Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009721.1 Corchorus olitorius cultivar O-4 contig09753, 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: 3738
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34


Found at i:2101 original size:349 final size:352

Alignment explanation


    Indices: 1438--2140  Score: 952
    Period size: 349  Copynumber: 2.0  Consensus size: 352

       1428 CAAAACATTA

                          *                 *             *              *   
       1438 TCCAAGTCGGTTTAGGAGAAGATCAATTTTGTTCAGAAATTTCAAGGGCAAAATCATCCACTGAA
          1 TCCAAGTCGGTTTAAGAGAAGATCAATTTTGTCCAGAAATTTCAAGAGCAAAATCATCCACCGAA

             *           *                                                  *
       1503 AGTGCAGAATTAGGTATCGAGGTAGGCATAATAAAAGTTGTAGATCTTGGAATACTATTTCCAAT
         66 ACTGCAGAATTAGATATCGAGGT--G-ATAATAAAAGTTGTAGATCTTGGAATACTATTTCCAAC

                                             *    *                          
       1568 GGTACCTCATTTGCATTTTTCTGAGATATGAATTAAAAGTTACGAATTTTCTTCCAAAACTACTC
        128 GGTACCTCATTTGCATTTTTCTGAGATATGAATCAAAAATTACGAATTTTCTTCCAAAACTACTC

                      *                   **    *                *           
       1633 TTGTGAAGGTCCTCATTTGAATAGGATTTAGTAATGTTGCATCAAGGCTGAATTATTACTGCATC
        193 TTGTGAAGGTACTCATTTGAATAGGATTTAACAATGCTGCATCAAGGCTGAATCATTACTGCATC

                               **                 *                          
       1698 ACAATTATTGATTGGACTTGGACTCCTTCTTTGGCCTTCCATATTAACGAATTGGGT-CTAAGAA
        258 ACAATTATTGATTGGACTTAAACTCCTTCTTTGGCCTTACATATTAACGAATTGGGTGC-AAGAA

               *        *      *           
       1762 TATTACATTTAGGCTTCAAGACATCTGGCTC
        322 TATCACATTTAGACTTCAAAACATCTGGCTC

                                                                   *       * 
       1793 TCCAAGTCGGTTTAAGAGAAGATCAATTTTGTCCAGAAATTTCAAGAGCAAAATCGTCCACCGGA
          1 TCCAAGTCGGTTTAAGAGAAGATCAATTTTGTCCAGAAATTTCAAGAGCAAAATCATCCACCGAA

                *          *               *                          *      
       1858 ACTGTAGAATTAGATCTCGAGGT-AT-ATAATAGTTGTAGATCTTGGAAT-CTACTTTTCAACGG
         66 ACTGCAGAATTAGATATCGAGGTGATAATAAAAGTTGTAGATCTTGGAATACTA-TTTCCAACGG

                                   * *               *                  *    
       1920 TACCTCATTTGCATTTTTCTGAGCTCT-ACATCAAAAATTATGAATTTTCTTCCAAAACTGCTCT
        130 TACCTCATTTGCATTTTTCTGAGATATGA-ATCAAAAATTACGAATTTTCTTCCAAAACTACTCT

                         *                             *                     
       1984 TGTGAA-GTACTCCTTTGAATAGGATTTAACAATGCTGCATCAGGGCTGAATCATTACTGCATCA
        194 TGTGAAGGTACTCATTTGAATAGGATTTAACAATGCTGCATCAAGGCTGAATCATTACTGCATCA

            *                       **        *            *                 
       2048 TAATTACTT-ATTGGACTTAAACTTTTTCTTTGGGCTTACATATTAATGAATTGGGTGCAAGAAT
        259 CAATTA-TTGATTGGACTTAAACTCCTTCTTTGGCCTTACATATTAACGAATTGGGTGCAAGAAT

                *                        
       2112 ATCAGATTTAGACTTCAAAACATCTGGCT
        323 ATCACATTTAGACTTCAAAACATCTGGCT

       2141 TGGCAATTTG


Statistics
Matches: 306,  Mismatches: 38, Indels: 14
        0.85            0.11        0.04

Matches are distributed among these distances:
 349  131  0.43
 350   95  0.31
 351    2  0.01
 355   78  0.25

ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Consensus pattern (352 bp):   
TCCAAGTCGGTTTAAGAGAAGATCAATTTTGTCCAGAAATTTCAAGAGCAAAATCATCCACCGAA
ACTGCAGAATTAGATATCGAGGTGATAATAAAAGTTGTAGATCTTGGAATACTATTTCCAACGGT
ACCTCATTTGCATTTTTCTGAGATATGAATCAAAAATTACGAATTTTCTTCCAAAACTACTCTTG
TGAAGGTACTCATTTGAATAGGATTTAACAATGCTGCATCAAGGCTGAATCATTACTGCATCACA
ATTATTGATTGGACTTAAACTCCTTCTTTGGCCTTACATATTAACGAATTGGGTGCAAGAATATC
ACATTTAGACTTCAAAACATCTGGCTC

Found at i:3190 original size:11 final size:11

Alignment explanation


    Indices: 3174--3207  Score: 52
    Period size: 11  Copynumber: 3.1  Consensus size: 11

       3164 GAGGATTAAG

                       
       3174 AACAATTCCTA
          1 AACAATTCCTA

                        
       3185 AACAATGT-CTA
          1 AACAAT-TCCTA

                       
       3196 AACAATTCCTA
          1 AACAATTCCTA

             
       3207 A
          1 A

       3208 TATTGGAGTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  10    1  0.05
  11   19  0.90
  12    1  0.05

ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26


Consensus pattern (11 bp):   
AACAATTCCTA
Done.