Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001298.1 Corchorus olitorius cultivar O-4 contig01298, 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: 1851
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38


Found at i:1529 original size:339 final size:329

Alignment explanation


    Indices: 695--1847  Score: 1247
    Period size: 321  Copynumber: 3.5  Consensus size: 329

        685 GGGCGTGACA

                             *    *                                         *
        695 ATCACGGTTTTTTGGCTGAAAATGCGTTCCGGGGCCCCGGGTCAGTTTTGCATGATTTTCGGTGG
          1 ATCACGGTTTTTT-GCTAAAAACGCGTTCCGGGGCCCCGGGTCAGTTTTGCATGATTTTCGGTGC

            *    *      *                             *                      
        760 TAAAATTCCTTGTAATATCTATATTCATCTAACCAAATCTCAACCACATTGAATTTAAGGATTTG
         65 CAAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTG-ATTTAAGGATTTG

               *                                 *  *                  *     
        825 TTTATACGAGCATCTAAATCTT-TTT---TTT-ATT-TAATTTAATTT-AGAA-AAATATGAAAA
        129 TTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTTGAGAAGAAATAGGAAAA

                   * *                 *            *   *          *         
        882 ACGATATCAAAAGCGTGAAAAGTCC-TCCAATTTTTTTCGTGTTCAATTATATATATTTTATGAG
        194 ACGATATTAGAAGCGTGAAAAG-CCTTTCAATTTTTTTCGCGTTGAATTATATATTTTTTATGAG

               *               *             *  *        *           *       
        946 TATCATGGCTAAAAATTGAGAAAAAAATATTTCAGGCCAATTTTTACAAAATTTTAGTCGAAATC
        258 TATTATGGCTAAAAATTGAAAAAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC

              *    
       1011 GTGTACC
        323 GTATACC

                           *                      *         *              **
       1018 ATCACGGTTTTTTG-GAAAAACGCGTTCCGGGGCCCCGTGTCAGTTTTACATGATTTTCGGTGGA
          1 ATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGGTCAGTTTTGCATGATTTTCGGTGCC

                       *                           *                 *       
       1082 AAAACTCCTTGTAATATCTATATTCATCTAACCAAATCTTAGCCACATTAGATTTAATGATTTGT
         66 AAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATT-GATTTAAGGATTTGT

                        * *    *                *            *               
       1147 TTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATTAATTTGAAAAGAAATAGGAAAAA
        130 TTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTTGAGAAGAAATAGGAAAAA

                   *     *   *                              *                
       1212 CGATATTTGAAGCATGAGAAGCCTTTCAATCTTTTTT-GCGTTGAATTTTATATTTTTTATGAGT
        195 CGATATTAGAAGCGTGAAAAGCCTTTCAAT-TTTTTTCGCGTTGAATTATATATTTTTTATGAGT

               *    *                                                        
       1276 ATTGTGGCCAAAAATTGTAAAAAAAAATATTTCGGGTCAATTTTTGCAAAA-TTTAGCCGAAATC
        259 ATTATGGCTAAAAATTG-AAAAAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC

            *      
       1340 ATATACC
        323 GTATACC

                                       *  *                                  
       1347 ATTCACGGGTTTTTTTTTTTGCTAAAACCGTGTTCCGGGGCCCCGGGTCAGTTTTGCATGATTTT
          1 A-TCAC-GG-----TTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGGTCAGTTTTGCATGATTTT

            ** *     *        *              *       *         *             
       1412 TTGCGCCAAGACTCCTTAAAATATATCTATATTTATCTAACTAAATCTCAGGCACATTGTATTTA
         59 CGGTGCCAAAACTCCTT-GAA-ATATCTATATTCATCTAACCAAATCTCAGCCACATTG-ATTTA

                        *     *                                              
       1477 AGGATTTGTTTTCACGAGTATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTTG-GAAGTAA
        121 AGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTTGAGAAG--A

                                              *               *  *     *     
       1541 AATAGGAAAAAACGATATTAGAAGCGTGAAAAAGACTTTCAATTTTTTTTGGCATTGAACTATAT
        184 AATAGG-AAAAACGATATTAGAAGCGTG-AAAAGCCTTTCAA-TTTTTTTCGCGTTGAATTATAT

                            * **   *        **    ***      *                 
       1606 ATTTTTTATGAGTATTTTCTCTAGAAATTG-AGGAAAAGCCTTTCGGCTCAATTTTTGCAAAATT
        246 ATTTTTTATGAGTATTATGGCTAAAAATTGAAAAAAAAATATTTCGGGTCAATTTTTGCAAAATT

                                   
       1670 TTAGCCGAAATCGTGTACTAACC
        311 TTAGCCGAAATC--GTA-T-ACC

                       **           *              * *       *        *      
       1693 ATCACGGTTTTCGGCTAAAAACGCATTCCGGGG-CCCGGCTTAGTTTTGTATGATTTTTGGTGCC
          1 ATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGGTCAGTTTTGCATGATTTTCGGTGCC

              *                                                              
       1757 AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGT
         66 AAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATT-GATTTAAGGATTTGT

                      *   *           
       1822 TTTTACGAGCGTCTGAATCTTGTTTC
        130 TTTTACGAGCATCTAAATCTTGTTTC

       1848 AATT


Statistics
Matches: 695,  Mismatches: 100, Indels: 57
        0.82            0.12        0.07

Matches are distributed among these distances:
 321  120  0.17
 322    5  0.01
 323   13  0.02
 325    3  0.00
 326    3  0.00
 327    9  0.01
 328    5  0.01
 329   87  0.13
 330   39  0.06
 331    2  0.00
 336   76  0.11
 337   52  0.07
 338   41  0.06
 339  108  0.16
 340    7  0.01
 341   45  0.06
 342   30  0.04
 343   37  0.05
 344    4  0.01
 345    5  0.01
 346    4  0.01

ACGTcount: A:0.31, C:0.15, G:0.16, T:0.37


Consensus pattern (329 bp):   
ATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGGTCAGTTTTGCATGATTTTCGGTGCC
AAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGATTTAAGGATTTGTT
TTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTTGAGAAGAAATAGGAAAAAC
GATATTAGAAGCGTGAAAAGCCTTTCAATTTTTTTCGCGTTGAATTATATATTTTTTATGAGTAT
TATGGCTAAAAATTGAAAAAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTA
TACC
Done.