Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011448.1 Corchorus olitorius cultivar O-4 contig11481, 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, 780

Length: 1300
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Found at i:1270 original size:649 final size:643

Alignment explanation


    Indices: 74--1278  Score: 1707
    Period size: 649  Copynumber: 1.9  Consensus size: 643

         64 CACCGACTCA

                             *                               *   *           
         74 GTTTGGCATGATTTTAGGTAGAAAGACTCCTTTGAATATCTATATTCATGTAATCAAATCTCAAC
          1 GTTTGGCATGATTTTAGATAGAAAGACTCCTTTGAATATCTATATTCATCTAACCAAATCTCAAC

              *                                                              
        139 CATATTGGATCTAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAATTACAAATAA
         66 CACATTGGATCTAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAATTACAAATAA

               *                                                             
        204 ATTTGGAAAAAAAGGAAAAACGATATTAGAAGCATGAAAAACCGTTCAATTTTTTTGGCGTTGAA
        131 ATTCGG---AAAA-GAAAAACGATATTAGAAGCATGAAAAACCGTTCAATTTTTTTGGCGTTGAA

                                        *                                    
        269 CTATATATTTTTTCTGAGTATTGTGACATAAAATTAAGAGAAAAAAATTTCGGCTCAATTTTTAG
        192 CTATATATTTTTTCTGAGTATTGTGACAAAAAATTAAGAGAAAAAAATTTCGGCTCAATTTTTAG

                   *           *                                             
        334 CCGAAATCGTGTACATCACGATTTTTGGCTAAAAAACGAGTTTCGAGGCCCCGGCTCAGTTTTGC
        257 CCGAAATAGTGTACATCACAATTTTTGGC-AAAAAACGAGTTTCGAGGCCCCGGCTCAGTTTTGC

                                                                     ** *    
        399 ATGATTTTTGGCAGAAAAAATCCTTGAAATATCTATATTCATCTAACCAAATATCAGTTGTTTCG
        321 ATGATTTTTGGCAGAAAAAATCCTTGAAATATCTATATTCATCTAACCAAATATCAGCCGATTCG

                                 *                           * * ***         
        464 AATTTATGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATTATATTTAAATTCGAA
        386 AATTTATGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAAATTCGAA

                *                                               *         *  
        529 AAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAACTATATAT
        451 AAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGCTGAACTATACAT

                                                                             
        594 ATTTTCTAAGTATTGTGGCAGAAAAATTGAGGAAAAACCTTCCGTGTCAGTTTTTCTAAAATTCT
        516 ATTTTCTAAGTATTGTGGCAGAAAAATT-AGGAAAAACCTTCCGTGTCAGTTTTTCTAAAATTCT

                                                                            
        659 AGCCGAAATCGTGTACTAACCATCACAGAGTTTGGCAAAAAGCTCACCTCGAGGCCCCGGCTTT
        580 AGCCGAAATCGTGTACTAACCATCACAGAGTTTGGCAAAAAGCTCACCTCGAGGCCCCGGCTTT

                *          *                                                *
        723 GTTTTGCATGATTTTTGATAGAAAGACTCC-TTGAAATATCTATATTCATCTAACCAAATCTCAG
          1 GTTTGGCATGATTTTAGATAGAAAGACTCCTTTG-AATATCTATATTCATCTAACCAAATCTCAA

                                                  *                         *
        787 CCACATTGGA-CTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATT-CAGAT
         65 CCACATTGGATC-TAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAATTACA-AA

                      *       *             *                                
        850 TAAATTCGG-GAA-AAAATCGATATTAGAAGCGTG-AAAACAC-TTCAATTTTTTTTGGCGTTGA
        128 TAAATTCGGAAAAGAAAAACGATATTAGAAGCATGAAAAAC-CGTTCAA-TTTTTTTGGCGTTGA

            *                                              **      *         
        911 GCTATATATTTTTTCTGAGTATTGTGGA-AAAAAATTAAGA-AAAAATTTTTCGGGTCAATTTTT
        191 ACTATATATTTTTTCTGAGTATTGT-GACAAAAAATTAAGAGAAAAAAATTTCGGCTCAATTTTT

                                                *                            
        974 AGCCGAAATAGTGTACTAACCATCACAATTTTTGG-GAAAAACGAGTTTCGAGGCCCCGGCTCAG
        255 AGCCGAAATAGTG---T-A-CATCACAATTTTTGGCAAAAAACGAGTTTCGAGGCCCCGGCTCAG

                  *           *    * *                                *      
       1038 TTTTGCTTGATTTTTGGCGGAAAGATTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
        315 TTTTGCATGATTTTTGGCAGAAAAAATCCTTGAAATATCTATATTCATCTAACCAAATATCAGCC

                   *                                                         
       1103 GCATT-GGATTTGA-GGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACA
        380 G-ATTCGAATTT-ATGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACA

                               *                                           * 
       1166 AATTCGGGAAAACAAAAGGGAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGGTG
        443 AATTC--G-AAA-AAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA-TTTTTTTGGCG

                         *      *                     *      
       1231 CTGAACTATACATTTTTTCTGAGTATTGTGGCA-AAAAATTATGAAAAA
        503 CTGAACTATACATATTTTCTAAGTATTGTGGCAGAAAAATTAGGAAAAA

       1279 AAGTTTTCGG


Statistics
Matches: 494,  Mismatches: 44, Indels: 37
        0.86            0.08        0.06

Matches are distributed among these distances:
 642   42  0.09
 643   70  0.14
 644    2  0.00
 645  144  0.29
 646    4  0.01
 647   15  0.03
 648   16  0.03
 649  162  0.33
 650   39  0.08

ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35


Consensus pattern (643 bp):   
GTTTGGCATGATTTTAGATAGAAAGACTCCTTTGAATATCTATATTCATCTAACCAAATCTCAAC
CACATTGGATCTAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAATTACAAATAA
ATTCGGAAAAGAAAAACGATATTAGAAGCATGAAAAACCGTTCAATTTTTTTGGCGTTGAACTAT
ATATTTTTTCTGAGTATTGTGACAAAAAATTAAGAGAAAAAAATTTCGGCTCAATTTTTAGCCGA
AATAGTGTACATCACAATTTTTGGCAAAAAACGAGTTTCGAGGCCCCGGCTCAGTTTTGCATGAT
TTTTGGCAGAAAAAATCCTTGAAATATCTATATTCATCTAACCAAATATCAGCCGATTCGAATTT
ATGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAAATTCGAAAAAAA
GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGCTGAACTATACATATTTT
CTAAGTATTGTGGCAGAAAAATTAGGAAAAACCTTCCGTGTCAGTTTTTCTAAAATTCTAGCCGA
AATCGTGTACTAACCATCACAGAGTTTGGCAAAAAGCTCACCTCGAGGCCCCGGCTTT
Done.