Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003917.1 Kokia drynarioides strain JFW-HI SEQ_116987, 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, 816

Length: 1361
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41


Found at i:1309 original size:418 final size:419

Alignment explanation


    Indices: 598--1361  Score: 966
    Period size: 418  Copynumber: 1.8  Consensus size: 419

        588 GCAATTTTTT

                                                 *                           
        598 GAACATTCCATGCTCAAGAAATCACATCATTAGGTCCGAATAGCTTGTCATTTCGTAAACAACTT
          1 GAACATTCCATGCTCAAGAAATCACATCATTAGGTCCAAATAGCTTGTCATTTCGTAAACAACTT

                             *                  *                   *  *     
        663 TTGGTCTTTGAATTAAAGACTTATTTACGTGAAAATTGTCTCTCTCCTGGTTCATGGCCGAACAT
         66 TTGGTCTTTGAATTAAAAACTTATTTACGTGAAAATGGTCTCTCTCCTGGTTCATGACCAAACAT

                     *                *     *   * **                         
        728 CTGAACATGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACAATC
        131 CTGAACATGCCAAACTTTTACAAGTTATTTTAAAACCTCAGTTCCTTAAAGTATTCAAGACAATC

                                ** **                    *  *           *    
        793 CATTCCTTCGAGCAATTTTCTGAGTATTCCATGCTCGAGAAATCGTATCATTTCCACCAAGTAGT
        196 CATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATAATTTCCACCAAATAGT

                *                                                            
        858 TTTTTATTTTGTAAACAACTATTACTCTTTGAATT-AAACTTATTTATGTGAGAACGGTTTCTCT
        261 TTTTCATTTTGTAAACAACTATTACTCTTTGAATTAAAACTTATTTATGTGAGAACGGTTTCTCT

               *   *     *                                                   
        922 CTTGGTTGTTGGTTGAACTTCCAAGCCTTCCAAACTTTTTCGAGTTCTATTATAGCTTCATTTCC
        326 CTTAGTTCTTGGTCGAACTTCCAAGCCTTCCAAACTTTTTCGAGTTCTATTATAGCTTCATTTCC

                                         
        987 TTACAGTATTCAAAACGATCCATTCCTTC
        391 TTACAGTATTCAAAACGATCCATTCCTTC

                   *        *      *       *           *         *           
       1016 GAACATTTCATGCTCAGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTT
          1 GAACATTCCATGCTCAAGAAATCACATCATTAGGTCCAAATAGCTTGTCATTTCGTAAACAACTT

                                                     *              * *  *   
       1081 TTGGT-TTTAGAATTAAAAACTTATTTACGT-AATAATGGTTTCTC-CCTTGGTTCTTTACTAAA
         66 TTGGTCTTT-GAATTAAAAACTTATTTACGTGAA-AATGGTCTCTCTCC-TGGTTCATGACCAAA

               *      *              *                                       
       1143 C-TTTCGAACTTGCCAAACTTTTACGAGTTATTTTAAAACCTCAGTTCCTTAAAGTATTCAAGAC
        128 CATCT-GAACATGCCAAACTTTTACAAGTTATTTTAAAACCTCAGTTCCTTAAAGTATTCAAGAC

               *     *                               *                ***    
       1207 AATTCATTCTTTCGAGCAATTTTCCAAACATTCCATGCTCGGGAAAGT-GCATAATTTTTTCCAA
        192 AATCCATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCGAGAAA-TCGCATAATTTCCACCAA

                       *      *  *    *  ** *                             ** 
       1271 ATA-TTTTATCCTTTTGTTAATAACTTTTGGTGTTTGAATTAAAAACTTATTTATGTGAGAATTG
        256 ATAGTTTT-TCATTTTGTAAACAACTATTACTCTTTGAATT-AAAACTTATTTATGTGAGAACGG

                                       
       1335 TTTCTCTCTTAGTTCTTGGTCGAACTT
        319 TTTCTCTCTTAGTTCTTGGTCGAACTT


Statistics
Matches: 288,  Mismatches: 50, Indels: 14
        0.82            0.14        0.04

Matches are distributed among these distances:
 417   13  0.05
 418  230  0.80
 419    1  0.00
 420   44  0.15

ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40


Consensus pattern (419 bp):   
GAACATTCCATGCTCAAGAAATCACATCATTAGGTCCAAATAGCTTGTCATTTCGTAAACAACTT
TTGGTCTTTGAATTAAAAACTTATTTACGTGAAAATGGTCTCTCTCCTGGTTCATGACCAAACAT
CTGAACATGCCAAACTTTTACAAGTTATTTTAAAACCTCAGTTCCTTAAAGTATTCAAGACAATC
CATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATAATTTCCACCAAATAGT
TTTTCATTTTGTAAACAACTATTACTCTTTGAATTAAAACTTATTTATGTGAGAACGGTTTCTCT
CTTAGTTCTTGGTCGAACTTCCAAGCCTTCCAAACTTTTTCGAGTTCTATTATAGCTTCATTTCC
TTACAGTATTCAAAACGATCCATTCCTTC
Done.