Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002795.1 Corchorus olitorius cultivar O-4 contig02797, 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, 713

Length: 1189
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Found at i:1086 original size:326 final size:325

Alignment explanation


    Indices: 26--1089  Score: 1142
    Period size: 324  Copynumber: 3.3  Consensus size: 325

         16 GGGGCCCCAT

                                  *          *    *           *    *         
         26 CTCAGTTTTGCATGATTTTTGGTGCCAAGACTCATT-GGATA--TATATTAATCTGACCAAATCT
          1 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCGAATATCTATATTCATCTAACCAAATCT

                    *    *                              *             *      
         88 CAGCAACATTGGATTTAACTATTTGTTTTTACGAGCATCGGAAACCAGTTTCGATTTATTAATT-
         66 CAGCAACAATGGAATTAAC-ATTTGTTTTTACGAGCATCGGAAATCAGTTTCGATTTAATAATTA

                                                          *         *        
        152 AAAAAAATAGGTAAATCGATATTATTAACGTGAAAAGCCCTTCAATTTTTTTGGCGGTGAATTAT
        130 AAAAAAATAGGTAAATCGATATTATTAACGTGAAAAGCCCTTCAATATTTTTGGCGCTGAATTAT

                 *                  *           *              *         *   
        217 ATATTATTTATGAGTATTGTGGCCTGAAATTAAGGAAAAATCTTTCGGGT-CA-TTTTTTGCAAA
        195 ATATTTTTTATGAGTATTGTGGCCAGAAATTAAGGAGAAATCTTTCGGGTAAATTTTTTTGTAAA

                                                     *  *   *     *          
        280 ATTTTAGCCGAAATCGTGTACTAA-TCATCACAGTTTTTGGCTAGAAATGCGTTCTAGG-GCCCC
        260 ATTTTAGCCGAAATCGTGTACTAACT-ATCACAGTTTTTGGATAAAAACGCGTTATAGGAGCCCC

              
        343 GA
        324 GA

             *         *           *                      *              *   
        345 CCCAGTTTTGCCTGATTTTTGGCACCAAGACTCCTTCGAATATCTACATTCATCTAACCAATTCT
          1 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCGAATATCTATATTCATCTAACCAAATCT

                *     *         *             *     *        *             **
        410 CAGCCAC-ATTGAATTTAAGGATTTGTTTTTACGGGCATCTG-AATCATATTTCGATTTAAT-CG
         66 CAGCAACAATGGAA-TTAA-CATTTGTTTTTACGAGCATCGGAAATCA-GTTTCGATTTAATAAT

            *   **  * *  *   *                 *        *      *        *    
        472 GAAATTAATTCGGAAAAACATGATATTA-TAATCGCGAAAAGCCATTCAATCTTTTTGGCACTGA
        128 TAAAAAAAATAGGTAAATC--GATATTATTAA-CGTGAAAAGCCCTTCAATATTTTTGGCGCTGA

                                        * *     *                     *      
        536 ATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAGAAAAT-TTTC----AATTTAGTT
        190 ATTATATATTTTTTATGAGTATTGTGGCCAGAAATTAAGGAG-AAATCTTTCGGGTAAATT--TT

                                                   *        *        *     * 
        596 TTTGTAAAATTTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGGTTAAAAACGTGTTATGG
        252 TTTGTAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGATAAAAACGCGTTATAG

               *     
        661 GA-TCCC-A
        317 GAGCCCCGA

                                  **          *  *                  *        
        668 TCTCAGTTTTGCATGATTTTTGATGCCAAGACTCATTGGAATATCTATATTCATCTGACCAAATC
          1 -CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCGAATATCTATATTCATCTAACCAAATC

                     *    *                                            *     
        733 TCAGCAACATTGGATTTAACGATTTGTTTTTACGAGCATCGGAAATCAGTTTCGATTTACTAATT
         65 TCAGCAACAATGGAATTAAC-ATTTGTTTTTACGAGCATCGGAAATCAGTTTCGATTTAATAATT

                                                                  *  *       
        798 AAAAAAAATAGGTAAATCGATATTATTAACGTGAAAAGCCCTTCAATATTTTTGCCGTTGAATTA
        129 AAAAAAAATAGGTAAATCGATATTATTAACGTGAAAAGCCCTTCAATATTTTTGGCGCTGAATTA

                           *      *                                          
        863 TATATTTTTTTATGATTATTGTCGCCAGAAATTAAGGAGAAATCTTTCGGGTAAATTTTTTTGTA
        194 TATA-TTTTTTATGAGTATTGTGGCCAGAAATTAAGGAGAAATCTTTCGGGTAAATTTTTTTGTA

                     * *     *                      *              * *    *  
        928 AAATTTTAGGCAAAATCATGTACTAACTATCACAGTTTTTTGATAAAAACGCGTTTTCGGAGGCC
        258 AAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGATAAAAACGCGTTATAGGAGCCC

               
        993 CGA
        323 CGA

                  *  *   * *                     *                         * 
        996 CTCAGTATTACATAAATTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATAT
          1 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCGAATATCTATATTCATCTAACCAAATCT

                          *               
       1061 CAGCAACAATGGAAATAGA-ATTTGTTTTT
         66 CAGCAACAATGGAATTA-ACATTTGTTTTT

       1090 CCGGGCTTCT


Statistics
Matches: 598,  Mismatches: 115, Indels: 57
        0.78            0.15        0.07

Matches are distributed among these distances:
 319   31  0.05
 320    4  0.01
 321    7  0.01
 322   69  0.12
 323   49  0.08
 324  266  0.44
 325   25  0.04
 326   70  0.12
 327   71  0.12
 328    6  0.01

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37


Consensus pattern (325 bp):   
CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCGAATATCTATATTCATCTAACCAAATCT
CAGCAACAATGGAATTAACATTTGTTTTTACGAGCATCGGAAATCAGTTTCGATTTAATAATTAA
AAAAAATAGGTAAATCGATATTATTAACGTGAAAAGCCCTTCAATATTTTTGGCGCTGAATTATA
TATTTTTTATGAGTATTGTGGCCAGAAATTAAGGAGAAATCTTTCGGGTAAATTTTTTTGTAAAA
TTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGATAAAAACGCGTTATAGGAGCCCCGA
Done.