Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000868.1 Kokia drynarioides strain JFW-HI SEQ_111986, 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: 6129
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36


Found at i:1411 original size:28 final size:29

Alignment explanation


    Indices: 1375--1474  Score: 96
    Period size: 28  Copynumber: 3.4  Consensus size: 29

       1365 AAAAATTACC

                           **            
       1375 AACTTTTAAGGG-TCCCAAATTTTTTTTT
          1 AACTTTTAAGGGCTCAAAAATTTTTTTTT

                                           
       1403 AACTTTTAAGGGCTCAAAAATTTTTTTATCT
          1 AACTTTTAAGGGCTCAAAAATTTTTTT-T-T

            *               *         **   
       1434 TAC-TTTAAGGGACTTAAAAAATTTTCCTTT
          1 AACTTTTAAGGG-C-TCAAAAATTTTTTTTT

                       
       1464 AACTTTTAAGG
          1 AACTTTTAAGG

       1475 AATTTAAAAT


Statistics
Matches: 59,  Mismatches: 7, Indels: 9
        0.79            0.09        0.12

Matches are distributed among these distances:
  28   12  0.20
  29   12  0.20
  30   12  0.20
  31   12  0.20
  32   11  0.19

ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45


Consensus pattern (29 bp):   
AACTTTTAAGGGCTCAAAAATTTTTTTTT

Found at i:1472 original size:31 final size:29

Alignment explanation


    Indices: 1396--1483  Score: 81
    Period size: 31  Copynumber: 2.9  Consensus size: 29

       1386 GTCCCAAATT

                                   *     
       1396 TTTTTTTAACTTTTAAGGG-C-TCAAAAA
          1 TTTTTTTAACTTTTAAGGGACTTAAAAAA

                    *                       
       1423 TTTTTTTATCTTACTTTAAGGGACTTAAAAAA
          1 TTTTTTTAAC-T--TTTAAGGGACTTAAAAAA

                                * *      
       1455 TTTTCCTTTAACTTTTAAGGAATTTAAAA
          1 TTTT--TTTAACTTTTAAGGGACTTAAAA

       1484 TCTCATTTTA


Statistics
Matches: 49,  Mismatches: 5, Indels: 10
        0.77            0.08        0.16

Matches are distributed among these distances:
  27    9  0.18
  28    1  0.02
  30    8  0.16
  31   15  0.31
  32   10  0.20
  33    1  0.02
  34    5  0.10

ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47


Consensus pattern (29 bp):   
TTTTTTTAACTTTTAAGGGACTTAAAAAA

Found at i:1948 original size:201 final size:202

Alignment explanation


    Indices: 1589--1958  Score: 539
    Period size: 201  Copynumber: 1.8  Consensus size: 202

       1579 ATTGTCTATA

                    *                                            *     *     
       1589 AAAAATATGTTCTCTTTAAACATAAAATATGAAAAGTATAGAAAAACTAAATTTCAAATGATTGA
          1 AAAAATATATTCTCTTTAAACATAAAATATGAAAAGTATAGAAAAACTAAATTCCAAATAATTGA

                                              *                   *          
       1654 TTTAACATCAAACATACGTTAATATCATAAAAGTTGTTTTATAAAAAGAGAAAATATATTGACTT
         66 TTTAACATCAAACATACGTTAATATCATAAAAGTCGTTTTATAAAAAGAGAAAAGATATTGACTT

                         *                                                   
       1719 ACACGTGTCAAGCCAAGAAAAATTATTAAAATGAATGAGGTGAACATGACATACACATATGAAGG
        131 ACACGTGTCAAGCAAAGAAAAATTATTAAAATGAATGAGGTGAACATGACATACACATATGAAGG

                   
       1784 TGTCCAT
        196 TGTCCAT

                         *            *       *  *    *                      
       1791 AAAAATATATT-TTTTTAAACATAAATTATGAAAGGTGTAGAGAAACTAAATTCCAAATAATTGA
          1 AAAAATATATTCTCTTTAAACATAAAATATGAAAAGTATAGAAAAACTAAATTCCAAATAATTGA

               *  *         *   *        *                                *  
       1855 TTTTACGTCAAACATATGTTGATATCATAGAAGTCGTTTTATAAAAAGAGAAAAGATATTG-GTT
         66 TTTAACATCAAACATACGTTAATATCATAAAAGTCGTTTTATAAAAAGAGAAAAGATATTGACTT

                                               *     
       1919 GACACGTGTCAAGCGAAAG-AAAATTATTAAAATGGATGAG
        131 -ACACGTGTCAAGC-AAAGAAAAATTATTAAAATGAATGAG

       1959 ATAAACATTA


Statistics
Matches: 148,  Mismatches: 18, Indels: 5
        0.87            0.11        0.03

Matches are distributed among these distances:
 200    2  0.01
 201  133  0.90
 202   13  0.09

ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30


Consensus pattern (202 bp):   
AAAAATATATTCTCTTTAAACATAAAATATGAAAAGTATAGAAAAACTAAATTCCAAATAATTGA
TTTAACATCAAACATACGTTAATATCATAAAAGTCGTTTTATAAAAAGAGAAAAGATATTGACTT
ACACGTGTCAAGCAAAGAAAAATTATTAAAATGAATGAGGTGAACATGACATACACATATGAAGG
TGTCCAT

Found at i:2350 original size:23 final size:23

Alignment explanation


    Indices: 2302--2351  Score: 57
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       2292 ATTATGAAAC

                                 * 
       2302 TATATATTGATATATAATAAATT
          1 TATATATTGATATATAATAAAAT

                 *     *            
       2325 TATATTTTGATCTATGAA-AAAAT
          1 TATATATTGATATAT-AATAAAAT

                
       2348 TATA
          1 TATA

       2352 ATTAAATTTT


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  23   21  0.91
  24    2  0.09

ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46


Consensus pattern (23 bp):   
TATATATTGATATATAATAAAAT
Done.