Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011761.1 Corchorus olitorius cultivar O-4 contig11794, 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: 1675
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22


Found at i:615 original size:154 final size:154

Alignment explanation


    Indices: 1--1674  Score: 2203
    Period size: 154  Copynumber: 10.9  Consensus size: 154

                                                                 *           
          1 AATGATTATAGTT-CGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTG-CGAATCGAAGACG
          1 AATGATTATAGTTAC-GCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACG

                                                                    *        
         64 ATTCAAAACGTCACTAAT-GG-CCCGATAT-G-CCAAAAT-AAAAGTGTTCCAAATCAGCT-AAA
         65 ATTCAAAACGTCACTAATGGGCCCCGAT-TGGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAA

                                       
        123 ACTTCACAAGTGGACTAATCTCACCAA
        129 ACTTCACAA-TGGACTAATCTCACCAA

                          *                     *    *  *                    
        150 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGCATCGAAGGTTGCCAAATCGAAGACGA
          1 AATGATTATAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA

                                                                 *           
        215 TTCAAAACGTCACTAATGGGCCCCGATTAGGCCCAAAATAAAAAGTGTTCCAATTTAGCTAAAAA
         66 TTCAAAACGTCACTAATGGGCCCCGATT-GGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAAA

                                 *    
        280 CTTCACAGA-GGACTAATCTCCCCAA
        130 CTTCACA-ATGGACTAATCTCACCAA

              *     *                                 ** *                   
        305 AACGATTACAGTTACGCCATAAACAATGGAAAGAAAAGCATTTTGCGTTGCCAAATCGAAGACGA
          1 AATGATTATAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA

                                                                *    *       
        370 TTCAAAACGTCACTAAT-GGCCCCGATTGGCCCAAAATAAAAAGTGTTCCAATTTAGATAAAAAC
         66 TTCAAAACGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAAAC

                                    
        434 TTCACAATGGACTAATCTCACCAA
        131 TTCACAATGGACTAATCTCACCAA

                    *                       *                                
        458 AATGATTACAGTTACGCCATAAACAATGGAAAAAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
          1 AATGATTATAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA

                  **                                            *            
        523 TTCAAATTGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTCCAATTTAGCTAAAAAC
         66 TTCAAAACGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAAAC

                                    
        588 TTCACAATGGACTAATCTCACCAA
        131 TTCACAATGGACTAATCTCACCAA

                    *                       *          *                     
        612 AATGATTACAGTTACGCCATAAACAATGGAAAAAAAAGCATTGGGGGTTGCCAAATCGAAGACGA
          1 AATGATTATAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA

                  *                                          * **            
        677 TTCAAATCGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTCGATTTTAGCTAAAAAC
         66 TTCAAAACGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAAAC

                                    
        742 TTCACAATGGACTAATCTCACCAA
        131 TTCACAATGGACTAATCTCACCAA

                    *                                    *     *             
        766 AATGATTACAGTTACGCCATAAACAATGGAAAGAAAAGCATAT-ATGGTTGGCAAATCGAAGACG
          1 AATGATTATAGTTACGCCATAAACAATGGAAAGAAAAGCAT-TGAGGGTTGCCAAATCGAAGACG

               *      **                *   *                 *              
        830 ATTAAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCAAAATTAGCTAAAAA
         65 ATTCAAAACGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAAA

                    *                  
        895 CTTCAACAGTGGACTAATCTCACCTAA
        130 CTTC-ACAATGGACTAATCTCACC-AA

                           *                                   *             
        922 AATGAATTATAGTTAGGCCATAAACAATGGAAAGAAAA-CATTGAGGGTTTACCAAATCGAAGAC
          1 AATG-ATTATAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGG-TTGCCAAATCGAAGAC

                *                   **   *   *        *              *       
        986 GATTTAAAACGTCACTAATGGGCCTTGATGGGCACAAAATAACAAGTGTTCCAAATGAAGCTAAA
         64 GATTCAAAACGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTCCAAAT-TAGCTAAA

               *     *           *     
       1051 AACATCACAGTGGACTAATCTGACCAA
        128 AACTTCACAATGGACTAATCTCACCAA

                   *                    *                  *                *
       1078 AATGATTGTAGTTA-GTCCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACA
          1 AATGATTATAGTTACG-CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACG

                      **                *                     *    **        
       1142 ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAA-TGTTGCAAAGGAGCTAAAA
         65 ATTCAAAACGTCACTAATGGGCCCCGATTGGCCCAAAATAA-AAAGTGTTCCAAATTAGCTAAAA

                    *  *              
       1206 ACTTCACAGT-CACTAATCTCACCAA
        129 ACTTCACAATGGACTAATCTCACCAA

                          *                               *         *        
       1231 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATTGAAGACGA
          1 AATGATTATAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA

              *      **      *   *     *            *    *        *          
       1296 TTGAAAACGGAACTAATTGGCTCCGATAGGCCCAAAATAACAAGTCTTCCAAATGAGCTAAAAAC
         66 TTCAAAACGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAAAC

                  * *               
       1361 TTCACAGTCGACTAAT-TCACCAA
        131 TTCACAATGGACTAATCTCACCAA

                          *                               *                  
       1384 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
          1 AATGATTATAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA

                     **                        *     *    *        *  *      
       1449 TTCAAAACGGAACTAATGGGCCCCG-TTAGGCCCATAATAACAAGTATTCCAAATCAGTTAAAAA
         66 TTCAAAACGTCACTAATGGGCCCCGATT-GGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAAA

                   *     *     *     
       1513 CTTCACAGTGGACCAATCTGACCAA
        130 CTTCACAATGGACTAATCTCACCAA

                          *     *                         *                  
       1538 AATGATTATAGTTAGGCCATCAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
          1 AATGATTATAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA

              *      **      *   *     *             *    *        *         
       1603 TTGAAAACGGAACTAATTGGCTCCGATAGGCCCAAAATAACGAAGTCTTCCAAATGAGCTAAAAA
         66 TTCAAAACGTCACTAATGGGCCCCGATTGGCCCAAAATAA-AAAGTGTTCCAAATTAGCTAAAAA

                   
       1668 CTTCACA
        130 CTTCACA

       1675 G


Statistics
Matches: 1382,  Mismatches: 114, Indels: 52
        0.89            0.07        0.03

Matches are distributed among these distances:
 149   45  0.03
 150   30  0.02
 151    3  0.00
 152   10  0.01
 153  408  0.30
 154  483  0.35
 155  240  0.17
 156   39  0.03
 157  112  0.08
 158   12  0.01

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


Consensus pattern (154 bp):   
AATGATTATAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
TTCAAAACGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAAAC
TTCACAATGGACTAATCTCACCAA

Done.