genome.fa.s11721.2.7.7.80.10.50.1000.txt.html

Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011721.1 Corchorus olitorius cultivar O-4 contig11754, 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, 663

Length: 1106
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21


Found at i:466 original size:154 final size:154

Alignment explanation


    Indices: 1--1106  Score: 1719
    Period size: 154  Copynumber: 7.2  Consensus size: 154

                                                                             
          1 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
          1 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG

                                                    *                  *     
         66 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCAAAAAACTTCA-AAGTGGAATAATC
         66 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAA-TGGACTAATC

             *                     * 
        130 TTACCAAAATGATTATAGTTAGGTC
        130 TCACCAAAATGATTATAGTTAGGCC

                   *                           *                    **       
        155 ATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCATATCGAAGACGATTCAAAACGTCACTAATG
          1 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG

                   *  *                                           *          
        220 GGCCCCGGTAAGCCCAAAA-ATA-AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
         66 GGCCCCGATAGGCCCAAAATA-ACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATC

                             *       
        283 TCACCAAAATGATTATAATTAGGCC
        130 TCACCAAAATGATTATAGTTAGGCC

                         *    *            *                        **       
        308 ATAAACAATGGAAGGAAATGCATTGAGGGTTTCCAAATCGAAGACGATTCAAAACGTCACTAATG
          1 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG

                                  *              *                           
        373 GGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGTGCTAAAAACTTCACAATGGACTAATCT
         66 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCT

                                    
        438 CACCAAAATGATTATAGTTAGGCC
        131 CACCAAAATGATTATAGTTAGGCC

                                                                             
        462 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
          1 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG

                          *    *                                             
        527 GGCCCCGATAGGCCTAAAAAAACAAGTGTTCCAAATGAGCTAAAAACTTCA-AAGTGGACTAATC
         66 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAA-TGGACTAATC

             *                       
        591 TTACCAAAATGATTATAGTTAGGCC
        130 TCACCAAAATGATTATAGTTAGGCC

                   *                                                         
        616 ATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
          1 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG

                                        *           *                     *  
        681 GGCCCCGATAGGCCCAAAATAACAAGTGATCCAAATGAGCAAAAAACTTCA-AAGTGGACTATTC
         66 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAA-TGGACTAATC

             * *                  ** 
        745 TTATCAAAATGATTATAGTTAGTTC
        130 TCACCAAAATGATTATAGTTAGGCC

                   *                  **                                     
        770 ATAAACATTGGAAAGAAAAGCATTGATTGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
          1 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG

            *                                                     *          
        835 CGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC-AATAAACTTCACAGTGGACTAATC
         66 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA-AAACTTCACAATGGACTAATC

                                     
        899 TCACCAAAATGATTATAGTTAGGCC
        130 TCACCAAAATGATTATAGTTAGGCC

                                                                    **       
        924 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATG
          1 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG

                                              *                  *           
        989 GG----GATAGGCCCAAAATAACAAGTGTTCCAATTGAGCTAAAAACTTCACAGTGGACTAATCT
         66 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCT

                                    
       1050 CACCAAAATGATTATAGTTAGGCC
        131 CACCAAAATGATTATAGTTAGGCC

                              *              
       1074 ATAAACAATGGAAAGAAACGCAATTGAAGGGTT
          1 ATAAACAATGGAAAGAAAAGC-ATTG-AGGGTT


Statistics
Matches: 883,  Mismatches: 59, Indels: 22
        0.92            0.06        0.02

Matches are distributed among these distances:
 150   99  0.11
 151    6  0.01
 152    6  0.01
 153  141  0.16
 154  630  0.71
 155    1  0.00

ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21


Consensus pattern (154 bp):   
ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCT
CACCAAAATGATTATAGTTAGGCC

Done.