Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010398.1 Kokia drynarioides strain JFW-HI SEQ_125279, 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, 633

Length: 1056
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41


Found at i:895 original size:393 final size:392

Alignment explanation


    Indices: 156--895  Score: 863
    Period size: 393  Copynumber: 1.9  Consensus size: 392

        146 TCTAAATGTT

                                   *                 *       *               
        156 TTTTTAATTTTGTAAACAACTTTGGTCTTTGAAGTGAAAACTTATTTACGTGAAATTGTTTCTCT
          1 TTTTTAATTTTGTAAACAACTTTCGTCTTTGAAGTGAAAACATATTTACATGAAATTGTTTCTCT

                   *     *        *                        * *               
        221 CTTGGTTTTTGGATGAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCC
         66 CTTGGTTCTTGGACGAACTTCTAAACTTGTCAAACTTTTACGAGTTCCTCTATAACTTCGGTTCC

                 *                            *                   *          
        286 TTAAATTATTCAAGCCGATCCTATCCTTCGACCAGTTTTTCGAACATTCAATGATCGAAAAATCG
        131 TTAAACTATTCAAGCCGATCCTATCCTTCGACCAATTTTTCGAACATTCAATGACCGAAAAATCG

               *               *  *                                     *    
        351 CATTATTTGGTCTAAATAATTTGTCATTTCGTAAACAACTTTTGCTCTTTGAATTAAAAACCTAT
        196 CATCATTTGGTCTAAATAAGTTATCATTTCGTAAACAACTTTTGCTCTTTGAATTAAAAAACTAT

                   *            * * *                       *     * *  *     
        416 TTACGTGCGAACTGTTTCTCTCTTTGTTCTTGGCTGAACATTCGAACTTGTCAAGCTTTTATGAG
        261 TTACGTGAGAACTGTTTCTCCCATGGTTCTTGGCTGAACATTCGAACTAGTCAAACCTTAATGAG

            *             *                                                  
        481 TTCTTTTATAACCTCAGTTCCTTAAACTTATTTATGCTTGGGAAATCACATCGTTTGATCTAAAT
        326 CTCTTTTATAACCTAAGTTCCTTAAACTTATTTATGCTTGGGAAATCACATCGTTTGATCTAAAT

              
        546 AG
        391 AG

                 *         *                    *                            
        548 TTTTTCATTTTGTAATCAACTTTTCGTCTTTGAA-TTAAAA-ATATTTACATGACAATTGTTTCT
          1 TTTTTAATTTTGTAAACAAC-TTTCGTCTTTGAAGTGAAAACATATTTACATGA-AATTGTTTCT

                                            *                                
        611 CTCTTGGTTCTTGGACGAACTTCTAAACTTGTTAAACTTTTTATC-AGTTCCTCTATAACTTCGG
         64 CTCTTGGTTCTTGGACGAACTTCTAAACTTGTCAAAC-TTTTA-CGAGTTCCTCTATAACTTCGG

                              **             * **              *   *   *    *
        675 TTCCTTAAACTATTCAAGGTGATCC-ATTCCTTTGTGCAATTTTTC-AAGCTTTCCATGCCCGAG
        127 TTCCTTAAACTATTCAAGCCGATCCTA-TCCTTCGACCAATTTTTCGAA-CATTCAATGACCGAA

                                     *                    *     *            
        738 AAAT-GACATCATTTGGTCTAAATAGGTTATCATTTTC-TAAACAATTTTTGGTCTTTGAATTAA
        190 AAATCG-CATCATTTGGTCTAAATAAGTTATCA-TTTCGTAAACAACTTTTGCTCTTTGAATTAA

                *      *       *                *                 *          
        801 AAAATTATTTAGGTGAGAATTGTTTCTCCCATGGTTTTTGGAC-GAAC-TTCCGTACTAG-CGAA
        253 AAAACTATTTACGTGAGAACTGTTTCTCCCATGGTTCTTGG-CTGAACATT-CGAACTAGTC-AA

                               *    *         
        863 ACACTTAAT-AGCTCTTTTGTAACTTAAGTTCCT
        315 AC-CTTAATGAGCTCTTTTATAACCTAAGTTCCT

        896 GAGAGTATTC


Statistics
Matches: 288,  Mismatches: 48, Indels: 23
        0.80            0.13        0.06

Matches are distributed among these distances:
 391   10  0.03
 392   73  0.25
 393  195  0.68
 394   10  0.03

