Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006821.1 Corchorus olitorius cultivar O-4 contig06846, 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, 817

Length: 1362
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36


Found at i:652 original size:4 final size:4

Alignment explanation


    Indices: 645--673  Score: 58
    Period size: 4  Copynumber: 7.2  Consensus size: 4

        635 TATATATATA

                                                
        645 TATT TATT TATT TATT TATT TATT TATT T
          1 TATT TATT TATT TATT TATT TATT TATT T

        674 CTCTTATTAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   25  1.00

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (4 bp):   
TATT

Found at i:1351 original size:331 final size:330

Alignment explanation


    Indices: 682--1359  Score: 721
    Period size: 330  Copynumber: 2.1  Consensus size: 330

        672 TTCTCTTATT

                                                 *   **                      
        682 AAATCTCAGCCACATTGTATTTAAAGATTTGTTTGTATGAATTTCTAAATCTTGTTTCGATTTAA
          1 AAATCTCAGCCACATTGTATTTAAAGATTTGTTTGTACGAACATCTAAATCTTGTTTCGATTTAA

                         *                  **          *         * *        
        747 TCAGAATTAATTTTGAAATAAAATAGGAAAAATGATATTAGAAATGTGAAAAAGGCTTTCAATTT
         66 TCAGAATTAATTTCGAAATAAAATAGGAAAAACAATATTAGAAACGTGAAAAAGCCCTTCAATTT

                 * * **                        *  *                      * * 
        812 TTTTGGTGTTTAATTATATATTTTTTGAGTATTTTCGCTAGAAATCAAGGAAAAATCTTTCGGGT
        131 TTTTGATATCAAATTATATATTTTTTGAGTATTTTAGCCAGAAATCAAGGAAAAATCTTTCAGAT

               *     *           *     *                *                 *  
        877 CAATTTTTGTAAAATTTAACCGAAATCGTGTACTAACCATCACGGTTTTCGGCTAAAAACGCGTT
        196 CAAATTTTGCAAAATTTAACCAAAATCATGTACTAACCATCACGCTTTTCGGCTAAAAACGCATT

             *    *   *                                                  * * 
        942 CCGGGATCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGAATCCTTAAAATATCTATATTTATC
        261 CAGGGACCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGAATCCTTAAAATATCTATATTCAAC

                 
       1007 TAACC
        326 TAACC

                                     *         *     *     *                 
       1012 AAATCTCAGCCACATTAG-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
          1 AAATCTCAGCCACATT-GTATTTAAAGATTTGTTTGTACGAACATCTAAATCTTGTTTCGATTTA

              *    *                                     *                   
       1076 ATTAGAGTTTAA-TTCGAAA-AAAATAGGAAAAACAATATTAGAAGCGTTG-AAAA-CCCTTCAA
         65 ATCAGA-ATTAATTTCGAAATAAAATAGGAAAAACAATATTAGAAACG-TGAAAAAGCCCTTCAA

                                 *                              **      *    
       1137 TCTTTTTT-ATATCAAATTATGTATTTTTTATGAGTATTTTAGCCA-AAAGTTGAGGAAATATCT
        128 T-TTTTTTGATATCAAATTATATA-TTTTT-TGAGTATTTTAGCCAGAAA-TCAAGGAAAAATCT

                   *             *    *                                      
       1200 TTCAGATGAAATTTTGCAACATTTTAGCCAAAATCATGTACTAACCATCACGACTTTT-GGCTAA
        189 TTCAGATCAAATTTTGCAA-AATTTAACCAAAATCATGTACTAACCATCACG-CTTTTCGGCTAA

                                     *                      **   *  *  *     
       1264 AAA-GCATTACAGGG-CCACGACTCTGTTTTGCATGATTTTTGGCT-CTGAGACTCTTTGAAATA
        252 AAACGCATT-CAGGGACC-CGACTCAGTTTTGCATGATTTTTGG-TGCCAAGAATCCTTAAAATA

               *           * 
       1326 TCTTTATTCAACTAATC
        314 TCTATATTCAACTAACC

                             
       1343 AAATCTCAGCCACATTG
          1 AAATCTCAGCCACATTG

       1360 GAT


Statistics
Matches: 286,  Mismatches: 50, Indels: 24
        0.79            0.14        0.07

Matches are distributed among these distances:
 328   17  0.06
 329   41  0.14
 330  112  0.39
 331  111  0.39
 332    5  0.02

ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Consensus pattern (330 bp):   
AAATCTCAGCCACATTGTATTTAAAGATTTGTTTGTACGAACATCTAAATCTTGTTTCGATTTAA
TCAGAATTAATTTCGAAATAAAATAGGAAAAACAATATTAGAAACGTGAAAAAGCCCTTCAATTT
TTTTGATATCAAATTATATATTTTTTGAGTATTTTAGCCAGAAATCAAGGAAAAATCTTTCAGAT
CAAATTTTGCAAAATTTAACCAAAATCATGTACTAACCATCACGCTTTTCGGCTAAAAACGCATT
CAGGGACCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGAATCCTTAAAATATCTATATTCAAC
TAACC
Done.