTGAAACAAATGTTAGGAAAGCTCATATTTTACA

                               *  *                       *      **          
         66 ATCATATCCGAGTCTTATATGATATTAGAAAAGCTCTTTTGATAACTCAAGATTGAATAAGAACT
         66 ATCATATCCGAGTCTTATAAGAGATTAGAAAAGCTCTTTTGATAACCCAAGATCAAATAAGAACT

                                              *                            * 
        131 AAAATGTAAAATTTAAATTTAACAGGTTGATGTCTCAACACCAGGATTTCCAAATTGTAACCCTA
        131 AAAATGTAAAATTTAAATTTAACAGGTTGA-GTCGCAACACCAGGATTTCCAAATTGTAACCCCA

                  *                                          *             
        196 CTCACTGTCCATTCCTCTTCACAATGTTAAGGGTCCGACGTCACGATGTGACTTGCTATTTTC
        195 CTCACTATCCATTCCTCTTCACAATGTTAAGGGTCCGACGTCACGATGTAACTTGCTATTTTC

                                                                             
        259 ATAAGGTCCATATGGTACCAATTTACAACACCTGAAACAAATGTTAGGAAAGCTCATATTTTACA
          1 ATAAGGTCCATATGGTACCAATTTACAACACCTGAAACAAATGTTAGGAAAGCTCATATTTTACA

                                   *            *            *            ** 
        324 ATCATATCCGAGTCTTATAAGAGCTTAGGAAAA-CTTTTTTGATAACCCGAGATCAAATAAGGCC
         66 ATCATATCCGAGTCTTATAAGAGATTA-GAAAAGCTCTTTTGATAACCCAAGATCAAATAAGAAC

                                   *               *   *           *     *   
        388 TAAAATGTAAAATTTTAAATTTATC-GAGTTGCA-TCGCGACATCAGGATTTCCAGATTGTGACC
        130 TAAAATGTAAAA-TTTAAATTTAACAG-GTTG-AGTCGCAACACCAGGATTTCCAAATTGTAACC

                                                 **     ***                  
        451 CCACTCACTATCCATTCCTCTTCACAATGTTAAGGGTTTGACGTTGTGATGTAACTTGCTATTTT
        192 CCACTCACTATCCATTCCTCTTCACAATGTTAAGGGTCCGACGTCACGATGTAACTTGCTATTTT

             
        516 C
        257 C

                                 *   *     *     *       
        517 ATAAGGTCCATATGGTACCAACTTAAAACACTTGAAAAAAATGTT
          1 ATAAGGTCCATATGGTACCAATTTACAACACCTGAAACAAATGTT

        562 CACATGCCTT


Statistics
Matches: 271,  Mismatches: 28, Indels: 8
        0.88            0.09        0.03

Matches are distributed among these distances:
 258  250  0.92
 259   20  0.07
 260    1  0.00

ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32


Consensus pattern (257 bp):   
ATAAGGTCCATATGGTACCAATTTACAACACCTGAAACAAATGTTAGGAAAGCTCATATTTTACA
ATCATATCCGAGTCTTATAAGAGATTAGAAAAGCTCTTTTGATAACCCAAGATCAAATAAGAACT
AAAATGTAAAATTTAAATTTAACAGGTTGAGTCGCAACACCAGGATTTCCAAATTGTAACCCCAC
TCACTATCCATTCCTCTTCACAATGTTAAGGGTCCGACGTCACGATGTAACTTGCTATTTTC

Found at i:3601 original size:11 final size:11

Alignment explanation


    Indices: 3585--3614  Score: 60
    Period size: 11  Copynumber: 2.7  Consensus size: 11

       3575 ATTATTATTA

                       
       3585 TAAATTACCAT
          1 TAAATTACCAT

                       
       3596 TAAATTACCAT
          1 TAAATTACCAT

                    
       3607 TAAATTAC
          1 TAAATTAC

       3615 TAATAAATTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37


Consensus pattern (11 bp):   
TAAATTACCAT

Found at i:3621 original size:11 final size:11

Alignment explanation


    Indices: 3584--3623  Score: 53
    Period size: 11  Copynumber: 3.6  Consensus size: 11

       3574 TATTATTATT

                       
       3584 ATAAATTACCA
          1 ATAAATTACCA

            *          
       3595 TTAAATTACCA
          1 ATAAATTACCA

            *        * 
       3606 TTAAATTACTA
          1 ATAAATTACCA

                   
       3617 ATAAATT
          1 ATAAATT

       3624 TAACAAAATA


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   26  1.00

ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38


Consensus pattern (11 bp):   
ATAAATTACCA

Found at i:9978 original size:15 final size:14

Alignment explanation


    Indices: 9955--10005  Score: 66
    Period size: 15  Copynumber: 3.4  Consensus size: 14

       9945 TGTGAACGTT

                          
       9955 TTTTAAAAATAAAA
          1 TTTTAAAAATAAAA

                           
       9969 TTTTATAAAATAAAA
          1 TTTTA-AAAATAAAA

             *              
       9984 TATTAAAAATAATTAA
          1 TTTTAAAAATAA--AA

                  
      10000 TTTTAA
          1 TTTTAA

      10006 TAACCAAAAT


Statistics
Matches: 32,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  14   12  0.38
  15   13  0.41
  16    7  0.22

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (14 bp):   
TTTTAAAAATAAAA

Found at i:11441 original size:49 final size:49

Alignment explanation


    Indices: 11369--11468  Score: 200
    Period size: 49  Copynumber: 2.0  Consensus size: 49

      11359 TAATTAAAGT

                                                             
      11369 ATTTGAACCGCTAAACTTTTAGTCTATATCATGTGATTCAAACATACCA
          1 ATTTGAACCGCTAAACTTTTAGTCTATATCATGTGATTCAAACATACCA

                                                             
      11418 ATTTGAACCGCTAAACTTTTAGTCTATATCATGTGATTCAAACATACCA
          1 ATTTGAACCGCTAAACTTTTAGTCTATATCATGTGATTCAAACATACCA

              
      11467 AT
          1 AT

      11469 ATATGTATAG


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  49   51  1.00

ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35


Consensus pattern (49 bp):   
ATTTGAACCGCTAAACTTTTAGTCTATATCATGTGATTCAAACATACCA
Done.