Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007851.1 Kokia drynarioides strain JFW-HI SEQ_122490, 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: 11478
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33


Found at i:1386 original size:17 final size:17

Alignment explanation


    Indices: 1366--1403  Score: 76
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       1356 TTGCTGTAGG

                             
       1366 ACAGTCCATATAAAGAA
          1 ACAGTCCATATAAAGAA

                             
       1383 ACAGTCCATATAAAGAA
          1 ACAGTCCATATAAAGAA

                
       1400 ACAG
          1 ACAG

       1404 ACTCTTTGTG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.53, C:0.18, G:0.13, T:0.16


Consensus pattern (17 bp):   
ACAGTCCATATAAAGAA

Found at i:7332 original size:30 final size:29

Alignment explanation


    Indices: 7298--7500  Score: 165
    Period size: 30  Copynumber: 6.8  Consensus size: 29

       7288 TTATTTAAAA

                         *    *           
       7298 TTTGATCCCCAAACTTTCAAAAAATTATAT
          1 TTTGA-CCCCAAATTTTCCAAAAATTATAT

                   ** *  *               *
       7328 TTTGAACTTCGAACTTTCCAAAAATTATAG
          1 TTTG-ACCCCAAATTTTCCAAAAATTATAT

                    * *       *     *     
       7358 TTTGACCTTCGAATTTTCTAAAAAATATAT
          1 TTTGACC-CCAAATTTTCCAAAAATTATAT

             *           *                
       7388 TGTGACCCCAAAAATTTCCAAAAATTATAT
          1 TTTGACCCC-AAATTTTCCAAAAATTATAT

                      *      *            
       7418 TTTGACCCTCTAATTTTTCAAAAATTATAT
          1 TTTGACCC-CAAATTTTCCAAAAATTATAT

                     *                    *
       7448 TTTGACCCTTAAATTTTCCAAAAATT-TAAA
          1 TTTGACCC-CAAATTTTCCAAAAATTAT-AT

                              *    
       7478 TTTGACCCCCAAATTTTCTAAAA
          1 TTTGA-CCCCAAATTTTCCAAAA

       7501 TTTCATTTTT


Statistics
Matches: 141,  Mismatches: 26, Indels: 12
        0.79            0.15        0.07

Matches are distributed among these distances:
  29    4  0.03
  30  132  0.94
  31    5  0.04

ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38


Consensus pattern (29 bp):   
TTTGACCCCAAATTTTCCAAAAATTATAT

Found at i:7406 original size:60 final size:60

Alignment explanation


    Indices: 7342--7500  Score: 187
    Period size: 60  Copynumber: 2.6  Consensus size: 60

       7332 AACTTCGAAC

                           *       *  *                                 
       7342 TTTCCAAAAATTATAGTTTGACCTTCGAATTTTCTAAAAAATATATTGTGACCCCAAAAA
          1 TTTCCAAAAATTATAATTTGACCCTCAAATTTTCTAAAAAATATATTGTGACCCCAAAAA

                           *          *              *      *      **   *
       7402 TTTCCAAAAATTATATTTTGACCCTCTAATTTT-TCAAAAATTATATTTTGACCCTTAAAT
          1 TTTCCAAAAATTATAATTTGACCCTCAAATTTTCT-AAAAAATATATTGTGACCCCAAAAA

                                     *              
       7462 TTTCCAAAAATT-TAAATTTGACCCCCAAATTTTCTAAAA
          1 TTTCCAAAAATTAT-AATTTGACCCTCAAATTTTCTAAAA

       7501 TTTCATTTTT


Statistics
Matches: 85,  Mismatches: 11, Indels: 6
        0.83            0.11        0.06

Matches are distributed among these distances:
  59    2  0.02
  60   82  0.96
  61    1  0.01

ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39


Consensus pattern (60 bp):   
TTTCCAAAAATTATAATTTGACCCTCAAATTTTCTAAAAAATATATTGTGACCCCAAAAA

Found at i:7422 original size:90 final size:89

Alignment explanation


    Indices: 7304--7493  Score: 222
    Period size: 90  Copynumber: 2.1  Consensus size: 89

       7294 AAAATTTGAT

                   *                       *                                 
       7304 CCCCAAACTTTCAAAAAATTATATTTTGAACTTCGAACTTTCCAAAAATTATAGTTTGA-CCTTC
          1 CCCCAAAATTTCAAAAAATTATATTTTGAACCTCGAACTTTCCAAAAATTATAGTTTGACCCTT-

            *       *                
       7368 GAATTTTCTAAAAAATATATTGTGA
         65 AAATTTTCCAAAAAATATATTGTGA

                         *                *    *  *   *           *          
       7393 CCCCAAAAATTTCCAAAAATTATATTTTGACCCTCTAATTTTTCAAAAATTATATTTTGACCCTT
          1 CCCC-AAAATTTCAAAAAATTATATTTTGAACCTCGAACTTTCCAAAAATTATAGTTTGACCCTT

                           *  *       
       7458 AAATTTTCCAAAAATTTAAATT-TGA
         65 AAATTTTCCAAAAA-ATATATTGTGA

                *      
       7483 CCCCCAAATTT
          1 CCCCAAAATTT

       7494 TCTAAAATTT


Statistics
Matches: 85,  Mismatches: 13, Indels: 6
        0.82            0.12        0.06

Matches are distributed among these distances:
  89   10  0.12
  90   66  0.78
  91    9  0.11

ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38


Consensus pattern (89 bp):   
CCCCAAAATTTCAAAAAATTATATTTTGAACCTCGAACTTTCCAAAAATTATAGTTTGACCCTTA
AATTTTCCAAAAAATATATTGTGA

Found at i:8968 original size:16 final size:16

Alignment explanation


    Indices: 8947--8980  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       8937 GAAAGCTGCC

                            
       8947 ATAAACTCAAGACCCT
          1 ATAAACTCAAGACCCT

                         *  
       8963 ATAAACTCAAGACTCT
          1 ATAAACTCAAGACCCT

              
       8979 AT
          1 AT

       8981 TCAGCAGAGC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.44, C:0.26, G:0.06, T:0.24


Consensus pattern (16 bp):   
ATAAACTCAAGACCCT
Done.