Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006889.1 Corchorus olitorius cultivar O-4 contig06914, 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, 651

Length: 1085
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32


Found at i:812 original size:331 final size:329

Alignment explanation


    Indices: 1--1085  Score: 1352
    Period size: 334  Copynumber: 3.3  Consensus size: 329

                                           *                                 
          1 CTTTTCACGCTTCTAATATCGTATTTCCTACCTTTTCCAAA-TAATTTTTTGATTAAATCGAAAC
          1 CTTTTCACGCTTCTAATATCGTATTTCCTACTTTTTCCAAATTAA-TTTTTGATTAAATCGAAAC

                       *                               *   *             *   
         65 AAGATTCAGATACTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
         65 AAGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGACTGTGATTTGATTAGATAAAT

                                                        *        *           
        130 ATA-ATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCG
        130 ATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCC-GGGACCCGGAACGCG

                     *                           *  *                        
        194 TTTTTAGCAGAAAACTGTGA----ACA-TACACGATTCCGATTCAAATTTTGCAAAACATGACCC
        194 TTTTTAGCAAAAAACTGTGATGGTA-AGTACACGATTTCGGTTCAAATTTTGCAAAAC-TGACCC

                           *                                                 
        254 GAAAAAAATTTTTCGTCAATTTTTGTCCACAATACTCATAAAAAATATATAATTCAACACCAAAA
        257 G-AAAAAATTTTTCGAC-ATTTTTG-CCACAATACTCATAAAAAATATATAATTCAACACCAAAA

                       
        319 ACATTGAAGGG
        319 ACATTGAAGGG

            *                             *       *                    *   * 
        330 TTTTTCACGCTTC-AA-A---TA--T--T-GTTTTTCCTAATTAATTTTT-ATTAAATCAAAATA
          1 CTTTTCACGCTTCTAATATCGTATTTCCTACTTTTTCCAAATTAATTTTTGATTAAATCGAAACA

                                                *    **    *      *          
        384 AGATTCAGATGCTCGTAAAAACATATCCATT-AATCTAATGCAACTAAT-ATTTAATTAGATAAA
         66 AGATTCAGATGCTCGTAAAAACATATCC-TTAAATCCAATGTGACT-GTGATTTGATTAGATAAA

                                    *  *                          *       *  
        447 TATAGATATTTCAAGGAGTCTCGGGGCTAAAAATCATGCAAAACTAAGCCGGGAACCGGAACACG
        129 TATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGACCCGGAACGCG

                                            *           *                  * 
        512 TTTTTAGCAAAAAACTGTGATGGTAAGTACACAATTTCGGTTCAGATTTTGCAAAAACTGACCTG
        194 TTTTTAGCAAAAAACTGTGATGGTAAGTACACGATTTCGGTTCAAATTTTGC-AAAACTGACCCG

                                           *              *      *           
        577 AAAAAATTTTTCGACACTTTTTGCCACAATAATCATAAAAAATATAAAATTCATCACCAAAAACA
        258 AAAAAATTTTTCGACA-TTTTTGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAACA

                    
        642 TTGAAGGG
        322 TTGAAGGG

                        * *               *            *                     
        650 CTTTTCACGCTTTTTATATCGTATTTCCTATTTTTTCCAAATTCATTTTTGATTAAATCGAAACA
          1 CTTTTCACGCTTCTAATATCGTATTTCCTACTTTTTCCAAATTAATTTTTGATTAAATCGAAACA

                         *           *                                *      
        715 AGATTCAGATGCTTGTAAAAACATAGCCTTAAATCCAATGTGACTGTGATTTGATTAGGTAAATA
         66 AGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGACTGTGATTTGATTAGATAAATA

                          *     **              **              *       *    
        780 TAGATATTTCAAGGTGTCTCATCGCCAAAAATCATGGTAAAC-AGAGCCGGGGCCCGGAATGCGT
        131 TAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTA-AGCCGGGACCCGGAACGCG-

                           *    *     *      *        * *                    
        844 TTTTTTAAGCAAAAATC-GTTATGGTTAGTACATGATTTCGGCTAAAATTTTGCTAAAACTGACC
        194 -TTTTT-AGCAAAAAACTGTGATGGTAAGTACACGATTTCGGTTCAAATTTTGC-AAAACTGACC

                  *                                                          
        908 CGAAAATATTTTTCATGA-ATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACACCAAA
        256 CGAAAAAATTTTTC--GACATTTTT-GCCACAATACTCATAAAAAATATATAATTCAACACCAAA

                        
        972 AACATTGAAGGG
        318 AACATTGAAGGG

                                                                             
        984 CTTTTCACGCTTCTAATATCGTATTTCCTACTTTTTCCAAATTAATTTTTGATTAAATCGAAACA
          1 CTTTTCACGCTTCTAATATCGTATTTCCTACTTTTTCCAAATTAATTTTTGATTAAATCGAAACA

                      **                         
       1049 AGATTCAGATATTCGTAAAAACATATCCTTAAATCCA
         66 AGATTCAGATGCTCGTAAAAACATATCCTTAAATCCA


Statistics
Matches: 645,  Mismatches: 80, Indels: 57
        0.82            0.10        0.07

Matches are distributed among these distances:
 318   97  0.15
 319   57  0.09
 320   63  0.10
 321   22  0.03
 322   30  0.05
 323    5  0.01
 324    2  0.00
 325    2  0.00
 327    2  0.00
 328    2  0.00
 329   13  0.02
 330   21  0.03
 331  114  0.18
 333   61  0.09
 334  152  0.24
 335    2  0.00

ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32


Consensus pattern (329 bp):   
CTTTTCACGCTTCTAATATCGTATTTCCTACTTTTTCCAAATTAATTTTTGATTAAATCGAAACA
AGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGACTGTGATTTGATTAGATAAATA
TAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGACCCGGAACGCGTT
TTTAGCAAAAAACTGTGATGGTAAGTACACGATTTCGGTTCAAATTTTGCAAAACTGACCCGAAA
AAATTTTTCGACATTTTTGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAACATTGA
AGGG

Done.