Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005156.1 Kokia drynarioides strain JFW-HI SEQ_119001, 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: 2512
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37


Found at i:580 original size:126 final size:127

Alignment explanation


    Indices: 399--647  Score: 329
    Period size: 126  Copynumber: 2.0  Consensus size: 127

        389 TGTTTTACCG

                         *                **              *         *        
        399 TTGTGTATTCATAGCTTAAGTAGATTCCAATTGCAACCTTTATACATAGTATTCACGACTTTCTC
          1 TTGTGTATTCATAACTTAAGTAGATTCCAACAGCAACCTTTATACAGAGTATTCACAACTTTCTC

               *                              *               *           
        464 TAATAGATTTTATATGCGAGGAGTTGTGGATCCTGAACCATACGGTAGCTTGTTTGCATCCT
         66 TAACAGATTTTATATGCGAGGAGTTGTGGATCCTCAACCATACGGTAGCTCGTTTGCATCCT

                                              *  *       *                *  
        526 TTGTGTATTCATAACTT-AGTAGATTCCAACAGCGACTTTTATACGGAGTATTCACAACTTTTTC
          1 TTGTGTATTCATAACTTAAGTAGATTCCAACAGCAACCTTTATACAGAGTATTCACAACTTTCTC

             *    *      *   *   *                    *               
        590 TGACAGCTTTTATCTGCTAGGGGTTGTGGATCCTCAACCATATGGTAGCTCGTTTGCA
         66 TAACAGATTTTATATGCGAGGAGTTGTGGATCCTCAACCATACGGTAGCTCGTTTGCA

        648 CCTGTATGTA


Statistics
Matches: 104,  Mismatches: 18, Indels: 1
        0.85            0.15        0.01

Matches are distributed among these distances:
 126   88  0.85
 127   16  0.15

ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37


Consensus pattern (127 bp):   
TTGTGTATTCATAACTTAAGTAGATTCCAACAGCAACCTTTATACAGAGTATTCACAACTTTCTC
TAACAGATTTTATATGCGAGGAGTTGTGGATCCTCAACCATACGGTAGCTCGTTTGCATCCT

Found at i:1744 original size:35 final size:35

Alignment explanation


    Indices: 1648--1822  Score: 141
    Period size: 34  Copynumber: 5.1  Consensus size: 35

       1638 TTTTACTTCC

                                              * 
       1648 TTGATTGTTTA--ATATATGAATGAATTGAAAATCT
          1 TTGATTGTTTATGATATATGAATGAATT-AAAATTT

                                      *           
       1682 TT--TTGCTATTA--ATATATGAATGGATT-AAATTCT
          1 TTGATTG-T-TTATGATATATGAATGAATTAAAATT-T

              *    *              *            
       1715 TTTATTGATTATGATATATGAAAGAATTAAAATTT
          1 TTGATTGTTTATGATATATGAATGAATTAAAATTT

            *         **                   *  *
       1750 GTGATTGTTTGCGATATATGAATGAATT-AAGTTA
          1 TTGATTGTTTATGATATATGAATGAATTAAAATTT

                        *               *     *
       1784 TTGATTGTTTATAATATATGAATGAATTGAAATTC
          1 TTGATTGTTTATGATATATGAATGAATTAAAATTT

                
       1819 TTGA
          1 TTGA

       1823 ACGGTAGATA


Statistics
Matches: 113,  Mismatches: 19, Indels: 17
        0.76            0.13        0.11

Matches are distributed among these distances:
  32    7  0.06
  33    7  0.06
  34   47  0.42
  35   47  0.42
  36    5  0.04

ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45


Consensus pattern (35 bp):   
TTGATTGTTTATGATATATGAATGAATTAAAATTT

Found at i:1801 original size:34 final size:33

Alignment explanation


    Indices: 1648--1822  Score: 126
    Period size: 35  Copynumber: 5.1  Consensus size: 33

       1638 TTTTACTTCC

                                                
       1648 TTGATTG-TT-TAATATATGAATGAATTGAAAATCT
          1 TTGATTGTTTATAATATATGAATGAATT--AAAT-T

                    *                *          
       1682 TT--TTG-CTATTAATATATGAATGGATTAAATTCT
          1 TTGATTGTTTA-TAATATATGAATGAATTAAA-T-T

              *    *    *         *           
       1715 TTTATTGATTATGATATATGAAAGAATTAAAATT
          1 TTGATTGTTTATAATATATGAATGAATT-AAATT

                       ***                 *  
       1749 TGTGATTGTTTGCGATATATGAATGAATTAAGTT
          1 T-TGATTGTTTATAATATATGAATGAATTAAATT

                                               
       1783 ATTGATTGTTTATAATATATGAATGAATTGAAATT
          1 -TTGATTGTTTATAATATATGAATGAATT-AAATT

                 
       1818 CTTGA
          1 -TTGA

       1823 ACGGTAGATA


Statistics
Matches: 114,  Mismatches: 17, Indels: 19
        0.76            0.11        0.13

Matches are distributed among these distances:
  32    7  0.06
  33    5  0.04
  34   48  0.42
  35   49  0.43
  36    5  0.04

ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45


Consensus pattern (33 bp):   
TTGATTGTTTATAATATATGAATGAATTAAATT
Done.