Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004953.1 Corchorus capsularis cultivar CVL-1 contig04971, 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, 1000

Length: 1875
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Found at i:614 original size:333 final size:327

Alignment explanation


    Indices: 1--1190  Score: 1216
    Period size: 333  Copynumber: 3.6  Consensus size: 327

                     *               *                    *        *       * 
          1 AGTTTTGCATGATTTTTGGCGCCAAAACTCATTGAAATATCTATATTTATCTAACGAAATCTCGA
          1 AGTTTTGCACGATTTTTGGCGCCAAGACTCATTGAAATATCTATATCTATCTAACCAAATCT-TA

                *            *    *       *     *        *         *         
         66 -CCATATTGGATTTAAGGATTTATTTTTACGAGCATCTCAATTC-GGTTTCGATTTAATTAGAAA
         65 CCCACATTGGATTTAAGTATTTGTTTTTACAAGCATATCAA-TCATGTTT-GATTCAATTAGAAA

                     *         *                         *  *              **
        129 TTAATTCGAAAAAAATAGAAAAAAACAATATTAGAAGCGTGAGAAACCCTTCAATCTTTTTGGCA
        128 TTAATTCG-GAAAAATAG-GAAAAACAATATTAGAAGCGTGA-AAGCCTTTCAATCTTTTTGGTG

                                         *                        * *        
        194 TTGAATTATATATTTTTTATGAATATAGTTGCCGAAAATTGAGGAGAAATTTTTTGGGTCAATTT
        190 TTGAATTATATATTTTTTATGAATATAGTGGCCGAAAATTGAGGAGAAATTTTTCGAGTCAATTT

                                           *                     *           
        259 TTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTCGACTAAAACCGCGTTCTGGA
        255 TTGCAAAATTTTAGCTGAAATCGTGTACTAAACATCACGGTTTT-GACTAAAAACGCGTTCTGGA

              *      
        324 TCTCGGCTC
        319 TCCCGGCTC

             *                        **     *                  *            
        333 AATTTTGCACGATTTTTGGCGCCAAGTGTCATTTAAATATCTATATCCT-TCCAACCAAATCTTA
          1 AGTTTTGCACGATTTTTGGCGCCAAGACTCATTGAAATATCTATAT-CTATCTAACCAAATCTTA

                *                   *         *     *           *            
        397 CCCAAATTGGATTTAAGGATATTTTTTTTTACAAACATATGAATCATGTTTCCATTCAATTA-AG
         65 CCCACATTGGATTTAA-G-TATTTGTTTTTACAAGCATATCAATCATGTTT-GATTCAATTAGA-

                                       *           *                *     *  
        461 AATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCATGAATAGCCTTTCAATATTTTTTGT
        126 AATTAATTCGG-AAAAATAGGAAAAACAATATTAGAAGCGTGAA-AGCCTTTCAATCTTTTTGGT

                                   *   *      *           *               *  
        526 GTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGA-GAAAAATTCTTTCGAGTCTAT
        189 GTTGAATTATATATTTTTTATGAATATAGTGGCCGAAAATTGAGGAGAAATT-TTTCGAGTCAAT

                           *  *                 *            *          *   *
        590 GTTTT-CAAAATTTTTGCCGAAATCGGTGTACTAAATATCACGG-TTTGGCTAAAAACGCTTTCA
        253 -TTTTGCAAAATTTTAGCTGAAATC-GTGTACTAAACATCACGGTTTTGACTAAAAACGCGTTCT

              *          
        653 GGGTCCCCGGCTC
        316 GGAT-CCCGGCTC

                  *  *         *                          *        *      * *
        666 AGTTTTCCATGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTTATCTAACGAAATCTCAG
          1 AGTTTTGCACGATTTTTGGCGCCAAGACTCATTGAAATATCTATATCTATCTAACCAAATCTTAC

                                         *     *                  *          
        731 CCACATTGGATTTAAGTATTTGTTTTTACGAGCATCTCAATCCGAT-TTTGATTTAATTAGAAAT
         66 CCACATTGGATTTAAGTATTTGTTTTTACAAGCATATCAAT-C-ATGTTTGATTCAATTAGAAAT

                                                 *        *                  
        795 TAATTCGGAAAAATAGGAAAAAAAAACAATATTAGAATCGTGGGAAGGCCTTT-AATCTTTTTGG
        129 TAATTCGGAAAAATAGG----AAAAACAATATTAGAAGCGT--GAAAGCCTTTCAATCTTTTTGG

                         *            * *       * *               *          
        859 TGTTGAATTATATGTTTTTTATGAATTTGGTGGCCGGATATTGAGGAGAAATTTCTC-AGGTCAA
        188 TGTTGAATTATATATTTTTTATGAATATAGTGGCCGAAAATTGAGGAGAAATTTTTCGA-GTCAA

                             *     *   *      *                              
        923 TTTTTGCAAAATTTTAGTTGAAACCGTATACTAATCATCACGGTTTTGTACTAAAAACGCGTTCT
        252 TTTTTGCAAAATTTTAGCTGAAATCGTGTACTAAACATCACGGTTTTG-ACTAAAAACGCGTTCT

            *   *        
        988 AGAGCCCCGGCTC
        316 GGA-TCCCGGCTC

                            *   *     *  *    *            *                 
       1001 AGTTTTGCACGATTTTGGGCTCCAAGTCTGATTGGAATATCTATATCCATCTAACCAAATCTTAC
          1 AGTTTTGCACGATTTTTGGCGCCAAGACTCATTGAAATATCTATATCTATCTAACCAAATCTTAC

                            *                     *            *             
       1066 CCACATTGGATTTAAGCATTTGTTTTTA-AGAGCATATGAATCATGTTATGGTTCAATTA-AGAA
         66 CCACATTGGATTTAAGTATTTGTTTTTACA-AGCATATCAATCATGTT-TGATTCAATTAGA-AA

                *        *          * *                                   
       1129 TTAACTCGGAAAATTAGGAAAAACGACATTAGAAGCGTGAATAGCCTTTCAATCTTTTTGGT
        128 TTAATTCGGAAAAATAGGAAAAACAATATTAGAAGCGTGAA-AGCCTTTCAATCTTTTTGGT

       1191 ATTAAGAAGA


Statistics
Matches: 702,  Mismatches: 122, Indels: 69
        0.79            0.14        0.08

Matches are distributed among these distances:
 329    3  0.00
 330   15  0.02
 331   69  0.10
 332   96  0.14
 333  203  0.29
 334  163  0.23
 335  150  0.21
 336    3  0.00

ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36


Consensus pattern (327 bp):   
AGTTTTGCACGATTTTTGGCGCCAAGACTCATTGAAATATCTATATCTATCTAACCAAATCTTAC
CCACATTGGATTTAAGTATTTGTTTTTACAAGCATATCAATCATGTTTGATTCAATTAGAAATTA
ATTCGGAAAAATAGGAAAAACAATATTAGAAGCGTGAAAGCCTTTCAATCTTTTTGGTGTTGAAT
TATATATTTTTTATGAATATAGTGGCCGAAAATTGAGGAGAAATTTTTCGAGTCAATTTTTGCAA
AATTTTAGCTGAAATCGTGTACTAAACATCACGGTTTTGACTAAAAACGCGTTCTGGATCCCGGC
TC

Done.