Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006239.1 Corchorus capsularis cultivar CVL-1 contig06258, 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, 900

Length: 1501
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24


Found at i:520 original size:154 final size:154

Alignment explanation


    Indices: 1--1501  Score: 2157
    Period size: 154  Copynumber: 9.7  Consensus size: 154

                                     *                                 *     
          1 ATTCAAAATAGCACTAATGGGCCCCAAAAGGGCCCG-AAT-ACAAGTGTTCTGAATGAGGTAAAA
          1 ATTCAAAATAGCACTAATGGGCCCCGAAA-GGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAA

               *    *         *   *       *          *                       
         64 ACTACACAGTGGACTAATATCACCAAAAATGATTATAGTTATGCCATAAACAATGGAAAGAAAAG
         65 ACTTCACAATGGACTAATCTCATC-AAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAG

                                      
        129 CTTTGCGGTTTGTCATATCGAATACG
        129 CTTTGCGGTTTGTCATATCGAATACG

                                                               *           * 
        155 ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTAAATGAGCTAAAGA
          1 ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA

                               *               *               *            *
        220 CTTCACAATGGACTAATCTTATCAAAATAATTTATTGTTAGGCCATAAACATTGGAAAGAAAA-T
         66 CTTCACAATGGACTAATCTCATCAAAATAA-TTATAGTTAGGCCATAAACAATGGAAAGAAAAGC

                 *      *  *          
        284 TATTGTGGTTTGCCAAATCGAATACG
        130 T-TTGCGGTTTGTCATATCGAATACG

                                                                             
        310 ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA
          1 ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA

                                      *                                      
        375 CTTCACAATGGACTAATCTCATCAAATTAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCT
         66 CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCT

                                *   
        440 TTGCGGTTTGTCATATCGAAGACG
        131 TTGCGGTTTGTCATATCGAATACG

              *     *          *    *        *                 *             
        464 ATACAAAACAGCACTAATGCGCCCTGAAAGGCCTGAAATAACAAGTGTTCTTAATGAGCTAAAAA
          1 ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA

                                                                             
        529 CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCT
         66 CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCT

                                *   
        594 TTGCGGTTTGTCATATCGAAGACG
        131 TTGCGGTTTGTCATATCGAATACG

              *     *          *                        *             *      
        618 ATACAAAACAGCACTAATGCGCCCCGAAAGGCCCGAAATAACAAATGTTCTGAATGAGTTAAAAA
          1 ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA

                                                              *             *
        683 CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACATTGGAAAGAAAAGCA
         66 CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCT

               *      *  *   *      
        748 TTGTGGTTTGCCAAATCAAATACG
        131 TTGCGGTTTGTCATATCGAATACG

                             *                            *                  
        772 ATTCAAAATAGCACTAAAGGGCCCCGAAAGGCCCGAAATAACAAGTTTTCTGAATGAGCTAAAAA
          1 ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA

                                      *                                     *
        837 CTTCACAATGGACTAATCTCATCAAATTAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
         66 CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCT

               *      *  *   *      
        902 TTGTGGTTTGCCAAATCAAATACG
        131 TTGCGGTTTGTCATATCGAATACG

                                                           *                 
        926 ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTTTTTCTGAATGAGCTAAAA
          1 ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAG-TGTTCTGAATGAGCTAAAA

                                       *                                     
        991 ACTTCACAATGGACTAATCTCATCAAATTAA-TATAGTTA-G-CAT-AAC-ATGGAAAG-AAAGC
         65 ACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC

                                 *   
       1050 TTTGCGGTTTGTCATATCGAAGACG
        130 TTTGCGGTTTGTCATATCGAATACG

              *     *            *            *                    *         
       1075 ATACAAAACAGCACTAATGCGCCCCCGAAAGGCCTGAAATAACAAGTGTTCTAGATTGAAGTCTA
          1 ATTCAAAATAGCACTAATG-GGCCCCGAAAGGCCCGAAATAACAAGTGTTCT-GAATG-AG-CTA

                       *              *      *          *                    
       1140 AAAACTTCACAGTGGACTAATCTCAACCAAAATGATTATAGTTATGCCATAAACAATGGAAAGAA
         62 AAAACTTCACAATGGACTAATCTC-ATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAA

                                       *   
       1205 AAGCGTTTGCGGGTTTGTCATATCGAAGACG
        126 AAGC-TTTGC-GGTTTGTCATATCGAATACG

              *     *          *             *                               
       1236 ATACAAAACAGCACTAATGCGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGAATGAGCTAAAAA
          1 ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA

                                 *                   *                     * 
       1301 CTTCACAATGGACTAATCTCAACAAAATAATTATAGTTAGGACATAAACAATGGAAAGAAAA-TT
         66 CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCT

                *      *  *          
       1365 ATTGTGGTTTGCCAAATCGAATACG
        131 -TTGCGGTTTGTCATATCGAATACG

                                                  *                          
       1390 ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAACAACAAGTGTTCTAGAATGAGCTAAAA
          1 ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCT-GAATGAGCTAAAA

                                                               
       1455 ACTTCACAATGGACTAATCTCATC-AAAT-ATTATAG-TA-GCCATAAACA
         65 ACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACA


Statistics
Matches: 1233,  Mismatches: 93, Indels: 45
        0.90            0.07        0.03

Matches are distributed among these distances:
 149   46  0.04
 150   36  0.03
 151   14  0.01
 152   31  0.03
 153   21  0.02
 154  650  0.53
 155  272  0.22
 156   41  0.03
 157   29  0.02
 158   10  0.01
 159    9  0.01
 160   35  0.03
 161   39  0.03

ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24


Consensus pattern (154 bp):   
ATTCAAAATAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA
CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCT
TTGCGGTTTGTCATATCGAATACG

Done.