Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003808.1 Corchorus capsularis cultivar CVL-1 contig03816, 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, 616

Length: 1028
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35


Found at i:824 original size:192 final size:196

Alignment explanation


    Indices: 362--1028  Score: 678
    Period size: 192  Copynumber: 3.4  Consensus size: 196

        352 TAATTTTTCT

                     *              *    *          *                *       
        362 TATAAGATTGTTATACAATACACTTTTCAGTGTAAATTTTAGACTCCATAAGCGGGTTAAGAAGT
          1 TATAAGATTATTATACAATACAC-ATTCAATGTAAATTTTGGACTCCATAAGCGGGTAAAGAAGT

                                   *   *     *                               
        427 TGACACATACCCCA-TTCATAATCAATTAAATAGTTAATATTAATACATATTTCTTCTTAAGGGG
         65 TGACACATACCCCATTTCATAATAAATAAAATATTTAATATTAATACATA-TTC--CTTAAGGGG

                                        *     *   *    *    *      *       * 
        491 ACACATGTCAACCCTTAAAC-CCTGCACATGCAGACTGTTAAATTCGAGTGACAGTGTATAGTTT
        127 ACACATGTCAACCCTTAAACTCCTGCACGTGCAGTCTGCTAAACTCGACTGAC-GAG-AT-GTAT

                       
        555 AATTTTTCTTA
        189 AA---TTCTTA

                               *       *             *      *                
        566 TATAAGATTATTATACAATCCAC-TGTGAATGTAAATTTTGAACTCCACAAGCGGGTTAAA-AAG
          1 TATAAGATTATTATACAATACACAT-TCAATGTAAATTTTGGACTCCATAAGCGGG-TAAAGAAG

                        *               *        *                    *      
        629 TTGACACATACCTCATTTCATAATAAATGAAATATTTCATATTAATACATATTCCTTATGGGGAC
         64 TTGACACATACCCCATTTCATAATAAATAAAATATTTAATATTAATACATATTCCTTAAGGGGAC

                                  *     *    *            *                * 
        694 ACATGTCAACCCTTAAACTCC-ACACGTACAGTGTGCTAAACTCGATTGACG-G-TGTATAATAC
        129 ACATGTCAACCCTTAAACTCCTGCACGTGCAGTCTGCTAAACTCGACTGACGAGATGTATAATTC

               
        756 TT-
        194 TTA

                *                       *               *                    
        758 TATAGGATTATTATACAATACACATTCAGTGTAAATTTTGGACTTCATAAGCGGGTAAAGAAGTT
          1 TATAAGATTATTATACAATACACATTCAATGTAAATTTTGGACTCCATAAGCGGGTAAAGAAGTT

                                  *               *              *    *      
        823 GACACATACCCCATTTCATAATTAATAAAATATTTAATTTTAATACATATTCCCTAAGAGGACAC
         66 GACACATACCCCATTTCATAATAAATAAAATATTTAATATTAATACATATTCCTTAAGGGGACAC

                                            *          *                     
        888 ATGAT-AACCCTTAAA-TCCTGCACGTGCAGTTTGCTAAACTCCACTGACGACGCATTGTATAAT
        131 ATG-TCAACCCTTAAACTCCTGCACGTGCAGTCTGCTAAACTCGACTGACGA-G-A-TGTATAAT

             *  *
        951 TGTTC
        192 TCTTA

                 *                       *                                   
        956 TAATAGGACTTATTATACAATA-A-ATTGTAATGTAAA-TTTGGACTCCATAAGCGGG-ATAAGA
          1 T-ATAAGA-TTATTATACAATACACATT-CAATGTAAATTTTGGACTCCATAAGCGGGTA-AAGA

             *          
       1017 AATTGACACATA
         62 AGTTGACACATA


Statistics
Matches: 395,  Mismatches: 50, Indels: 42
        0.81            0.10        0.09

Matches are distributed among these distances:
 191    7  0.02
 192  146  0.37
 193    6  0.02
 194    1  0.00
 196    5  0.01
 197   12  0.03
 198   37  0.09
 199   15  0.04
 200   14  0.04
 201   49  0.12
 202    3  0.01
 203   45  0.11
 204   55  0.14

ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33


Consensus pattern (196 bp):   
TATAAGATTATTATACAATACACATTCAATGTAAATTTTGGACTCCATAAGCGGGTAAAGAAGTT
GACACATACCCCATTTCATAATAAATAAAATATTTAATATTAATACATATTCCTTAAGGGGACAC
ATGTCAACCCTTAAACTCCTGCACGTGCAGTCTGCTAAACTCGACTGACGAGATGTATAATTCTT
A
Done.