Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014721.1 Corchorus olitorius cultivar O-4 contig14754, 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: 2040
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38


Found at i:26 original size:2 final size:2

Alignment explanation


    Indices: 21--50  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

         11 CTACCCCCTC

                                                        
         21 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

         51 GTGTGTTTCT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
CT

Found at i:258 original size:62 final size:62

Alignment explanation


    Indices: 181--700  Score: 817
    Period size: 62  Copynumber: 8.5  Consensus size: 62

        171 TCGTGTCTGT

                            *      *                                      
        181 CTTCCTCTGTCTTCTCTTGTACCCTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC

                 *                 *                                         
        243 CTTCCCCTGTCTTCTCGTGTACCCTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTCCCTT
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGG-C-CT--CTT

             
        308 C
         62 C

            *                                                            *
        309 TTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTA
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC

                            *                          *           *      
        371 CTTCCTCTGTCTTCTCTTGTACCTTCGTGCCTGCTGGCCT--CTTCCT-------TC-CTTC
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC

                                                                          
        423 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC

                          *                                  *             
        485 CTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGTGGAGGCCTCTCTC
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCT-TC

                                                                          
        548 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC

                    *                                                     
        610 CTTCCTCTATCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC

                                         
        672 CTTCCTCTGTCTTCTCGTGTACCTTCGTG
          1 CTTCCTCTGTCTTCTCGTGTACCTTCGTG

        701 TCTGTCGTGT


Statistics
Matches: 423,  Mismatches: 20, Indels: 30
        0.89            0.04        0.06

Matches are distributed among these distances:
  52   42  0.10
  53    1  0.00
  54    5  0.01
  60    5  0.01
  61    1  0.00
  62  247  0.58
  63   61  0.14
  64    4  0.01
  65    1  0.00
  66   56  0.13

ACGTcount: A:0.03, C:0.41, G:0.21, T:0.35


Consensus pattern (62 bp):   
CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC

Found at i:560 original size:125 final size:124

Alignment explanation


    Indices: 419--700  Score: 528
    Period size: 125  Copynumber: 2.3  Consensus size: 124

        409 CTCTTCCTTC

                                                                             
        419 CTTCCTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTT
          1 CTTCCTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTT

                     *                                        *        
        484 CCTTCCTCTGTCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGTGGAGGCCT
         66 CCTTCCTCTATCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT

                                                                             
        543 CTCTCCTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCT
          1 CT-TCCTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCT

                            *                                           
        608 TCCTTCCTCTATCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
         65 TCCTTCCTCTATCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT

                                             
        668 CTTCCTTCCTCTGTCTTCTCGTGTACCTTCGTG
          1 CTTCCTTCCTCTGTCTTCTCGTGTACCTTCGTG

        701 TCTGTCGTGT


Statistics
Matches: 154,  Mismatches: 3, Indels: 2
        0.97            0.02        0.01

Matches are distributed among these distances:
 124   33  0.21
 125  121  0.79

ACGTcount: A:0.04, C:0.40, G:0.21, T:0.35


Consensus pattern (124 bp):   
CTTCCTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTT
CCTTCCTCTATCTTCCCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT

Found at i:1445 original size:20 final size:20

Alignment explanation


    Indices: 1420--1459  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1410 ATGAGACTCC

                                
       1420 TTTTCTACATTACATATGAT
          1 TTTTCTACATTACATATGAT

                  *             
       1440 TTTTCTGCATTACATATGAT
          1 TTTTCTACATTACATATGAT

       1460 ATAGCTCAAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50


Consensus pattern (20 bp):   
TTTTCTACATTACATATGAT
Done.