Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016943.1 Corchorus olitorius cultivar O-4 contig16976, 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: 7602
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:98 original size:43 final size:43

Alignment explanation


    Indices: 51--371  Score: 378
    Period size: 41  Copynumber: 7.6  Consensus size: 43

         41 GAAATGCCTT

                                                        
         51 TGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATG-CCC
          1 TGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGATGCCCC

                               *                      * 
         94 TGTGTTATATATGTGTTTGGGGACTTTG-ATATA-A-ATGCCTC
          1 TGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAGATGCCCC

                                                *      
        135 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCC
          1 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCC

                               *             *       * 
        178 TGTGTTATATATGTGTTTGGGGACTTTG--ATATAGATGCCTC
          1 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCC

                                             *  **     
        219 TGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGCGCCCC
          1 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCC

                               *        *           * * 
        262 TGTG-T-TATATGTGTTTGGGGAC-TTGGATATAG-G-TGTCTC
          1 TGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAGATGCCCC

                                         *               
        301 TGTGTTATATATGTGTTTGAGGACTTTTGGAATAGA-ATTGCCCC
          1 TGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGA-TGCCCC

                               *       
        345 TGTGTTATATATGTGTTTGGGGACTTT
          1 TGTGTTATATATGTGTTTGAGGACTTT

        372 TTGGTTATTG


Statistics
Matches: 239,  Mismatches: 24, Indels: 30
        0.82            0.08        0.10

Matches are distributed among these distances:
  39    7  0.03
  40    9  0.04
  41  106  0.44
  42   14  0.06
  43   76  0.32
  44   27  0.11

ACGTcount: A:0.21, C:0.10, G:0.27, T:0.43


Consensus pattern (43 bp):   
TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCC

Found at i:156 original size:84 final size:84

Alignment explanation


    Indices: 42--371  Score: 506
    Period size: 84  Copynumber: 3.9  Consensus size: 84

         32 CATAATGGAG

                    *                                                        
         42 AAATGCCTTTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATG-CCCTGTGTTATATAT
          1 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGATGCCCCTGTGTTATATAT

                                
        106 GTGTTTGGGGACTTTGATAT
         65 GTGTTTGGGGACTTTGATAT

                                                         *                   
        126 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATG
          1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG

                               
        191 TGTTTGGGGACTTTGATAT
         66 TGTTTGGGGACTTTGATAT

             *                                        *  **                  
        210 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGCGCCCCTGTG-T-TATATG
          1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG

                         *     
        273 TGTTTGGGGACTTGGATAT
         66 TGTTTGGGGACTTTGATAT

             **  *                                *                          
        292 AGGTGTCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGA-ATTGCCCCTGTGTTATATA
          1 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGA-TGCCCCTGTGTTATATA

                            
        356 TGTGTTTGGGGACTTT
         64 TGTGTTTGGGGACTTT

        372 TTGGTTATTG


Statistics
Matches: 227,  Mismatches: 14, Indels: 9
        0.91            0.06        0.04

Matches are distributed among these distances:
  82   55  0.24
  83   33  0.15
  84  120  0.53
  85   19  0.08

ACGTcount: A:0.21, C:0.10, G:0.26, T:0.42


Consensus pattern (84 bp):   
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
TGTTTGGGGACTTTGATAT

Found at i:731 original size:11 final size:11

Alignment explanation


    Indices: 715--740  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

        705 GTTTCAAATA

                       
        715 ATATGTAGTAT
          1 ATATGTAGTAT

                       
        726 ATATGTAGTAT
          1 ATATGTAGTAT

                
        737 ATAT
          1 ATAT

        741 TAGAGATTAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46


Consensus pattern (11 bp):   
ATATGTAGTAT

Found at i:3556 original size:2 final size:2

Alignment explanation


    Indices: 3549--3579  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       3539 ACTTACACTG

                                                          
       3549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       3580 AGCTTGAATG


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


Consensus pattern (2 bp):   
AT

Done.