Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012393.1 Corchorus olitorius cultivar O-4 contig12426, 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: 18945
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:510 original size:17 final size:17

Alignment explanation


    Indices: 488--522  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        478 TGCATAATGT

                             
        488 TAATATACCAACAAGAA
          1 TAATATACCAACAAGAA

                             
        505 TAATATACCAACAAGAA
          1 TAATATACCAACAAGAA

             
        522 T
          1 T

        523 GCACTTTTTC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.57, C:0.17, G:0.06, T:0.20


Consensus pattern (17 bp):   
TAATATACCAACAAGAA

Found at i:1377 original size:27 final size:27

Alignment explanation


    Indices: 1334--1462  Score: 195
    Period size: 27  Copynumber: 4.8  Consensus size: 27

       1324 CGACCTGAGG

                   **                  
       1334 CGAAGTGAAAGGATCCACTGCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                   *    *              
       1361 CGAAGTGTGAGGGTCCACTGCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                                       
       1388 CGAAGTGGGAGGATCCACTGCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                               *  *    
       1415 CGAAGTGGGAGGATCCACTACTAGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                    *            
       1442 CGAAGTGGAAGGATCCACTGC
          1 CGAAGTGGGAGGATCCACTGC

       1463 GGCAACAGTC


Statistics
Matches: 93,  Mismatches: 9, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   93  1.00

ACGTcount: A:0.22, C:0.19, G:0.40, T:0.19


Consensus pattern (27 bp):   
CGAAGTGGGAGGATCCACTGCTGGGGT

Found at i:5552 original size:15 final size:15

Alignment explanation


    Indices: 5522--5563  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5512 TTACTCTGCT

                            
       5522 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       5538 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       5553 TTGCTTTCTGT
          1 TTGTTTTCTGT

       5564 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:10281 original size:18 final size:18

Alignment explanation


    Indices: 10258--10296  Score: 69
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      10248 CACCTATTCC

                   *          
      10258 TTAGCTTTTTGAAGCGAG
          1 TTAGCTTCTTGAAGCGAG

                              
      10276 TTAGCTTCTTGAAGCGAG
          1 TTAGCTTCTTGAAGCGAG

               
      10294 TTA
          1 TTA

      10297 AGTACTCCAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38


Consensus pattern (18 bp):   
TTAGCTTCTTGAAGCGAG

Found at i:15811 original size:23 final size:23

Alignment explanation


    Indices: 15755--15819  Score: 116
    Period size: 21  Copynumber: 2.9  Consensus size: 23

      15745 AAACAAGAAT

                                   
      15755 TGCATGAAGTCATTAAGATATAA
          1 TGCATGAAGTCATTAAGATATAA

                                   
      15778 TGC--GAAGTCATTAAGATATAA
          1 TGCATGAAGTCATTAAGATATAA

                                 
      15799 TGCATGAAGTCATTAAGATAT
          1 TGCATGAAGTCATTAAGATAT

      15820 TATATTTCTT


Statistics
Matches: 40,  Mismatches: 0, Indels: 4
        0.91            0.00        0.09

Matches are distributed among these distances:
  21   21  0.52
  23   19  0.47

ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31


Consensus pattern (23 bp):   
TGCATGAAGTCATTAAGATATAA

Found at i:18880 original size:2 final size:2

Alignment explanation


    Indices: 18873--18903  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      18863 GTGAAGCCTG

                                                          
      18873 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      18904 GTATGTTGGT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.