Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000454.1 Kokia drynarioides strain JFW-HI SEQ_111311, 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: 1901
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37


Found at i:762 original size:249 final size:246

Alignment explanation


    Indices: 4--776  Score: 893
    Period size: 251  Copynumber: 3.1  Consensus size: 246

          1 TCA

                  *     *              *                            * *      
          4 TCTCTTGTCACTCAGATAAACTTAATTTTTCTA-TCATTCAAACTTATTTCTTCTCGTATCTCAT
          1 TCTCTTCTCACTTAGATAAACTTAATTCTTC-ACTCATTCAAACTTATTTCTTCTCTTCTCTCA-

                           *                                   *             
         68 TTCTTCATC-TTTTCAATTAGTTAGTTGATGTTAAGATGATGAAAGGAAAACGAAAAGTGAGTAA
         64 TTCTTCATCTTTTTCTATTAGTTAGTTGATGTTAAGATGATGAAAGGAAAAGGAAAAGTGAGTAA

             *      *  * *     *          *                *                 
        132 TGAAGTTGCTGGCTAACCTTCAGATAAACCATTATA-TA--TATAT-GT-ACATCATCTTAGAAT
        129 TTAAGTTGATGCCAAACCTACAG-TAAACCTTTATATTATTTATATATTGACATCATCTTAGAAT

                                           *            *     *   
        192 TATATATATTTATATTTGCCATTACTTAATGTCAAAATGAACCTATATATGTTC
        193 TATATATATTTATATTTGCCATTACTTAATGCCAAAATGAACCTGTATATATTC

                           *               * *                          *  * 
        246 TCTCTTCTCACTTAGGTAAACTTAATTCTTCTCCCATTCAAACTTATTTCTTCTCTTCTCCCTTT
          1 TCTCTTCTCACTTAGATAAACTTAATTCTTCACTCATTCAAACTTATTTCTTCTCTTCTCTC-AT

                           *  **            *    *                           
        311 TCTTCATCTTTTTCTGTTTCTTAGTTGATGTTCAGATTATGAAAGGAAAAGGAAAAGTGAGTAA-
         65 TCTTCATCTTTTTCTATTAGTTAGTTGATGTTAAGATGATGAAAGGAAAAGGAAAAGTGAGTAAT

                               *  * *                                        
        375 TAAGGTT-ACTGCCAAACGTTAGAATAAACCTTTATATATATAAATTA-ATATTGACATCATCTT
        130 TAA-GTTGA-TGCCAAAC-CTACAGTAAACCTTTATAT-TAT---TTATATATTGACATCATCTT

              *                            *                            
        438 AGTATTATATATATTTATATTTGCCATTACTCAAT-CTCAAAATGAACCTGTATATATTC
        188 AGAATTATATATATTTATATTTGCCATTACTTAATGC-CAAAATGAACCTGTATATATTC

                                                                             
        497 TCTCTTCTCACTTAGATAAACTTAATTCTTCACTCATTCAAACTTATTTCTTCTCTTCTCTCATT
          1 TCTCTTCTCACTTAGATAAACTTAATTCTTCACTCATTCAAACTTATTTCTTCTCTTCTCTCATT

                          *       *  *             *       *                 
        562 CTTCATCTTTTTCTCTTAGTTAATTTATGTTAAGATGATTAAAGGAATAGGAAAAGTGAGTAATT
         66 CTTCATCTTTTTCTATTAGTTAGTTGATGTTAAGATGATGAAAGGAAAAGGAAAAGTGAGTAATT

                    *       *     *                                   *      
        627 AAGTTGATTCCAAACCCACAGTTAACCTTTATATGTATGTTTATATATTGACATCATCCTAGAAT
        131 AAGTTGATGCCAAACCTACAGTAAACCTTTATAT-TA--TTTATATATTGACATCATCTTAGAAT

             *        * *       *                *   *           *
        692 TGTATATATTGACATTTGCCTTTACTTAATGCCAAAACGAATCTGTATATATTT
        193 TATATATATTTATATTTGCCATTACTTAATGCCAAAATGAACCTGTATATATTC

                *                          
        746 TCTCCTCTCACTTAGATAAACTTAATTCTTC
          1 TCTCTTCTCACTTAGATAAACTTAATTCTTC

        777 TCCCATTTCT


Statistics
Matches: 445,  Mismatches: 64, Indels: 37
        0.82            0.12        0.07

Matches are distributed among these distances:
 242   63  0.14
 243   68  0.15
 244    2  0.00
 245    2  0.00
 248    3  0.01
 249  111  0.25
 250   70  0.16
 251  126  0.28

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


Consensus pattern (246 bp):   
TCTCTTCTCACTTAGATAAACTTAATTCTTCACTCATTCAAACTTATTTCTTCTCTTCTCTCATT
CTTCATCTTTTTCTATTAGTTAGTTGATGTTAAGATGATGAAAGGAAAAGGAAAAGTGAGTAATT
AAGTTGATGCCAAACCTACAGTAAACCTTTATATTATTTATATATTGACATCATCTTAGAATTAT
ATATATTTATATTTGCCATTACTTAATGCCAAAATGAACCTGTATATATTC

Found at i:1354 original size:24 final size:24

Alignment explanation


    Indices: 1327--1418  Score: 166
    Period size: 24  Copynumber: 3.8  Consensus size: 24

       1317 ATCAAATAAC

                                    
       1327 TAAACAGAGTTTAATTGAAACAAA
          1 TAAACAGAGTTTAATTGAAACAAA

                                    
       1351 TAAACAGAGTTTAATTGAAACAAA
          1 TAAACAGAGTTTAATTGAAACAAA

                                    
       1375 TAAACAGAGTTTAATTGAAACAAA
          1 TAAACAGAGTTTAATTGAAACAAA

                *         *     
       1399 TAAATAGAGTTTAACTGAAA
          1 TAAACAGAGTTTAATTGAAA

       1419 GATTATTTCT


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:0.53, C:0.08, G:0.13, T:0.26


Consensus pattern (24 bp):   
TAAACAGAGTTTAATTGAAACAAA

Done.