Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011010.1 Corchorus olitorius cultivar O-4 contig11042, 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, 755

Length: 1259
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25


Found at i:401 original size:21 final size:21

Alignment explanation


    Indices: 377--489  Score: 149
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        367 CTTAGGCATT

                         *       
        377 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
        398 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *    *     * 
        419 TCCAATGAACTTGTAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        440 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
        461 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        482 TCCAATGA
          1 TCCAATGA

        490 ACTTCTAGCA


Statistics
Matches: 83,  Mismatches: 8, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   81  0.98

ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:881 original size:154 final size:154

Alignment explanation


    Indices: 593--1252  Score: 1016
    Period size: 154  Copynumber: 4.3  Consensus size: 154

        583 CCTTGGCGCA

                                                  *              *           
        593 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAACGAAAAGCATTGAGATTTGCCAAATCG
          1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCG

                *        *  **                                               
        658 AAGATGATTCAAAGCGTCATTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
         66 AAGACGATTCAAAACGGAATTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC

                                    
        723 TAAAAACTTCACAGTGGACTAATC
        131 TAAAAACTTCACAGTGGACTAATC

              *                                                 *    *       
        747 TCTCCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGTCAAATCG
          1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCG

                                *    *                     *             *  *
        812 AAGACGATTCAAAACGGAATAAATGCGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATTAGA
         66 AAGACGATTCAAAACGGAATTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC

                       *            
        877 TAAAAACTTCATAGTGGACTAATC
        131 TAAAAACTTCACAGTGGACTAATC

                      *                                 *        *          *
        901 TCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGATTTGCCAAATCC
          1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCG

                             **                                              
        966 AAGACGATTCAAAAC-GTCTCTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
         66 AAGACGATTCAAAACGGAAT-TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG

               *       *             
       1030 CTAGAAACTTCTCAGTGGACTAATC
        130 CTAAAAACTTCACAGTGGACTAATC

                            *    *                              *      *     
       1055 TCACCAAAATGATTATGGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCCAATCG
          1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCG

                            ** *                                             
       1120 AAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
         66 AAGACGATTCAAAACGGAATTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC

                                    
       1185 TAAAAACTTCACAGTGGACTAATC
        131 TAAAAACTTCACAGTGGACTAATC

                                *                  *    
       1209 TCACCAAAATGATTATAGTTGGGCCATAAACAATGGAAAAAAAA
          1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA

       1253 AAACATT


Statistics
Matches: 454,  Mismatches: 50, Indels: 4
        0.89            0.10        0.01

Matches are distributed among these distances:
 153    2  0.00
 154  452  1.00

ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22


Consensus pattern (154 bp):   
TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCG
AAGACGATTCAAAACGGAATTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
TAAAAACTTCACAGTGGACTAATC

Done.