Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012911.1 Kokia drynarioides strain JFW-HI SEQ_127927, 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: 4215
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33

Warning! 100 characters in sequence are not A, C, G, or T


Found at i:736 original size:21 final size:22

Alignment explanation


    Indices: 695--736  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 22

        685 AATTCAATGT

                      *           
        695 CCAAATTACATACCAAAAATAC
          1 CCAAATTACAAACCAAAAATAC

                          *      
        717 CCAAATTA-AAACCCAAAATA
          1 CCAAATTACAAACCAAAAATA

        737 TACAAGTCTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  21   10  0.56
  22    8  0.44

ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17


Consensus pattern (22 bp):   
CCAAATTACAAACCAAAAATAC

Found at i:1196 original size:14 final size:13

Alignment explanation


    Indices: 1179--1218  Score: 53
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       1169 TATAGATCTA

                          
       1179 TATATTTCTTGTTT
          1 TATATTTCTT-TTT

                    *    
       1193 TATATTTCATTTT
          1 TATATTTCTTTTT

               *         
       1206 TATTTTTCTTTTT
          1 TATATTTCTTTTT

       1219 CATTTTGAAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  13   14  0.61
  14    9  0.39

ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75


Consensus pattern (13 bp):   
TATATTTCTTTTT

Found at i:2484 original size:29 final size:30

Alignment explanation


    Indices: 2413--2526  Score: 106
    Period size: 30  Copynumber: 3.8  Consensus size: 30

       2403 TTGGCCCCCG

                 *          * *      *  **
       2413 AACTTCCCAAAAATTTTAATTTGACCCTTG
          1 AACTTTCCAAAAATTTCATTTTGACACTCA

                            *         *    
       2443 AA-TTTCCTAAAAATTCCATTTTGACTC-CA
          1 AACTTTCC-AAAAATTTCATTTTGACACTCA

                            *             
       2472 AACTTTCCAAAAATTTGATTTTGACACTCA
          1 AACTTTCCAAAAATTTCATTTTGACACTCA

              *    *                 
       2502 AATTTTCAAAAAATTTCATTTTGAC
          1 AACTTTCCAAAAATTTCATTTTGAC

       2527 CAGTAAACTT


Statistics
Matches: 68,  Mismatches: 13, Indels: 6
        0.78            0.15        0.07

Matches are distributed among these distances:
  29   22  0.32
  30   46  0.68

ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39


Consensus pattern (30 bp):   
AACTTTCCAAAAATTTCATTTTGACACTCA

Found at i:2485 original size:59 final size:59

Alignment explanation


    Indices: 2413--2526  Score: 147
    Period size: 59  Copynumber: 1.9  Consensus size: 59

       2403 TTGGCCCCCG

                            *        *  **       *                     
       2413 AACTTCCCAAAAATTTTAATTTGACCCTTGAATTTCCTAAAAATTCCATTTTGACTCCA
          1 AACTTCCCAAAAATTTGAATTTGACACTCAAATTTCCAAAAAATTCCATTTTGACTCCA

                 *            *                *         *         
       2472 AACTTTCCAAAAATTTGATTTTGACACTCAAATTTTCAAAAAATTTCATTTTGAC
          1 AACTTCCCAAAAATTTGAATTTGACACTCAAATTTCCAAAAAATTCCATTTTGAC

       2527 CAGTAAACTT


Statistics
Matches: 46,  Mismatches: 9, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  59   46  1.00

ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39


Consensus pattern (59 bp):   
AACTTCCCAAAAATTTGAATTTGACACTCAAATTTCCAAAAAATTCCATTTTGACTCCA
Done.