Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013184.1 Kokia drynarioides strain JFW-HI SEQ_128203, 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, 863

Length: 1439
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.37

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:340 original size:195 final size:195

Alignment explanation


    Indices: 8--403  Score: 605
    Period size: 195  Copynumber: 2.0  Consensus size: 195

          1 AATTTTG

                                 *                                   *    *  
          8 TCATTTTGTAAAAAAGTTTTGGCCTTTGAATAGAAAACTTATTTATATGAGAATTGTTTCTCTCT
          1 TCATTTTGTAAAAAAGTTTTGACCTTTGAATAGAAAACTTATTTATATGAGAATTGTCTCTCCCT

             *                  *                               *            
         73 TTGTTGTTGGACGAACTTCCGAACTTGCCAAACTTTTACGAGTTCTTTCTTATATCCGGTTCCTT
         66 TGGTTGTTGGACGAACTTCCAAACTTGCCAAACTTTTACGAGTTCTTTCTTAAATCCGGTTCCTT

                            * *   *                                      *   
        138 AAAATGTTCAAGAAAATCTATTTCTTCGAGTAATTTTTCGAACATTCAATGCGAGGGAAATTGCA
        131 AAAATGTTCAAGAAAACCCATTCCTTCGAGTAATTTTTCGAACATTCAATGCGAGGGAAATCGCA

                        *                                  *                 
        203 TCATTTTGTAAACAAGTTTTGACCTTTGAATTA-AAAACTTATTTATGTGAGAATTGTCTCTCCC
          1 TCATTTTGTAAAAAAGTTTTGACCTTTGAA-TAGAAAACTTATTTATATGAGAATTGTCTCTCCC

                               *        *                    *       *       
        267 TTGGTTGTTGGACGAACTTGCAAACTTGTCAAACTTTTACGAGTTCTTTTTTAAATCTGGTTCCT
         65 TTGGTTGTTGGACGAACTTCCAAACTTGCCAAACTTTTACGAGTTCTTTCTTAAATCCGGTTCCT

                          *                        *        *                
        332 TAAAATGTTCAAGACAACCCATTCCTTCGAGTAATTTTTTGAACATTCCATGCGAGGGAAATCGC
        130 TAAAATGTTCAAGAAAACCCATTCCTTCGAGTAATTTTTCGAACATTCAATGCGAGGGAAATCGC

             
        397 A
        195 A

                  
        398 TCATTT
          1 TCATTT

        404 AGTCTAAATA


Statistics
Matches: 181,  Mismatches: 19, Indels: 2
        0.90            0.09        0.01

Matches are distributed among these distances:
 195  179  0.99
 196    2  0.01

ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39


Consensus pattern (195 bp):   
TCATTTTGTAAAAAAGTTTTGACCTTTGAATAGAAAACTTATTTATATGAGAATTGTCTCTCCCT
TGGTTGTTGGACGAACTTCCAAACTTGCCAAACTTTTACGAGTTCTTTCTTAAATCCGGTTCCTT
AAAATGTTCAAGAAAACCCATTCCTTCGAGTAATTTTTCGAACATTCAATGCGAGGGAAATCGCA

Found at i:594 original size:224 final size:215

Alignment explanation


    Indices: 207--880  Score: 692
    Period size: 224  Copynumber: 3.1  Consensus size: 215

        197 ATTGCATCAT

                              * *      *             * *  *    * *    *      
        207 TTTGTAAACAAGTTTTGACCTTTGAATTAAAAACTTATTTATGTGAGAATTGTCTCTCCCTTGGT
          1 TTTGTAAACAAGTTTTGATCATTGAATGAAAAACTTATTTACGCGACAATTATGTCTCTCTTGGT

             *            *        *       *     *            *             *
        272 TGTTGGACGAACTTGCAAACTTGTCAAACTTTTACGAGTTCTTTTTTAAATCTGGTTCCTTAAAA
         66 TCTTGGACGAACTTCCAAACTTGCCAAACTTGTACGAATTCTTTTTTAAAACTGGTTCCTTAAAG

                        *                     *                              
        337 TGTTCAAGACAACCCATTCCTTCGAGTAATTTTTTGAACATTCCATGCGAGGGAAATCGCATCAT
        131 TGTTCAAGACAATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCGAGGGAAATCGCATCAT

              *                 
        402 TTAGTCTAAATAGTTTTTCA
        196 TTGGTCTAAATAGTTTTTCA

                           *                *            *  *            *   
        422 TTTCGTAAACAAGTTCTGATCATT-AAGTGAAGAACTTATTTACGTGAGAATTATGTCTCTTTTG
          1 TTT-GTAAACAAGTTTTGATCATTGAA-TGAAAAACTTATTTACGCGACAATTATGTCTCTCTTG

                     *                                *                      
        486 GTTCTTGGATGAACTTCCAAACTT-CCAAACTTGT-CGAATTTTTACAAGTTCTTAAACAACTTC
         64 GTTCTTGGACGAACTTCCAAACTTGCCAAACTTGTACGAATTCTT-----TT-TT-AA-AAC-T-

                         *        *     *      *  *               *      *   
        549 GGTTCCTTAAAGTATTCAAGACGATCCAATCCTTCAAGCAATTTTTCGAACATTACATGCTCA-G
        119 GGTTCCTTAAAGTGTTCAAGACAATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGC-GAGG

               *  **               *     *   
        613 GAAGTCATATCATTTGGTCTAAAAAGTTTGTCA
        183 GAAATCGCATCATTTGGTCTAAATAGTTTTTCA

                *    *       ** *      *             *         * *           
        646 TTTGAAAACTAGTTTTGGCCTTTGAATTAAAAACTTATTTATGCGACAATTGTTTCTCTCTTGGT
          1 TTTGTAAACAAGTTTTGATCATTGAATGAAAAACTTATTTACGCGACAATTATGTCTCTCTTGGT

             *              *      *       *     *            *              
        711 TGTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTTTAAATCTGGTTCCTTAAAG
         66 TCTTGGACGAACTTCCAAACTTGCCAAACTTGTACGAATTCTTTTTTAAAACTGGTTCCTTAAAG

                                             *                  *            
        776 TGTTCAAGACAAT-CATTCCTTCGAGTAATTTTCCGAACATTCCATGCGAGGTAAATCGCATCAT
        131 TGTTCAAGACAATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCGAGGGAAATCGCATCAT

                                
        840 TTGGTCTAAATAGTTTTTCA
        196 TTGGTCTAAATAGTTTTTCA

                                 
        860 TTTTGTAAACAAGTTTTGATC
          1 -TTTGTAAACAAGTTTTGATC

        881 TTTCAATTAA


Statistics
Matches: 367,  Mismatches: 74, Indels: 36
        0.77            0.16        0.08

Matches are distributed among these distances:
 213    1  0.00
 214   64  0.17
 215   52  0.14
 216   69  0.19
 217    2  0.01
 218    2  0.01
 219    4  0.01
 220    4  0.01
 221    2  0.01
 222    2  0.01
 223   65  0.18
 224   92  0.25
 225    8  0.02

ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39


Consensus pattern (215 bp):   
TTTGTAAACAAGTTTTGATCATTGAATGAAAAACTTATTTACGCGACAATTATGTCTCTCTTGGT
TCTTGGACGAACTTCCAAACTTGCCAAACTTGTACGAATTCTTTTTTAAAACTGGTTCCTTAAAG
TGTTCAAGACAATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCGAGGGAAATCGCATCAT
TTGGTCTAAATAGTTTTTCA
Done.