Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004184.1 Corchorus capsularis cultivar CVL-1 contig04192, 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, 655

Length: 1092
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:641 original size:325 final size:319

Alignment explanation


    Indices: 19--1087  Score: 1072
    Period size: 325  Copynumber: 3.3  Consensus size: 319

          9 CCGACTCAAA

                             *            *             *    **              
         19 TTTGCATGATTTTTTGTGCA-AAA-ACTCCTTGAAATATCTATATTCATAGAACCAAATCTCAGC
          1 TTTGCATGA-TTTTTG-CCAGAAACACTCCATGAAATATCTATACTCATCTAACCAAATCTCAGC

              *       *                       *   *    *              *    * 
         82 CAGATTGGATATAAGGATTTGTTTTTACGAAGATTTGATTCTTATTTCGATTTAATTATAAATTA
         64 CACATTGGATTTAAGGATTTG-TTTTACG-AGATATGAATCTTGTTTCGATTTAATTAGAAATAA

                                                       *                **   
        147 ATTC--AAAAAAATGG-AAAACTGATATTATAAGCGTGAAATAGCCG-TCAATTTTTTGGTATTG
        127 ATTCGGAAAAAAATGGAAAAAC-GATATTATAAGCGTGAAA-ACCCGTTC-ATTTTTTGGCGTTG

                            *   *      *           *   *       *       *   * 
        208 AATTATATA-TTTTTTATGAATATT-TTGCAAAAAAAAAGTG-TGTAAAAAATTTTCAGATCAGT
        189 AATTATATATTTTTTTCTGAGTATTGTGGC---AAAAAATTGACG-AAAAACTTTTCAGGTCAAT

                    *              *               *        *    *   *       
        270 TTTTAGCCTAAATCGTGTACTAATCATCACGGTTTTTGGTTAAAAACGGGTGTTGGGTTCCAGGC
        250 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTGTCGGGGTCCAGGC

                 
        335 TCAGT
        315 TCAGT

                                  *          *                      *     *  
        340 TTTGCATGATTTTTGCCAGAAAGACTCCATGAATTA-CTTATACTCATCTAACCAAGTCTCAACC
          1 TTTGCATGATTTTTGCCAGAAACACTCCATGAAATATC-TATACTCATCTAACCAAATCTCAGCC

               *                                                             
        404 ACAATGGATTTAAGGATTTGTTTTACGAGTATATGAATCTTGTTTCGATTTAATTAGAAATAAAT
         65 ACATTGGATTTAAGGATTTGTTTTACGAG-ATATGAATCTTGTTTCGATTTAATTAGAAATAAAT

                                              *                              
        469 TCGGAAAAAAAAATGGAAAAACGATATTATAAGCATGAAAACCCGTTCATTTCTTTGGCGTTGAA
        129 TCGG--AAAAAAATGGAAAAACGATATTATAAGCGTGAAAACCCGTTCATTT-TTTGGCGTTGAA

                                 *                                   *       
        534 TTATATATATTTTTTTCTGAGCATTGTGGCAAAAAATTGACGAAAAACTTTTCAGGTTAATTTTT
        191 -T-TATATATTTTTTTCTGAGTATTGTGGCAAAAAATTGACGAAAAACTTTTCAGGTCAATTTTT

                           *                                          **     
        599 AGCCGAAATCGTGTAGTAACCATCACGGTTTTTGGCTAAAAACGCGTGTCGGGGTCCATTCTCAG
        254 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTGTCGGGGTCCAGGCTCAG

             
        664 T
        319 T

                           *            *             *              *    *  
        665 TTTGCATGATTTTTGGCAGAAACACTCCCTGAAATATCTATATTCATCTAACCAAATATCAGTCA
          1 TTTGCATGATTTTTGCCAGAAACACTCCATGAAATATCTATACTCATCTAACCAAATCTCAGCCA

                *              *      *                    *               * 
        730 CATTTGATTTAAGGATTTCTTTTTACAAGCATATGAATCTTGTTTCGGTTTAATTAGAAATAATT
         66 CATTGGATTTAAGGATTT-GTTTTACGAG-ATATGAATCTTGTTTCGATTTAATTAGAAATAAAT

                        *              *             *                       
        795 TCGGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAAATCC-TTCAGTTTTTTGGCGTTGAA
        129 TCGGAAAAAAATGGAAAAACGATATTATAAGCGTG--AAAACCCGTTCA-TTTTTTGGCGTTGAA

                             *                    *                          
        859 TTATAT-TTTTTTTCTGCGTATTGTGGCAAAAAATTGAGGAAAAACTTTTC-GGTCAATTTTTAG
        191 TTATATATTTTTTTCTGAGTATTGTGGCAAAAAATTGACGAAAAACTTTTCAGGTCAATTTTTAG

                               *              *                         * *  
        922 CCGAAATCGTGTACTAACCTTCACGATTTTTTAATTTTTTGGCTAAAAACGCGT-TCCGGAGACC
        256 CCGAAATCGTGTACTAACCATCACG---------GTTTTTGGCTAAAAACGCGTGT-CGGGGTCC

            * *    **
        986 CGACTCAAA
        311 AGGCTCAGT

                             *            *             *    **              
        995 TTTGCATGATTTTTTGTGCA-AAA-ACTCCTTGAAATATCTATATTCATAGAACCAAATCTCAGC
          1 TTTGCATGA-TTTTTG-CCAGAAACACTCCATGAAATATCTATACTCATCTAACCAAATCTCAGC

              *       *              *    
       1058 CAGATTGGATATAAGGATTTGTTTTTCGAG
         64 CACATTGGATTTAAGGATTTGTTTTACGAG

       1088 TATTT


Statistics
Matches: 631,  Mismatches: 84, Indels: 58
        0.82            0.11        0.08

Matches are distributed among these distances:
 319    4  0.01
 320   49  0.08
 321   93  0.15
 322   41  0.06
 323   13  0.02
 324   68  0.11
 325  176  0.28
 326   62  0.10
 327   12  0.02
 328    3  0.00
 329    8  0.01
 330   90  0.14
 331    9  0.01
 332    3  0.00

ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36


Consensus pattern (319 bp):   
TTTGCATGATTTTTGCCAGAAACACTCCATGAAATATCTATACTCATCTAACCAAATCTCAGCCA
CATTGGATTTAAGGATTTGTTTTACGAGATATGAATCTTGTTTCGATTTAATTAGAAATAAATTC
GGAAAAAAATGGAAAAACGATATTATAAGCGTGAAAACCCGTTCATTTTTTGGCGTTGAATTATA
TATTTTTTTCTGAGTATTGTGGCAAAAAATTGACGAAAAACTTTTCAGGTCAATTTTTAGCCGAA
ATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTGTCGGGGTCCAGGCTCAGT
Done.