Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002325.1 Kokia drynarioides strain JFW-HI SEQ_114372, 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, 603

Length: 1006
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40


Found at i:696 original size:216 final size:216

Alignment explanation


    Indices: 1--699  Score: 893
    Period size: 216  Copynumber: 3.2  Consensus size: 216

                       * *                   *  *         *     *  *    *  * 
          1 GTCTTTGAATTCAGAACTTATTTACGTGAGAATGGTATCTCTCTTTCTTCTTAGATGAACGTCTA
          1 GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCGA

                              **            *   *                            
         66 AGCTTGTCAAACTTTTACTTGTTATTTTATAATTTCGGATCCTTAAAGTATTCAAGACGATCCAT
         66 A-CTTGTCAAACTTTTACAAGTTATTTTATAACTTCCGATCCTTAAAGTATTCAAGACGATCCAT

                              **          *               *                  
        131 TCCTT-CGAGCAATTTTTCAAACATTCCATTCTCGGGAAATCGCATTATTTGGTCTAAATAGTTT
        130 TCCTTACGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTT

                      *           
        195 GTCATTTTGCTAACAAGTTTTG
        195 GTCATTTTGCAAACAAGTTTTG

                  *               *      *                **      *          
        217 GTCTTTAAATTAAAAACTTATTCACGTGAAAATTGTTTCTCTCTTTAATCTTGGGCGAACTTTCG
          1 GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAAC-TTCG

                  *           *         *              *            * *      
        282 AACTTGCCAAACTTTTACGAGTTATTTTTTAACTT-CGATTCCCTAAAGTATTCAATAAGATCCA
         65 AACTTGTCAAACTTTTACAAGTTATTTTATAACTTCCGA-TCCTTAAAGTATTCAAGACGATCCA

                         *                      *      *  *                * 
        346 TTCCTTA-GAGCATTTTTTTGAACATTCCATGCTCGAGAAATCACAGCATTTGGTCTAAATAGCT
        129 TTCCTTACGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTT

                      *           *
        410 TGTCATTTTGTAAACAAGTTTTA
        194 TGTCATTTTGCAAACAAGTTTTG

                                                                             
        433 GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCG
          1 GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTT-CG

                         *   *     *                             *       **  
        498 AACTTGTCAAACTATTAAAAGTTCTTTTATAACTTCCGATCCTTAAAGTATTCTAGACGATTTAT
         65 AACTTGTCAAACTTTTACAAGTTATTTTATAACTTCCGATCCTTAAAGTATTCAAGACGATCCAT

                                             *         *   *                 
        563 T-CTTACGAGCAATTTTTTGAACATTCCATGCTAGGGAAATCGTATCGTTTGGTCTAAATAGTTT
        130 TCCTTACGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTT

                           *      
        627 GTCATTTTGCAAACATGTTTTG
        195 GTCATTTTGCAAACAAGTTTTG

                                    *               *          
        649 GTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTATCTTTGTTCT
          1 GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCT

        700 CGGATCCTTA


Statistics
Matches: 411,  Mismatches: 66, Indels: 12
        0.84            0.13        0.02

Matches are distributed among these distances:
 215    8  0.02
 216  396  0.96
 217    7  0.02

ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41


Consensus pattern (216 bp):   
GTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCGA
ACTTGTCAAACTTTTACAAGTTATTTTATAACTTCCGATCCTTAAAGTATTCAAGACGATCCATT
CCTTACGAGCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTG
TCATTTTGCAAACAAGTTTTG

Found at i:834 original size:76 final size:76

Alignment explanation


    Indices: 708--863  Score: 242
    Period size: 76  Copynumber: 2.1  Consensus size: 76

        698 CTCGGATCCT

                                                                            *
        708 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCG-GAAAATCT
          1 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCGAG-AAATCG

                        
        772 CATCATTTGGTC
         65 CATCATTTGGTC

                      *        *    *              **                        
        784 TAAAGTATTCCAGACGATCTATTCTTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAATCGC
          1 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGC

                       
        849 ATCATTTGGTC
         66 ATCATTTGGTC

                
        860 TAAA
          1 TAAA

        864 TAGTTTGTCA


Statistics
Matches: 73,  Mismatches: 6, Indels: 2
        0.90            0.07        0.02

Matches are distributed among these distances:
  76   72  0.99
  77    1  0.01

ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33


Consensus pattern (76 bp):   
TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGC
ATCATTTGGTC
Done.