Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020844.1 Corchorus olitorius cultivar O-4 contig20877, 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, 799

Length: 1333
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33


Found at i:873 original size:328 final size:329

Alignment explanation


    Indices: 2--1329  Score: 1359
    Period size: 328  Copynumber: 4.0  Consensus size: 329

          1 A

                         *       *           *                   *    *     *
          2 AAATTTTTTTTCTGAATATTTCGCCACAATACTGAT-AAAAAAATATAATTCAGCGCAAAAAAAA
          1 AAATTTTTTTTCTAAATATTTTGCCACAATACTCATAAAAAAAATATAATTCAACGC-CAAAAAG

                 **                                                          
         66 ATTTTCTGGGCTTTTCATGCTTCAAATATGGTTTTTCCGTTTTTTTATCCAATTAATTTCTGATA
         65 A-TTTAAGGGCTTTTCATGCTTCAAATATGG-TTTT-C-TTTTTTTATCCAATTAATTTCTGATA

                         *              *                                    
        131 AAACCCGAATCAACATTCAGAAGCTCGTTAAAACATATCCTTAAATTCAATG-TGACTGAGATTT
        126 AAACCCGAATCAAGATTCAGAAGCTCGTAAAAACATATCCTTAAATTCAATGTTG-CTGAGATTT

            *                      *      *      *  *     *  *               
        195 CATTAGATTAATATAGATATTTCTAGGAGTTTCGACGTCATAAAT-AATTCAAAACTGAGCCGGG
        190 GATTAGATTAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTA-GCAAAACTGAGCC-GG

                 *  *            *            *                 *  *         
        259 GGCCCGGAGCGCATTTTCAGCTGAAAACTGTGATAGTTAGTACACGATTTCAACTGAAATTTTGC
        253 GGCCCAGAACGCATTTTCAGCAGAAAAC-GTGATGGTTAGTACACGATTTCAGCTAAAATTTTGC

                     *   
        324 AAAACCTGAACCG
        317 AAAACCTGATCCG

                          *     *                               *           *
        337 AAAATTTTTTTTCTGAATATGTTGCCACAATACTCATAAAAAAAATATAATTGAACGCCAAAAAT
          1 -AAATTTTTTTTCTAAATATTTTGCCACAATACTCATAAAAAAAATATAATTCAACGCCAAAAAG

                * *                       *                              *   
        402 ATTTCATGGCTTTTCATGCTTCAAATATAGTTTTTCTTTTTTTTTTTTTAAATCCAATTAACTTC
         65 ATTTAAGGGCTTTTCATGCTTCAAATAT-GGTTTTC------TTTTTTT--ATCCAATTAATTTC

                      *    *           *                        *  *   * *   
        467 TGATAAAA-CGGAATGAAGATTTC-GATGCTCGTAAAAACATATCCTTAAATACATTGTAGATGA
        121 TGATAAAACCCGAATCAAGA-TTCAGAAGCTCGTAAAAACATATCCTTAAATTCAATGTTGCTGA

                          *                 *            *                   
        530 GATTTGATTAGATTCATATAGATATTTCAAGGTGTCTCGACGCCACAAATCTAGCAAAACTGAGC
        185 GATTTGATTAGATTAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTAGCAAAACTGAGC

                           **              *                           *     
        595 CGGGGCCCCAGAACGGGTTTTCAGCAAGAAATCGTGATGGTTAGTACACGATTTCAGCTCAAATT
        250 CGGGG-CCCAGAACGCATTTTCAGC-AGAAAACGTGATGGTTAGTACACGATTTCAGCTAAAATT

                    *        
        660 TTGCAAAAACTGATCCG
        313 TTGCAAAACCTGATCCG

                                      *           *    *       *  * * *      
        677 AAATTTTTTTCTCTAAAT-TTTTGCCCCAATACTCATAGAAAATATATAATCCAGCACTAAAAAG
          1 AAATTTTTTT-TCTAAATATTTTGCCACAATACTCATAAAAAAAATATAATTCAACGCCAAAAAG

