Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008930.1 Kokia drynarioides strain JFW-HI SEQ_123621, 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: 9792
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:112 original size:16 final size:15

Alignment explanation


    Indices: 86--119  Score: 59
    Period size: 16  Copynumber: 2.2  Consensus size: 15

         76 TATTGAATGG

                           
         86 ATATTAATAATAATA
          1 ATATTAATAATAATA

                            
        101 ATATTAAATAATAATA
          1 ATATT-AATAATAATA

               
        117 ATA
          1 ATA

        120 ATAGTATTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15    5  0.28
  16   13  0.72

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (15 bp):   
ATATTAATAATAATA

Found at i:1207 original size:35 final size:35

Alignment explanation


    Indices: 1168--1238  Score: 142
    Period size: 35  Copynumber: 2.0  Consensus size: 35

       1158 AGCTGCCACA

                                               
       1168 TGCCACTTGTTTTGGTTTTATTGCCCTGAAGCCCC
          1 TGCCACTTGTTTTGGTTTTATTGCCCTGAAGCCCC

                                               
       1203 TGCCACTTGTTTTGGTTTTATTGCCCTGAAGCCCC
          1 TGCCACTTGTTTTGGTTTTATTGCCCTGAAGCCCC

             
       1238 T
          1 T

       1239 AAACTTCCAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   36  1.00

ACGTcount: A:0.11, C:0.28, G:0.20, T:0.41


Consensus pattern (35 bp):   
TGCCACTTGTTTTGGTTTTATTGCCCTGAAGCCCC

Found at i:1390 original size:30 final size:29

Alignment explanation


    Indices: 1234--1515  Score: 220
    Period size: 29  Copynumber: 9.7  Consensus size: 29

       1224 TGCCCTGAAG

                *               **     * 
       1234 CCCCTAAACTTCCAAAAATTATATTTTGA
          1 CCCCAAAACTTCCAAAAATTCCATTTTTA

                  *              **        
       1263 CCCC--GACTTCTCAAAAATTATATTTTTGA
          1 CCCCAAAACTTC-CAAAAATTCCATTTTT-A

                *               *        
       1292 -CCCTAAACTTCCAAAAATTTCATTTTTA
          1 CCCCAAAACTTCCAAAAATTCCATTTTTA

                  *     *        *        
       1320 CCCTC-GAACTTTCAAAAATTACATTTTTA
          1 CCC-CAAAACTTCCAAAAATTCCATTTTTA

                                         * 
       1349 CCCTC-AAACTTCCAAAAATTCCATTTTCAA
          1 CCC-CAAAACTTCCAAAAATTCCATTTT-TA

                                *         
       1379 CCCCAAAACTTCCAAAAATTTCATTTTTTA
          1 CCCCAAAACTTCCAAAAATTCCA-TTTTTA

               *       *         *        
       1409 CCCAAAAACTTTCAAAAA-TCTATTTTTGA
          1 CCCCAAAACTTCCAAAAATTCCATTTTT-A

                       *        *         
       1438 CCCCAAAACTTTCAAAAATTAC-TATTTTA
          1 CCCCAAAACTTCCAAAAATTCCAT-TTTTA

                *               *         
       1467 CCCCTAAACTTCC-AAAATTTCATTTTTAA
          1 CCCCAAAACTTCCAAAAATTCCATTTTT-A

               *       *        
       1496 CCCAAAAACTTTCAAAAATT
          1 CCCCAAAACTTCCAAAAATT

       1516 AGCCTTTTAC


Statistics
Matches: 211,  Mismatches: 27, Indels: 29
        0.79            0.10        0.11

Matches are distributed among these distances:
  27    5  0.02
  28   35  0.17
  29  112  0.53
  30   55  0.26
  31    4  0.02

ACGTcount: A:0.38, C:0.26, G:0.02, T:0.35


Consensus pattern (29 bp):   
CCCCAAAACTTCCAAAAATTCCATTTTTA

Found at i:1524 original size:58 final size:59

Alignment explanation


    Indices: 1234--1529  Score: 301
    Period size: 58  Copynumber: 5.1  Consensus size: 59

       1224 TGCCCTGAAG

                                         *       *               *        
       1234 CCCCTAAACTTCCAAAAA-TT-ATATTTTGACCCC--GACTTCTCAAAAATTATATTTTTGA
          1 CCCCTAAACTTCCAAAAATTTCAT-TTTTAACCCCAAAACTT-TCAAAAATTACATTTTT-A

                                                *                       
       1292 -CCCTAAACTTCCAAAAATTTCATTTTT-ACCCTC-GAACTTTCAAAAATTACATTTTTA
          1 CCCCTAAACTTCCAAAAATTTCATTTTTAACCC-CAAAACTTTCAAAAATTACATTTTTA

                                 *      *             *        *         
       1349 -CCCTCAAACTTCCAAAAATTCCATTTTCAACCCCAAAACTTCCAAAAATTTCATTTTTTA
          1 CCCCT-AAACTTCCAAAAATTTCATTTTTAACCCCAAAACTTTCAAAAATTACA-TTTTTA

               **      *       *        *                               
       1409 CCCAAAAACTTTCAAAAATCT-ATTTTTGACCCCAAAACTTTCAAAAATTAC-TATTTTA
          1 CCCCTAAACTTCCAAAAATTTCATTTTTAACCCCAAAACTTTCAAAAATTACAT-TTTTA

                                             *                    *     
       1467 CCCCTAAACTTCC-AAAATTTCATTTTTAACCCAAAAACTTTCAAAAATTAGC-CTTTTA
          1 CCCCTAAACTTCCAAAAATTTCATTTTTAACCCCAAAACTTTCAAAAATTA-CATTTTTA

                 
       1525 CCCCT
          1 CCCCT

       1530 GGATGTTCAA


Statistics
Matches: 203,  Mismatches: 23, Indels: 24
        0.81            0.09        0.10

Matches are distributed among these distances:
  57   33  0.16
  58   97  0.48
  59   52  0.26
  60   19  0.09
  61    2  0.01

ACGTcount: A:0.36, C:0.26, G:0.02, T:0.35


Consensus pattern (59 bp):   
CCCCTAAACTTCCAAAAATTTCATTTTTAACCCCAAAACTTTCAAAAATTACATTTTTA

Done.