Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024905.1 Corchorus olitorius cultivar O-4 contig24938, 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: 5302
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38


Found at i:456 original size:22 final size:22

Alignment explanation


    Indices: 398--479  Score: 74
    Period size: 22  Copynumber: 3.6  Consensus size: 22

        388 TCATATAAAA

                         *  *      
        398 GTTAACAAAATTTCATTGGGAGG
          1 GTTAACAAAATTTGATAGGGA-G

                  *         *       
        421 TGCTTATCAAAATTTGCTAGGGAG
          1 -G-TTAACAAAATTTGATAGGGAG

                         *        
        445 GTTAACAAAATTTTATAGGGAG
          1 GTTAACAAAATTTGATAGGGAG

                **       
        467 GTTATGAAAATTT
          1 GTTAACAAAATTT

        480 TATGCAGTGG


Statistics
Matches: 48,  Mismatches: 9, Indels: 4
        0.79            0.15        0.07

Matches are distributed among these distances:
  22   29  0.60
  23    1  0.02
  24    2  0.04
  25   16  0.33

ACGTcount: A:0.35, C:0.07, G:0.23, T:0.34


Consensus pattern (22 bp):   
GTTAACAAAATTTGATAGGGAG

Found at i:480 original size:22 final size:22

Alignment explanation


    Indices: 424--482  Score: 82
    Period size: 22  Copynumber: 2.7  Consensus size: 22

        414 TGGGAGGTGC

                        **        
        424 TTATCAAAATTTGCTAGGGAGG
          1 TTATCAAAATTTTATAGGGAGG

               *                  
        446 TTAACAAAATTTTATAGGGAGG
          1 TTATCAAAATTTTATAGGGAGG

                *          
        468 TTATGAAAATTTTAT
          1 TTATCAAAATTTTAT

        483 GCAGTGGTTA


Statistics
Matches: 32,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   32  1.00

ACGTcount: A:0.37, C:0.05, G:0.20, T:0.37


Consensus pattern (22 bp):   
TTATCAAAATTTTATAGGGAGG

Found at i:563 original size:22 final size:22

Alignment explanation


    Indices: 529--773  Score: 152
    Period size: 22  Copynumber: 11.1  Consensus size: 22

        519 TGTTTCATTC

                  *         *     
        529 TCATAGGGAGGTTATCGAAATT
          1 TCATAGTGAGGTTATCAAAATT

                *   *              
        551 TCATGGTGTGGTTATCAAAATTT
          1 TCATAGTGAGGTTATCAAAA-TT

                *   *        *    
        574 TCATTGTGCGGTTA-C-CAATT
          1 TCATAGTGAGGTTATCAAAATT

             *        * *    *      
        594 TTATTTAGTGTGATTATTAAAATT
          1 TCA--TAGTGAGGTTATCAAAATT

             *    **  *           
        618 TTATAGACAGATTATCAAAATT
          1 TCATAGTGAGGTTATCAAAATT

               * *          *     
        640 TCACACTGAGGTTATCGAAATT
          1 TCATAGTGAGGTTATCAAAATT

                    *   * *       
        662 TCATAGTGTGGTCACCAAAATT
          1 TCATAGTGAGGTTATCAAAATT

               *    *      *   *  
        684 TCACAGTGTGGTTATTAAATTT
          1 TCATAGTGAGGTTATCAAAATT

                  *         *     
        706 TCATAGGGAGGTTATCGAAATT
          1 TCATAGTGAGGTTATCAAAATT

                 *             *  
        728 TCATAATGAGGTTATCAAATTT
          1 TCATAGTGAGGTTATCAAAATT

               * *  *         *   
        750 TCAAAATGTGGTTATCAATATT
          1 TCATAGTGAGGTTATCAAAATT

              
        772 TC
          1 TC

        774 TACATTGGAG


Statistics
Matches: 169,  Mismatches: 49, Indels: 10
        0.74            0.21        0.04

Matches are distributed among these distances:
  20    4  0.02
  21    2  0.01
  22  142  0.84
  23   14  0.08
  24    7  0.04

ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39


Consensus pattern (22 bp):   
TCATAGTGAGGTTATCAAAATT

Found at i:586 original size:23 final size:22

Alignment explanation


    Indices: 538--587  Score: 64
    Period size: 23  Copynumber: 2.2  Consensus size: 22

        528 CTCATAGGGA

                   *             *
        538 GGTTATCGAAATTTCATGGTGT
          1 GGTTATCAAAATTTCATGGTGC

                              *    
        560 GGTTATCAAAATTTTCATTGTGC
          1 GGTTATCAAAA-TTTCATGGTGC

                 
        583 GGTTA
          1 GGTTA

        588 CCAATTTTAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  22   10  0.42
  23   14  0.58

ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42


Consensus pattern (22 bp):   
GGTTATCAAAATTTCATGGTGC

Found at i:708 original size:66 final size:66

Alignment explanation


    Indices: 629--773  Score: 173
    Period size: 66  Copynumber: 2.2  Consensus size: 66

        619 TATAGACAGA

                             *                    *  *                * *    
        629 TTATCAAAATTTCACACTGAGGTTATCGAAATTTCATAGTGTGGTCACCAAAATTTCACAGTGTG
          1 TTATCAAAATTTCACACGGAGGTTATCGAAATTTCATAATGAGGTCACCAAAATTTCAAAATGTG

             
        694 G
         66 G

                *   *     * *                            * *    *            
        695 TTATTAAATTTTCATAGGGAGGTTATCGAAATTTCATAATGAGGTTATCAAATTTTCAAAATGTG
          1 TTATCAAAATTTCACACGGAGGTTATCGAAATTTCATAATGAGGTCACCAAAATTTCAAAATGTG

             
        760 G
         66 G

                   *     
        761 TTATCAATATTTC
          1 TTATCAAAATTTC

        774 TACATTGGAG


Statistics
Matches: 64,  Mismatches: 15, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  66   64  1.00

ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38


Consensus pattern (66 bp):   
TTATCAAAATTTCACACGGAGGTTATCGAAATTTCATAATGAGGTCACCAAAATTTCAAAATGTG
G

Found at i:4905 original size:13 final size:13

Alignment explanation


    Indices: 4887--4912  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       4877 TATTTTTATA

                         
       4887 AATATTTTAATTT
          1 AATATTTTAATTT

                         
       4900 AATATTTTAATTT
          1 AATATTTTAATTT

       4913 TAAAAAATTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (13 bp):   
AATATTTTAATTT
Done.