                                                                             
        741 ATTTAAGGGCTTTTCATGCTTCAAATATGG-TTT-TTTTTTTATCCAATTAATTTCTGATAAAA-
         65 ATTTAAGGGCTTTTCATGCTTCAAATATGGTTTTCTTTTTTTATCCAATTAATTTCTGATAAAAC

                  *                  *                  *  *                 
        803 CCGAATGAAGATTTC-GATA-CTCGGAAAAACATATCCTTAAATCCATTGTTGCTGAGATTTGAT
        130 CCGAATCAAGA-TTCAGA-AGCTCGTAAAAACATATCCTTAAATTCAATGTTGCTGAGATTTGAT

                  *                  *                   *                   
        866 TAGATTCATATTA-ATATTTCAAGGCGTCTCGACGCCAAAAATCTCGCAAAACTGAGCCGGGGCC
        193 TAGATTAATA-TAGATATTTCAAGGAGTCTCGACGCCAAAAATCTAGCAAAACTGAGCCGGGGCC

             *                      *                                 *      
        930 CTGAAACGCATTTTCAGCCAGAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTGTGCAAA
        257 CAG-AACGCATTTTCAG-CAGAAAACGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAA

                    * 
        995 ACCTGATCAG
        320 ACCTGATCCG

                *             *          * *   *       *                     
       1005 -AATATTTTTTC-ACAATTTTTTGCCACAGTGCTCTTAAAAAATATATAATTCAACGCCAAAAAG
          1 AAATTTTTTTTCTA-AATATTTTGCCACAATACTCATAAAAAAAATATAATTCAACGCCAAAAAG

                     *            *                                          
       1068 ATTTCAA-GCCTTTTCATGCTTAAAATATGGTTATTCGTTTTTTTATCCAATTAATTTCTGATAA
         65 ATTT-AAGGGCTTTTCATGCTTCAAATATGGTT-TTC-TTTTTTTATCCAATTAATTTCTGATAA

                                       *                      *  *  *        
       1132 AACCCGAATCAAGATTCAGAAGCTCGTTAAAACATATCCTTAAATTCAATATTACTAAGATTTGA
        127 AACCCGAATCAAGATTCAGAAGCTCGTAAAAACATATCCTTAAATTCAATGTTGCTGAGATTTGA

                                  *      *      *            *   *   *       
       1197 TTAGATTAATATAGATAATTTCTAGGAGTTTCGACGTCAAAAATCATA-TAAATCTGGGCCGGGC
        192 TTAGATTAATATAGAT-ATTTCAAGGAGTCTCGACGCCAAAAATC-TAGCAAAACTGAGCCGGG-

                *  **  *    *   *                  *             *           
       1261 GCCCGGAGTGCCTTTTTAGCTGAAAAC-T-AT-G--A-TTCACGATTTCAGCTGAAATTTTGCAA
        254 GCCCAGAACGCATTTTCAGCAGAAAACGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAA

              *       
       1320 AAGCTGATCC
        319 AACCTGATCC

       1330 AAAA


Statistics
Matches: 845,  Mismatches: 114, Indels: 76
        0.82            0.11        0.07

Matches are distributed among these distances:
 325    1  0.00
 326   37  0.04
 327   75  0.09
 328  198  0.23
 329    6  0.01
 330    9  0.01
 331   36  0.04
 332   66  0.08
 333   45  0.05
 334    7  0.01
 335   29  0.03
 336   40  0.05
 337   21  0.02
 338    1  0.00
 339   83  0.10
 340  160  0.19
 341   31  0.04

ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34


Consensus pattern (329 bp):   
AAATTTTTTTTCTAAATATTTTGCCACAATACTCATAAAAAAAATATAATTCAACGCCAAAAAGA
TTTAAGGGCTTTTCATGCTTCAAATATGGTTTTCTTTTTTTATCCAATTAATTTCTGATAAAACC
CGAATCAAGATTCAGAAGCTCGTAAAAACATATCCTTAAATTCAATGTTGCTGAGATTTGATTAG
ATTAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTAGCAAAACTGAGCCGGGGCCCAGA
ACGCATTTTCAGCAGAAAACGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAACCTGA
TCCG
Done.