Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009691.1 Corchorus olitorius cultivar O-4 contig09723, 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, 787

Length: 1312
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35


Found at i:898 original size:327 final size:324

Alignment explanation


    Indices: 140--1312  Score: 1611
    Period size: 327  Copynumber: 3.6  Consensus size: 324

        130 ATCAATTTTT

                                     *    *                    *             
        140 AGTTTTGCATGATTTTTGGCAGAAACACTCATTGAAATATCTATATTCATAAAACCAAATCTCAG
          1 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG

                  * *            *        * *    *              *            
        205 ------CCAATTT--GGATTTATTTTTACGGGTATCTGAATTTTGTTTCGATCTAATTAGAAATA
         66 AAAATTTCGATTTAAGGATTTCTTTTTACGAGCATCTTAATTTTGTTTCGATTTAATTAGAAATA

                 *                                *                     *    
        262 AATTCGGAAAAAAATTGGAAAAACAATATTCGAAGCGTTAAAAACCCTTAAATTTTTTTTTGCGT
        131 AATTCCGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAAA-TTTTTTTGGCGT

                                                                           * 
        327 TGAATCATATATTTTTTGAGAGTAGTGTGGCAAAAAAATGAGAAAAAAAGTTTTCGAGTCAATCT
        195 TGAATCATATATTTTTTGAGAGTAGTGTGGCAAAAAAATGAG-AAAAAAGTTTTCGAGTCAATTT

                               *           *                *                
        392 TTAGCCG-AAATCGTGTACAAACCATCACGGATTTTTGCTAAAAACGCATTTC-GGGACCCCGGC
        259 TTAGCCGAAAATCGTGTACGAACCATCACGGTTTTTTGCTAAAAACGCGTTTCAGGG-CCCCGGC

              
        455 TC
        323 TC

                                               *                             
        457 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGATATATCTATATTCATATAACCAAATCTCAG
          1 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG

            **     *                   *                                     
        522 CCAATTTGGATTTAAGGATTTCTTTTTTCGAGCATCTTAATTTTGTTTCGATTTAATTAGAAATA
         66 AAAATTTCGATTTAAGGATTTCTTTTTACGAGCATCTTAATTTTGTTTCGATTTAATTAGAAATA

                             *                            *               *  
        587 AATTCCGAAAAAAATTGAAAAAACAATATTCGAAGCGTGAAAAACCTTTAAATTTTATTTGGTGT
        131 AATTCCGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAAATTTT-TTTGGCGT

                                                                             
        652 TGAATCATATATTTTTTGAGAGTAGTGTGGC-AAAAAATGAGAAAATAAGTTTTCGAGTCAATTT
        195 TGAATCATATATTTTTTGAGAGTAGTGTGGCAAAAAAATGAGAAAA-AAGTTTTCGAGTCAATTT

                                                                        **   
        716 TTAGCCGAAAATCGTGTACGTTAACCATCACGGTTTTTTGCTAAAAACGCGTTTCAGGGCGTCGG
        259 TTAGCCGAAAATCGTGTACG--AACCATCACGGTTTTTTGCTAAAAACGCGTTTCAGGGCCCCGG

            *  
        781 TTC
        322 CTC

                                             *                               
        784 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTCAAATATCTATATTCATATAACCAAATCTCAG
          1 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG

                                *           *                                
        849 AAAATTTCGATTTAAGGATTGCTTTTTACGAGTATCTTAATTTTGTTTCGATTTAATTAGAAATA
         66 AAAATTTCGATTTAAGGATTTCTTTTTACGAGCATCTTAATTTTGTTTCGATTTAATTAGAAATA

                 *            *           *            *     *            *  
        914 AATTCGGAAAAAAATTGGCAAAACAATATTGGAAGCGTGAAAACCCCTTCAATTTTTTTGGCATT
        131 AATTCCGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAAATTTTTTTGGCGTT

                *             *    *                *    *          *     *  
        979 GAATTATATATTTTTTGTTGAGTTGTGTGGCAAAAAAACTAAGAATAAAGTTTTCGGGTCAACTT
        196 GAATCATATATTTTTTG-AGAGTAGTGTGGCAAAAAAA-TGAGAAAAAAGTTTTCGAGTCAATTT

                     ** *                       *        *        *          
       1044 TTAGCCGAACTTTGTGTACGAACCATCACGGTTTTTGGCTAAAAAAGCGTTTCAAGGCCCCGGCT
        259 TTAGCCGAAAATCGTGTACGAACCATCACGGTTTTTTGCTAAAAACGCGTTTCAGGGCCCCGGCT

             
       1109 C
        324 C

               *                                                             
       1110 AGTATTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCA-
          1 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG

                           *                             *                   
       1174 ACAAATTTCGATTTACGGATTTCTTTTTACGAGCATCTTAATTTTATTTCGATTTAATTA-AAAT
         66 A-AAATTTCGATTTAAGGATTTCTTTTTACGAGCATCTTAATTTTGTTTCGATTTAATTAGAAAT

                    *                *                         *        *  * 
       1238 AAATT-CGGAAAAAATTGGAAAAACGATATTCGAAGCGTGAAAAACCCTT-CATTTTTTGGGGGG
        130 AAATTCCGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAAATTTTTT-TGGCG

              *         
       1301 TTTAATCATATA
        194 TTGAATCATATA


Statistics
Matches: 760,  Mismatches: 77, Indels: 31
        0.88            0.09        0.04

Matches are distributed among these distances:
 317   61  0.08
 323   15  0.02
 324   88  0.12
 325  150  0.20
 326  179  0.24
 327  219  0.29
 328   42  0.06
 329    6  0.01

ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35


Consensus pattern (324 bp):   
AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAG
AAAATTTCGATTTAAGGATTTCTTTTTACGAGCATCTTAATTTTGTTTCGATTTAATTAGAAATA
AATTCCGAAAAAAATTGGAAAAACAATATTCGAAGCGTGAAAAACCCTTAAATTTTTTTGGCGTT
GAATCATATATTTTTTGAGAGTAGTGTGGCAAAAAAATGAGAAAAAAGTTTTCGAGTCAATTTTT
AGCCGAAAATCGTGTACGAACCATCACGGTTTTTTGCTAAAAACGCGTTTCAGGGCCCCGGCTC

Done.