ACGTcount: A:0.27, C:0.18, G:0.14, T:0.42


Consensus pattern (392 bp):   
TTTTTAATTTTGTAAACAACTTTCGTCTTTGAAGTGAAAACATATTTACATGAAATTGTTTCTCT
CTTGGTTCTTGGACGAACTTCTAAACTTGTCAAACTTTTACGAGTTCCTCTATAACTTCGGTTCC
TTAAACTATTCAAGCCGATCCTATCCTTCGACCAATTTTTCGAACATTCAATGACCGAAAAATCG
CATCATTTGGTCTAAATAAGTTATCATTTCGTAAACAACTTTTGCTCTTTGAATTAAAAAACTAT
TTACGTGAGAACTGTTTCTCCCATGGTTCTTGGCTGAACATTCGAACTAGTCAAACCTTAATGAG
CTCTTTTATAACCTAAGTTCCTTAAACTTATTTATGCTTGGGAAATCACATCGTTTGATCTAAAT
AG

Found at i:936 original size:216 final size:215

Alignment explanation


    Indices: 521--1043  Score: 541
    Period size: 215  Copynumber: 2.4  Consensus size: 215

        511 TTTATGCTTG

                  *     *    *            *           *        *             
        521 GGAAATCACATCGTTTGATCTAAATAGTTTTTCATTTTGTAATCAACTTTTCGTCTTTGAATT-A
          1 GGAAATGACATCATTTGGTCTAAATAGTTTATCATTTTGTAAACAACTTTTAGTCTTTGAATTAA

                       *   *           * *                   *     * **    **
        585 AAAATATTTACATGACAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTAAACTTGTTAAACTT
         66 AAAATATTTACGTGAGAATTGTTTCTCCCATGGTTCTTGGACGAACTTCCAAACTAGCGAAACAC

              *     *             **      *            **              **    
        650 TTTATCAGTTCCTCTATAACTTCGGTTCCTTAAACTATTCAAGGTGATCCATTCCTTTGTGCAAT
        131 TTAATCAGCTCCTCTATAACTTAAGTTCCTGAAACTATTCAAGACGATCCATTCCTTTGACCAAT

                   *            
        715 TTTTCAAGCTTTCCATGCCC
        196 TTTTCAAACTTTCCATGCCC

                                        *          *       *    *            
        735 GAGAAATGACATCATTTGGTCTAAATAGGTTATCATTTTCTAAACAATTTTTGGTCTTTGAATTA
          1 G-GAAATGACATCATTTGGTCTAAATAGTTTATCATTTTGTAAACAACTTTTAGTCTTTGAATTA

                        *                        *              **           
        800 AAAAATTATTTAGGTGAGAATTGTTTCTCCCATGGTTTTTGGACGAACTTCCGTACTAGCGAAAC
         65 AAAAA-TATTTACGTGAGAATTGTTTCTCCCATGGTTCTTGGACGAACTTCCAAACTAGCGAAAC

                         * * *                * *                            
        865 ACTTAAT-AGCTCTTTTGTAACTTAAGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCA
        129 ACTTAATCAGCTCCTCTATAACTTAAGTTCCTGAAACTATTCAAGACGATCCATTCCTTTGACCA

                                * 
        929 ATTTTTCAAACTTTCCATGCTC
        194 ATTTTTCAAACTTTCCATGCCC

              *      *      *           *   *     *                    *     
        951 GGGAATCG-TATCATTCGGTCTTAAA-ACTTTGTCATTATGTAAACAACTTTTAGTCTTCGAATT
          1 GGAAAT-GACATCATTTGGTC-TAAATAGTTTATCATTTTGTAAACAACTTTTAGTCTTTGAATT

                  *                       
       1014 AAAAACCTATTTACGTGAGAATTGTTTCTC
         64 AAAAA-ATATTTACGTGAGAATTGTTTCTC

       1044 TTGTGGTTCT


Statistics
Matches: 251,  Mismatches: 52, Indels: 11
        0.80            0.17        0.04

Matches are distributed among these distances:
 214    1  0.00
 215  124  0.49
 216   75  0.30
 217   51  0.20

ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40


Consensus pattern (215 bp):   
GGAAATGACATCATTTGGTCTAAATAGTTTATCATTTTGTAAACAACTTTTAGTCTTTGAATTAA
AAAATATTTACGTGAGAATTGTTTCTCCCATGGTTCTTGGACGAACTTCCAAACTAGCGAAACAC
TTAATCAGCTCCTCTATAACTTAAGTTCCTGAAACTATTCAAGACGATCCATTCCTTTGACCAAT
TTTTCAAACTTTCCATGCCC
Done.