Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008368.1 Corchorus capsularis cultivar CVL-1 contig08389, 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: 16673
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33


Found at i:3657 original size:180 final size:178

Alignment explanation


    Indices: 3297--3825  Score: 514
    Period size: 180  Copynumber: 3.0  Consensus size: 178

       3287 AACGGATTCT

                  *                           *   *         *     *  *  *    
       3297 ACAACATTTGAAGGGTCACATAATCCAAAAAGTATATAAATAAA-GGCGACACCTCCGAATATAT
          1 ACAACACTTGAAGGG-CACATAATCCAAAAAGTAAATATATAAAGGGCAACACCGCCAAACATAT

                                 *         **       *       *            *   
       3361 CATAGATATGATTATTATTTCGTCAAATGACGTGAGGTTATCCACAAATTAAGTAACAACTTCCA
         65 CATAGATATGATTATTATTTCATCAAATGACACGAGGTTAGCCACAAACTAAGTAACAACTCCCA

                     *                    **            *    
       3426 ATGCAGAAATGCATTTATTAACCCAAACATTGTATCCGTTTCAGTAATC
        130 ATGCAGAAACGCATTTATTAACCCAAACATCCTATCCGTTTCAGAAATC

                                      *          *                           
       3475 ACAACACTTGAAGGGCCACATAATCCGAAAAGTAAATGTATAAAGGGCAACACCGCCAAACATAT
          1 ACAACACTTGAAGGG-CACATAATCCAAAAAGTAAATATATAAAGGGCAACACCGCCAAACATAT

               *             *                 *          *     **  *        
       3540 CATGGATAT-ATTATTTCTTTCCATCAAATGACACAAGGTTAGCCAAAAACTGGGTGACAACTCC
         65 CATAGATATGATTA-TTATTT-CATCAAATGACACGAGGTTAGCCACAAACTAAGTAACAACTCC

                    *                  *  *       *      *      
       3604 CAATGCAGCAACGCCA-TTATTAACCCGAATATCCTATTCGTTTCGGAAATC
        128 CAATGCAGAAACG-CATTTATTAACCCAAACATCCTATCCGTTTCAGAAATC

                                     *                      *     *  *       
       3655 ACAACACTTGAAGGTG-ACATAATCTAAAAAG--AATATAT-AAGGTGTAACACTGCTAAACATA
          1 ACAACACTTGAAGG-GCACATAATCCAAAAAGTAAATATATAAAGG-GCAACACCGCCAAACATA

                         *                                      *      *  *  
       3716 TCATAGATATGATCATTATTTCATCAAATGACACGAGGTTAGCCACAAACTAGGTAACAGCTTCC
         64 TCATAGATATGATTATTATTTCATCAAATGACACGAGGTTAGCCACAAACTAAGTAACAACTCCC

             *       ** *    *  **   *         *         
       3781 AGTGCAGAAGTGAATTTTTTTGCCCGAACATCCTAACCGTTTCAG
        129 AATGCAGAAACGCATTTATTAACCCAAACATCCTATCCGTTTCAG

       3826 CTATCACCAT


Statistics
Matches: 284,  Mismatches: 59, Indels: 18
        0.79            0.16        0.05

Matches are distributed among these distances:
 175    1  0.00
 176   73  0.26
 177   35  0.12
 178   45  0.16
 179   42  0.15
 180   85  0.30
 181    3  0.01

ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26


Consensus pattern (178 bp):   
ACAACACTTGAAGGGCACATAATCCAAAAAGTAAATATATAAAGGGCAACACCGCCAAACATATC
ATAGATATGATTATTATTTCATCAAATGACACGAGGTTAGCCACAAACTAAGTAACAACTCCCAA
TGCAGAAACGCATTTATTAACCCAAACATCCTATCCGTTTCAGAAATC

Found at i:4930 original size:3 final size:3

Alignment explanation


    Indices: 4922--4965  Score: 81
    Period size: 3  Copynumber: 15.0  Consensus size: 3

       4912 TGGTAACCTC

                                                                       
       4922 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

       4966 ATGGGATTAA


Statistics
Matches: 40,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2    2  0.05
   3   38  0.95

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
TAT

Done.