Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014330.1 Kokia drynarioides strain JFW-HI SEQ_129367, 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: 12493
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35


Found at i:295 original size:18 final size:18

Alignment explanation


    Indices: 272--308  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        262 ACAGTTCATA

                              
        272 TCACTTTCAATTCCAATT
          1 TCACTTTCAATTCCAATT

                     *  *     
        290 TCACTTTCACTTTCAATT
          1 TCACTTTCAATTCCAATT

             
        308 T
          1 T

        309 TGATCACCAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49


Consensus pattern (18 bp):   
TCACTTTCAATTCCAATT

Found at i:2722 original size:50 final size:50

Alignment explanation


    Indices: 2618--2727  Score: 121
    Period size: 50  Copynumber: 2.2  Consensus size: 50

       2608 AGCGTAAAAC

                     *                                *  *   *
       2618 TTTTTTTTTTGTTTCAAGATGCCCTTTGCGAGTTCTCATCTCGACTTCTT
          1 TTTTTTTTTGGTTTCAAGATGCCCTTTGCGAGTTCTCATCTCAACCTCTA

                                *       * *   * *    *        
       2668 TTTTTTTTTGGTTTCAAGATTCCCTTTGTGGGTTTTGATCTTAACCTCTA
          1 TTTTTTTTTGGTTTCAAGATGCCCTTTGCGAGTTCTCATCTCAACCTCTA

                      
       2718 TTTTTCTTTT
          1 TTTTT-TTTT

       2728 TTTTTATCTC


Statistics
Matches: 49,  Mismatches: 10, Indels: 1
        0.82            0.17        0.02

Matches are distributed among these distances:
  50   45  0.92
  51    4  0.08

ACGTcount: A:0.12, C:0.18, G:0.14, T:0.56


Consensus pattern (50 bp):   
TTTTTTTTTGGTTTCAAGATGCCCTTTGCGAGTTCTCATCTCAACCTCTA

Found at i:4119 original size:36 final size:36

Alignment explanation


    Indices: 4070--4169  Score: 173
    Period size: 36  Copynumber: 2.8  Consensus size: 36

       4060 TCGTTATTCG

                    *           *               
       4070 TTTTACTCTCTGTTGACCTACAGGTCATTATGCTCA
          1 TTTTACTCCCTGTTGACCTAAAGGTCATTATGCTCA

                                                
       4106 TTTTACTCCCTGTTGACCTAAAGGTCATTATGCTCA
          1 TTTTACTCCCTGTTGACCTAAAGGTCATTATGCTCA

                              *         
       4142 TTTTACTCCCTGTTGACCAAAAGGTCAT
          1 TTTTACTCCCTGTTGACCTAAAGGTCAT

       4170 GCCTATTACC


Statistics
Matches: 61,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  36   61  1.00

ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39


Consensus pattern (36 bp):   
TTTTACTCCCTGTTGACCTAAAGGTCATTATGCTCA

Found at i:7972 original size:3 final size:3

Alignment explanation


    Indices: 7966--8016  Score: 50
    Period size: 3  Copynumber: 17.3  Consensus size: 3

       7956 TAACAACATA

                              *          *      *         *              * 
       7966 AAT AAT AA- AAT AAA AAT AAT AGT AAT GAT AAT AAC AAT AAT AAT ACT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                 
       8013 AAT A
          1 AAT A

       8017 TGACTACAAC


Statistics
Matches: 37,  Mismatches: 10, Indels: 2
        0.76            0.20        0.04

Matches are distributed among these distances:
   2    2  0.05
   3   35  0.95

ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27


Consensus pattern (3 bp):   
AAT

Found at i:8316 original size:15 final size:15

Alignment explanation


    Indices: 8283--8330  Score: 62
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       8273 GGAATGCTAG

                            
       8283 AAATAAATAAATAAGT
          1 AAATAAATAAATAA-T

                  *         
       8299 AAA-AAGTAAAATAAT
          1 AAATAAAT-AAATAAT

                           
       8314 AAATAAATAAATAAT
          1 AAATAAATAAATAAT

              
       8329 AA
          1 AA

       8331 GGAAAGGACC


Statistics
Matches: 28,  Mismatches: 2, Indels: 5
        0.80            0.06        0.14

Matches are distributed among these distances:
  15   16  0.57
  16   12  0.43

ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23


Consensus pattern (15 bp):   
AAATAAATAAATAAT

Found at i:8545 original size:5 final size:5

Alignment explanation


    Indices: 8535--8559  Score: 50
    Period size: 5  Copynumber: 5.0  Consensus size: 5

       8525 AGGGCGAAAT

                                         
       8535 TAAAA TAAAA TAAAA TAAAA TAAAA
          1 TAAAA TAAAA TAAAA TAAAA TAAAA

       8560 AATGACAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   20  1.00

ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20


Consensus pattern (5 bp):   
TAAAA

Done.