Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003315.1 Kokia drynarioides strain JFW-HI SEQ_116004, 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: 1902
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35


Found at i:513 original size:24 final size:24

Alignment explanation


    Indices: 485--576  Score: 157
    Period size: 24  Copynumber: 3.8  Consensus size: 24

        475 AGAAATAATC

                 *                  
        485 TTTCAGTTAAACTCTATTTATTTG
          1 TTTCAATTAAACTCTATTTATTTG

                                    
        509 TTTCAATTAAACTCTATTTATTTG
          1 TTTCAATTAAACTCTATTTATTTG

                           *        
        533 TTTCAATTAAACTCTGTTTATTTG
          1 TTTCAATTAAACTCTATTTATTTG

                           *    
        557 TTTCAATTAAACTCTGTTTA
          1 TTTCAATTAAACTCTATTTA

        577 GTTATTTGAT


Statistics
Matches: 66,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  24   66  1.00

ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53


Consensus pattern (24 bp):   
TTTCAATTAAACTCTATTTATTTG

Found at i:599 original size:48 final size:48

Alignment explanation


    Indices: 485--600  Score: 135
    Period size: 48  Copynumber: 2.4  Consensus size: 48

        475 AGAAATAATC

                 *       * *                            *  *
        485 TTTCAGTTAAACTCTATTTATTTGTTTCAATTAAACTCTATTTATTTG
          1 TTTCAATTAAACTATGTTTATTTGTTTCAATTAAACTCTATTTAGTTA

                         *                         *        
        533 TTTCAATTAAACTCTGTTTATTTGTTTCAATTAAACTCTGTTTAGTTA
          1 TTTCAATTAAACTATGTTTATTTGTTTCAATTAAACTCTATTTAGTTA

                *       *        
        581 TTT-GATTCAAATTATGTTTA
          1 TTTCAATT-AAACTATGTTTA

        601 GTCTAGATTA


Statistics
Matches: 59,  Mismatches: 8, Indels: 2
        0.86            0.12        0.03

Matches are distributed among these distances:
  47    3  0.05
  48   56  0.95

ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53


Consensus pattern (48 bp):   
TTTCAATTAAACTATGTTTATTTGTTTCAATTAAACTCTATTTAGTTA

Found at i:1650 original size:251 final size:248

Alignment explanation


    Indices: 1120--1899  Score: 929
    Period size: 251  Copynumber: 3.2  Consensus size: 248

       1110 AAGATGAAGA

                *                            *    *           *   *          
       1120 AATGGGAGAAGAATTAAGTTTATCTAAGTGAGAGGAGAAAATATATACAGATTCGTTTTG-GCAT
          1 AATGAGAGAAGAATTAAGTTTATCTAAGTGAGAAGAGAGAATATATACAGGTTCATTTTGAG-AT

                   *       * *        *       *                   *   *      
       1184 TAAGTAAAGGCAAATGTCAATATATACAATTCTAGGATGATGTCAATATATAAACATACATATAA
         65 TAAGTAATGGCAAATATAAATATATATAATTCTAAGATGATGTCAATAT-T-AATATATATATAA

                   *   **         *                        *       *         
       1249 AGG-TTAACTGTGGGTTTGG-AATCAACTTAATTACTCACTTTTCCTATTCCTTTAATCATCTTA
        128 AGGTTTATCT-AAGGTTTGGCAGT-AACTTAATTACTCACTTTTCCTTTTCCTTTCATCATCTTA

                *  *       *                                          
       1312 ACATAAATTAACTAAGAGAAAAAGATGAAG-AATGAGAGAAGAGAAGAAATAAGTTTG
        191 ACATCAACTAACTAACAGAAAAAGATGAAGAAATGAGAGAAGAGAAGAAATAAGTTTG

                  *                                                          
       1369 AATGAGTGAAGAATTAAGTTTATCTAAGTGAGAAGAGAGAATATATACAGGTTCATTTTGAGATT
          1 AATGAGAGAAGAATTAAGTTTATCTAAGTGAGAAGAGAGAATATATACAGGTTCATTTTGAGATT

            *                            *                                   
       1434 GAGTAATGGCAAATATAAATATATATAATACTAAGATGATGTCAATATTAATTTATATATATAAA
         66 AAGTAATGGCAAATATAAATATATATAATTCTAAGATGATGTCAATATTAA--TATATATATAAA

                        *                                            *    *  
       1499 GGTTTATTCTAACGTTTGGCAGTAACCTT-ATTACTCACTTTTCCTTTTCCTTTCATAATCTGAA
        129 GGTTTA-TCTAAGGTTTGGCAGTAA-CTTAATTACTCACTTTTCCTTTTCCTTTCATCATCTTAA

                      **                    * *                      
       1563 CATCAACTAAGAAACAGAAAAAGATGAAGAAAAGGGAGAAGAGAAGAAATAAGTTTG
        192 CATCAACTAACTAACAGAAAAAGATGAAGAAATGAGAGAAGAGAAGAAATAAGTTTG

                *                 *                  *     *             *   
       1620 AATGGGAGAAGAATTAAGTTTACCTAAGTGAGAAGAGAGAACATATATAGGTTCATTTTGACATT
          1 AATGAGAGAAGAATTAAGTTTATCTAAGTGAGAAGAGAGAATATATACAGGTTCATTTTGAGATT

                                                                             
       1685 AAGTAATGGCAAATATAAATATATATAATTCTAAGATGATGT-ACATA-T-ATATATA-AT---G
         66 AAGTAATGGCAAATATAAATATATATAATTCTAAGATGATGTCA-ATATTAATATATATATAAAG

                           * *   *     *              *                      
       1743 GTTTATCTGAAGGTTAGCCAGCAACTTCATTACTCACTTTTCGTTTTCCTTTCATCATCTTAACA
        130 GTTTATCT-AAGGTTTGGCAGTAACTTAATTACTCACTTTTCCTTTTCCTTTCATCATCTTAACA

                        **                     * *                 
       1808 TCAACTAACTAATTG-AAAAGATGAAGAAATGAGATACGAGAAGAAATAAGTTTG
        194 TCAACTAACTAACAGAAAAAGATGAAGAAATGAGAGAAGAGAAGAAATAAGTTTG

                 *    *              *     *      
       1862 AATGATAGAAAAATTAAGTTTATCTGAGTGACAAGAGA
          1 AATGAGAGAAGAATTAAGTTTATCTAAGTGAGAAGAGA

       1900 TGA


Statistics
Matches: 460,  Mismatches: 60, Indels: 29
        0.84            0.11        0.05

Matches are distributed among these distances:
 242   73  0.16
 243   62  0.13
 246    2  0.00
 247    8  0.02
 248    1  0.00
 249  111  0.24
 250   69  0.15
 251  134  0.29

ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31


Consensus pattern (248 bp):   
AATGAGAGAAGAATTAAGTTTATCTAAGTGAGAAGAGAGAATATATACAGGTTCATTTTGAGATT
AAGTAATGGCAAATATAAATATATATAATTCTAAGATGATGTCAATATTAATATATATATAAAGG
TTTATCTAAGGTTTGGCAGTAACTTAATTACTCACTTTTCCTTTTCCTTTCATCATCTTAACATC
AACTAACTAACAGAAAAAGATGAAGAAATGAGAGAAGAGAAGAAATAAGTTTG
Done.