Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001178.1 Corchorus olitorius cultivar O-4 contig01178, 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: 2072
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.35


Found at i:895 original size:437 final size:436

Alignment explanation


    Indices: 22--1019  Score: 1244
    Period size: 437  Copynumber: 2.3  Consensus size: 436

         12 AGCCTTAGTC

                       *   *  *      *           *                     *     
         22 TTTTTAGAATTGAAATATGAAAATTAGCTTTTGAGTCTTTCATGAAAGTTGTAGATCATAAAATT
          1 TTTTTAGAATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATT

                              *   * *      *      *                          
         87 ACCTTTTAATAGACACATGAATTACCTTAATTGGACAACTAGAACAAAGAATAAAAAAGAAATGA
         66 ACCTTTTAATAGACACATTAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAA-AAA-GA

                                *                                            
        152 AGCGTTAAATCGAGTAAAATTGAATTTGTAAAGGACTAAGTAGCATAACATAGAAAAGTATGAGG
        129 AGCGTTAAATCGAGTAAAATAGAATTTGTAAAGGACTAAGTAGCATAACATAGAAAAGTATGAGG

              *         *    *    *         *           *                    
        217 GTCATTTGATAACTAATTCAAATAAGAAAATATTTCTTAATGGATATCTTGAAACATAAAAATTC
        194 GTAATTTGATAAATAATCCAAAAAAGAAAATACTTCTTAATGGAGATCTTGAAACATAAAAATTC

             *                                             *          *     *
        282 CCTTTTGAACCCTTCATGAAACTCATAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTCGTAG
        259 CATTTTGAACCCTTCATGAAACTCATAGATCAAATTAACTTTCGGGTCCTTCATGAAAATCGTAA

                    *                                  *            *        
        347 ATCATACAGTAACCTTTTAACCGACACTTGAATAACTTTAATCGGACATGTGGATCGAAAATTAT
        324 ATCATACAATAACCTTTTAACCGACACTTGAATAACTTTAATCAGACATGTGGATCAAAAATTAT

             * *                    *    *  *               
        412 ATGGTATTAAATAGACCAACAATCGAAACGACCAAATTTAGGAAGCAT
        389 ACGATATTAAATAGACCAACAATCAAAACCACAAAATTTAGGAAGCAT

                 *                           *                               
        460 TTTTTTGAATTAAAACATAAAAATTTGCTTTTGGGTCCTTCATGAAAGTTGTAGATCATGAAATT
          1 TTTTTAGAATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATT

                                                                       *    *
        525 ACCTTTTAATAGACACATTAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAAACA-AAT
         66 ACCTTTTAATAGACACATTAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAAAAAGAAG

                               *                 *       *                   
        589 C-TTAAAT-GTTAGATTAAGATAGAATTTGTAAAGGATTAAGTAGTATAA-AGTAGAAAA-TATG
        131 CGTTAAATCG--AG--TAAAATAGAATTTGTAAAGGACTAAGTAGCATAACA-TAGAAAAGTATG

                                              *   *              *  *        
        650 AGGGTAATTTGATAAATAATCCAAAAAAGAAAATGCTTGTTAATGGAGATCTTTAAGCATAAAAA
        191 AGGGTAATTTGATAAATAATCCAAAAAAGAAAATACTTCTTAATGGAGATCTTGAAACATAAAAA

                                       *                                     
        715 TTCCATTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAGA-TTTCGGGTCCTTCATGAAAAT
        256 TTCCATTTTGAACCCTTCATGAAACTCATAGATCAAA-TTA-ACTTTCGGGTCCTTCATGAAAAT

                      *                       *                              
        779 CGTAAATCATGCAATAACCTTTTAACCGACACTTTAATAA-TTTCAATCAGACATGTGGA-CAAA
        319 CGTAAATCATACAATAACCTTTTAACCGACACTTGAATAACTTT-AATCAGACATGTGGATCAAA

                               *   ***                    *        
        842 AAGTTATACGATATTAAATTGACTGGCAATCAAAACCACAAAATTTCGGAAGCAT
        383 AA-TTATACGATATTAAATAGACCAACAATCAAAACCACAAAATTTAGGAAGCAT

             *        **      *                  *          *                
        897 TGTTTAGAATCCAAACATTAAAA-TTGACTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAAT
          1 TTTTTAGAATTAAAACATAAAAATTTG-CTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAAT

              *         * *           **                      *    *     
        961 TATCTTTTAATATAAAC-TTGAATCAGTTTAATCGGACAAATAGAA-AAAAAATACAAAAA
         65 TACCTTTTAATAGACACATT-AATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAAA

       1020 TAAAAGCCAA


Statistics
Matches: 485,  Mismatches: 64, Indels: 24
        0.85            0.11        0.04

Matches are distributed among these distances:
 433    1  0.00
 434    6  0.01
 435    5  0.01
 436  120  0.25
 437  242  0.50
 438  111  0.23

ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31


Consensus pattern (436 bp):   
TTTTTAGAATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATT
ACCTTTTAATAGACACATTAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAAAAAGAAG
CGTTAAATCGAGTAAAATAGAATTTGTAAAGGACTAAGTAGCATAACATAGAAAAGTATGAGGGT
AATTTGATAAATAATCCAAAAAAGAAAATACTTCTTAATGGAGATCTTGAAACATAAAAATTCCA
TTTTGAACCCTTCATGAAACTCATAGATCAAATTAACTTTCGGGTCCTTCATGAAAATCGTAAAT
CATACAATAACCTTTTAACCGACACTTGAATAACTTTAATCAGACATGTGGATCAAAAATTATAC
GATATTAAATAGACCAACAATCAAAACCACAAAATTTAGGAAGCAT

Found at i:1762 original size:77 final size:77

Alignment explanation


    Indices: 1675--1831  Score: 253
    Period size: 78  Copynumber: 2.0  Consensus size: 77

       1665 ATATTTATAG

                                                                        * *  
       1675 TTTTACTCAACTAAAAACTCTA-TTTTATTTAACTAAATCTAATATCTTTATAACTATTTTATTT
          1 TTTTACTCAACTAAAAACTCTATTTTTATTTAACTAAATCTAATATCTTTATAACTATTTCAGTT

                    *    
       1739 TACCATTTTACTA
         66 TACCA-TTAACTA

                                             *     *                         
       1752 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATTTAATATCTTTATAACTATTTCAGTT
          1 TTTTACTCAACTAAAAACTCTATTTTTATTTAACTAAATCTAATATCTTTATAACTATTTCAGTT

                        
       1817 TACCATTAACTA
         66 TACCATTAACTA

               
       1829 TTT
          1 TTT

       1832 CAACTAGAAA


Statistics
Matches: 74,  Mismatches: 5, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  77   31  0.42
  78   43  0.58

ACGTcount: A:0.35, C:0.15, G:0.01, T:0.50


Consensus pattern (77 bp):   
TTTTACTCAACTAAAAACTCTATTTTTATTTAACTAAATCTAATATCTTTATAACTATTTCAGTT
TACCATTAACTA

Done.