Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015081.1 Corchorus olitorius cultivar O-4 contig15114, 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: 11633
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33


Found at i:378 original size:59 final size:59

Alignment explanation


    Indices: 283--400  Score: 191
    Period size: 59  Copynumber: 2.0  Consensus size: 59

        273 AGTCTTAAGT

                              *           *                            
        283 CAGTTACCGCCCATCCAAGACTTAACCCCTGGAGTGGTGCAAGCTACGAACACTCCACA
          1 CAGTTACCGCCCATCCAAAACTTAACCCCTAGAGTGGTGCAAGCTACGAACACTCCACA

                     *                     *              *            
        342 CAGTTACCGGCCATCCAAAACTTAACCCCTATAGTGGTGCAAGCTATGAACACTCCACA
          1 CAGTTACCGCCCATCCAAAACTTAACCCCTAGAGTGGTGCAAGCTACGAACACTCCACA

        401 ATTGCACGCC


Statistics
Matches: 54,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  59   54  1.00

ACGTcount: A:0.31, C:0.34, G:0.17, T:0.19


Consensus pattern (59 bp):   
CAGTTACCGCCCATCCAAAACTTAACCCCTAGAGTGGTGCAAGCTACGAACACTCCACA

Found at i:2227 original size:143 final size:139

Alignment explanation


    Indices: 1906--2229  Score: 351
    Period size: 138  Copynumber: 2.3  Consensus size: 139

       1896 TTATTTCCGT

                 *                                        *            *     
       1906 GGAAATCTTCCTCCATGCTTAAACAATTTGACTTCTCTTAAA-CTCCTAGACCTCTCCATGAATC
          1 GGAAACCTTCCTCCATGCTTAAACAATTTGACTTCTCTTAAAGCTCATAGACCTCTCCAGGAATC

                                 *      *             *                      
       1970 AATTCAATGGAGACCTCTCCTGCGATTTGTCTAGCTCTCTTCGAGAATTGGATCTTAGCAGTAAC
         66 AATTCAATGGAGACCTCTCCTCCGATTTATCTAGCTCTCTTCAAGAATTGGATCTTAGCAGTAAC

                   * 
       2035 AGTTTCGGA
        131 AGTTTCGAA

                                                                             
       2044 GGAAACCTTCCTCCATGCTTAAACAATTTGACTAT-TCTTAAAGCT-ATAGACCTCTCTC-GGAA
          1 GGAAACCTTCCTCCATGCTTAAACAATTTGACT-TCTCTTAAAGCTCATAGACCTCTC-CAGGAA

                                  *                                **    *   
       2106 TCAATTCAATGG-GACCATCTCTTCCGATTTAT-TATTGCCAAGTTCTCTTCAAGTGTTGGTTCT
         64 TCAATTCAATGGAGACC-TCTCCTCCGATTTATCTA--G-C----TCTCTTCAAGAATTGGATCT

                       *         
       2169 TAGCTA-TAA-TGCTTTCGAA
        121 TAGC-AGTAACAG-TTTCGAA

                      * *                              
       2188 GGAAA-CTTCGTTCATGCTTAAACAATTTGACTTCTCTTAAAG
          1 GGAAACCTTCCTCCATGCTTAAACAATTTGACTTCTCTTAAAG

       2230 TTTTGTCTGT


Statistics
Matches: 158,  Mismatches: 14, Indels: 23
        0.81            0.07        0.12

Matches are distributed among these distances:
 137    6  0.04
 138   76  0.48
 139    5  0.03
 140    1  0.01
 142    1  0.01
 143   34  0.22
 144   34  0.22
 145    1  0.01

ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35


Consensus pattern (139 bp):   
GGAAACCTTCCTCCATGCTTAAACAATTTGACTTCTCTTAAAGCTCATAGACCTCTCCAGGAATC
AATTCAATGGAGACCTCTCCTCCGATTTATCTAGCTCTCTTCAAGAATTGGATCTTAGCAGTAAC
AGTTTCGAA

Found at i:2302 original size:18 final size:19

Alignment explanation


    Indices: 2279--2318  Score: 55
    Period size: 21  Copynumber: 2.1  Consensus size: 19

       2269 TATATTACCC

                               
       2279 TCATTT-AAAACTCCACTA
          1 TCATTTAAAAACTCCACTA

                                 
       2297 TCATTTCAAAAAACTCCACTA
          1 TCATTT--AAAAACTCCACTA

             
       2318 T
          1 T

       2319 AGTCTTAAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    6  0.32
  21   13  0.68

ACGTcount: A:0.40, C:0.28, G:0.00, T:0.33


Consensus pattern (19 bp):   
TCATTTAAAAACTCCACTA
Done.