Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017540.1 Corchorus olitorius cultivar O-4 contig17573, 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, 832

Length: 1387
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34


Found at i:877 original size:332 final size:333

Alignment explanation


    Indices: 12--1380  Score: 2007
    Period size: 332  Copynumber: 4.1  Consensus size: 333

          2 TTATATATAT

                                                                             
         12 TTTATGAGTATTGTGGCCAAAAAATTGAGGAGAAATG-TTTCAGGTCAATTTTTGCAAAATTTTA
          1 TTTATGAGTATTGTGGCC-AAAAATTGAGGAGAAATGTTTTCAGGTCAATTTTTGCAAAATTTTA

                    *     *       *  *  *            *                       
         76 GCCGAAATAATGTATTAACCATAACAGTGTTTGACTAAAAATGCGTTCCGGGGCCCGGCTCAGTT
         65 GCCGAAATCATGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGGGCCCGGCTCAGTT

                                                              *              
        141 TTGCATGATTTTTGGCGTCAAGACTCATTGAAATATCTATATTCATCTAGTGAAAGCTCAGACAA
        130 TTGCATGATTTTTGGCGTCAAGACTCATTGAAATATCTATATTCATCTAGCGAAAGCTCAGACAA

                    *                                                        
        206 ATTGGATTGAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATTTGAAATTAATT
        195 ATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATTTGAAATTAATT

                                                                             
        271 CA-AAAAAGAAAAGAAAAACGATATTAGATGCGTGAGAAGCCCTTCAATC-TTTTTGGCGTTGAG
        260 CAGAAAAA-AAAAGAAAAACGATATTAGATGCGTGAGAAGCCCTTCAATCATTTTTGGCGTTGAG

               *       
        334 TTATATATGT-
        324 TTAAATAT-TC

                                                                   *         
        344 TTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATG-TTTCAGGTCAATTTTTGCCAAATTTTAG
          1 TTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTTCAGGTCAATTTTTGCAAAATTTTAG

                                                 *                           
        408 CCGAAATCATGTACT--CCATCACGGTTTTTGACTAAGAACGCGTTCCGGGGCCCCGGCTCAGTT
         66 CCGAAATCATGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGGG-CCCGGCTCAGTT

                            * *      *                            *          
        471 TTGCATGATTTTTGGCTTTAAGACTTATTGAAATATCTATATTCATCTAGCGAATGCTCAGACAA
        130 TTGCATGATTTTTGGCGTCAAGACTCATTGAAATATCTATATTCATCTAGCGAAAGCTCAGACAA

                               *                                *          * 
        536 ATTGGATTTAAGGATTTGTATTTACGAGCATCTCAATCCGGTTTCGATTTAAATTGAAATTAAGT
        195 ATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATTTGAAATTAATT

                     *                     *                                 
        601 -AGAAAAAAGAAGAAAAACGATATTAGATGCATGAGAAGCCCTTCAATCATTTTTGG-GTTGAG-
        260 CAGAAAAAAAAAGAAAAACGATATTAGATGCGTGAGAAGCCCTTCAATCATTTTTGGCGTTGAGT

                      
        663 TAAAGTATTC
        325 TAAA-TATTC

                 *                                    *                     *
        673 TTTATAAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTTCAAGTCAATTTTTGCAAAATTTTAA
          1 TTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTTCAGGTCAATTTTTGCAAAATTTTAG

                                   *               *   *   *                 
        738 CCGAAATCATGTACTAACCATCATGGTTTTTGACTAAAAGCGCATTCTGGGGCCCCGGCTCAGTT
         66 CCGAAATCATGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGGG-CCCGGCTCAGTT

                                                       *          *          
        803 TTGCATGATTTTTGGCGTCAAGACTCATTGAAATATCTATATTTATCTAGCGAATGCTCAGACAA
        130 TTGCATGATTTTTGGCGTCAAGACTCATTGAAATATCTATATTCATCTAGCGAAAGCTCAGACAA

                       *     *                      **         **    *       
        868 ATTGGATTTAAAGATTTCTTTTTACGAG-ATTCTCAATCCATTTTCGATTTCTTTTGGAATTAAT
        195 ATTGGATTTAAGGATTTGTTTTTACGAGCA-TCTCAATCCGGTTTCGATTTAATTTGAAATTAAT

                 *                        *          *                 *     
        932 TCAGGGAAAAAAAAGAAAAACGATATTAGAAGCGTGAGAAGTCCTTCAAT-ATTTTTGGAGTTGA
        259 TCA-GAAAAAAAAAGAAAAACGATATTAGATGCGTGAGAAGCCCTTCAATCATTTTTGGCGTTGA

                *     *
        996 GTTATATATTT
        323 GTTAAATATTC

                   *          *                *        *      *             
       1007 TTTATGAATATTGTGGCCTAAAATTGAGG-GAAA-ATTTTCAGGACAATTTCTGCAAAATTTTAG
          1 TTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTTCAGGTCAATTTTTGCAAAATTTTAG

                *      *                                     *               
       1070 CCGACATCATGGACTAACCATCACGGTTTTTGACTAAAAACG-GTTTCCAGGGCCCGGCTCAGTT
         66 CCGAAATCATGTACTAACCATCACGGTTTTTGACTAAAAACGCG-TTCCGGGGCCCGGCTCAGTT

                                                                          *  
       1134 TTGCATGATTTTTGGCGTCAAGACTCATTGAAATATCTATATTCATCTAGCGAAAGCTCAGAGAA
        130 TTGCATGATTTTTGGCGTCAAGACTCATTGAAATATCTATATTCATCTAGCGAAAGCTCAGACAA

                *                                    *                       
       1199 ATTGTATTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGATTCGATTTAATTTGAAATTAATT
        195 ATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATTTGAAATTAATT

                                     *        *                              
       1264 C-GAAAAAAAAAGAAAAACGATATTTGATGCGTGTGAAGCCCTTCAATCA-TTTTGGCGTTGAGT
        260 CAGAAAAAAAAAGAAAAACGATATTAGATGCGTGAGAAGCCCTTCAATCATTTTTGGCGTTGAGT

               *     
       1327 TAAGTATTC
        325 TAAATATTC

                        *                           *    
       1336 TTTATGAGTATTTTGGCCAAAAATTGAGGACGAAATGTTTCCAGG
          1 TTTATGAGTATTGTGGCCAAAAATTGAGGA-GAAATGTTTTCAGG

       1381 GACAATT


Statistics
Matches: 927,  Mismatches: 91, Indels: 38
        0.88            0.09        0.04

Matches are distributed among these distances:
 328    4  0.00
 329  200  0.22
 330  186  0.20
 331  192  0.21
 332  252  0.27
 333   13  0.01
 334   77  0.08
 335    3  0.00

ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34


Consensus pattern (333 bp):   
TTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTTCAGGTCAATTTTTGCAAAATTTTAG
CCGAAATCATGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGGGCCCGGCTCAGTTT
TGCATGATTTTTGGCGTCAAGACTCATTGAAATATCTATATTCATCTAGCGAAAGCTCAGACAAA
TTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCCGGTTTCGATTTAATTTGAAATTAATTC
AGAAAAAAAAAGAAAAACGATATTAGATGCGTGAGAAGCCCTTCAATCATTTTTGGCGTTGAGTT
AAATATTC

Done.