Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005473.1 Kokia drynarioides strain JFW-HI SEQ_119522, 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: 3741
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31


Found at i:2665 original size:216 final size:215

Alignment explanation


    Indices: 2163--2850  Score: 876
    Period size: 216  Copynumber: 3.2  Consensus size: 215

       2153 AAAAAACTAT

                     *                           *                   *       
       2163 AAAAGAACTTGTAAAAGTTTGACAAGTTCGAAAGTTCATCCATGAACCAAGAGAGAAGCAATTCT
          1 AAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCATGAACCAAGAGAGAAACAATTCT

            * *  *      *               *                *                   
       2228 TAGGTTAATAAGATTTTAATTCAAAGACCAAAACTTGTTTACAAACTGACAAACTATTTAGACCA
         66 CACGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAGA-CA

                          *     *      *  *                   *    *      * *
       2293 ACAA-GATGCGATTCCCCGACCATGGACTGCTCAAAAAATTGCTCGATGGAACATAGATCATCTC
        130 A-AATGATGCGATTTCCCGAGCATGGAATGTTCAAAAAATTGCTC-ATGGGA-ATGGATC-TTTG

                        *           *
       2357 GAATACTTTAAGCAACAGAAGTTAT
        191 GAATACTTTAAGGAACAGAAGTTAA

                     *                                                       
       2382 AAAAGAACTTGTAAAAGTTTGACAAGTTCGAAAGCTT-GTCCATGAACCAAGAGAGAAACAATTC
          1 AAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG-TTCGTCCATGAACCAAGAGAGAAACAATTC

                *                                                            
       2446 TCACATAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAGACA
         65 TCACGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAGACA

                    *                                *                       
       2511 AAATGATGAGATTTCCCGAGCATGGAATGTTCAAAAAATTGATCATGGGAATGGATCTTTGTGAA
        130 AAATGATGCGATTTCCCGAGCATGGAATGTTCAAAAAATTGCTCATGGGAATGGATCTTTG-GAA

                   *      *       
       2576 TACTTTAGGGAACAAAAGTTAA
        194 TACTTTAAGGAACAGAAGTTAA

                *                                     *    *          *      
       2598 AAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAAAAATTCT
          1 AAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCATGAACCAAGAGAGAAACAATTCT

                  *    *    *                 ** *                      *  * 
       2663 CACGTACATAAATTTTCAATTCAAAGACTAAAACCCGATTACAAAATGACAAACTATTTAAACCA
         66 CACGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAGACAA

                      *   * *               *          *                     
       2728 AATGATGCGAATTCTCAAGCATGGAATGTTCAGAAAATTGCTCGTGGGAATGGATCTTCTGGAAT
        131 AATGATGCGATTTCCCGAGCATGGAATGTTCAAAAAATTGCTCATGGGAATGGATCTT-TGGAAT

                           *     
       2793 ACTTTAAGGAACAGATGTTAA
        195 ACTTTAAGGAACAGAAGTTAA

                *  *                             
       2814 AAAATAAATCGTAAAAGTTTGACAAGTTCGGAAAGTT
          1 AAAAGAACTCGTAAAAGTTTGACAAGTTC-GAAAGTT

       2851 TGACAGACTA


Statistics
Matches: 415,  Mismatches: 48, Indels: 14
        0.87            0.10        0.03

Matches are distributed among these distances:
 215    4  0.01
 216  241  0.58
 217   16  0.04
 218   37  0.09
 219  115  0.28
 220    2  0.00

ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26


Consensus pattern (215 bp):   
AAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCATGAACCAAGAGAGAAACAATTCT
CACGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAGACAA
AATGATGCGATTTCCCGAGCATGGAATGTTCAAAAAATTGCTCATGGGAATGGATCTTTGGAATA
CTTTAAGGAACAGAAGTTAA

Found at i:3490 original size:17 final size:17

Alignment explanation


    Indices: 3470--3502  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       3460 TTTAAGGACT

                              
       3470 TTTTAATTTTA-TTTAAG
          1 TTTT-ATTTTAGTTTAAG

                            
       3487 TTTTATTTTAGTTTAA
          1 TTTTATTTTAGTTTAA

       3503 TAAGTGTTTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    6  0.40
  17    9  0.60

ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67


Consensus pattern (17 bp):   
TTTTATTTTAGTTTAAG
Done.