Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000911.1 Corchorus capsularis cultivar CVL-1 contig00911, 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, 733

Length: 1222
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27


Found at i:413 original size:168 final size:167

Alignment explanation


    Indices: 110--420  Score: 417
    Period size: 168  Copynumber: 1.9  Consensus size: 167

        100 TGACGGCATC

                               *           *                  *    *         
        110 AAGTACAATCAAGCTGGTATCAAATATCAACTTTTCTAGAACCTTCCGCTGCAGTTAAATATCAG
          1 AAGTACAATCAAGCTGGTACCAAATATCAACATTTCTAGAACCTTCCGCTACAGTCAAATATCAG

                         *  *             *                                * 
        175 CAGATCCAAAGGTGTTGACCGGGTAAAAGGTGCTCTTCCAACAAGATGTACCTAACATGCAGTTT
         66 CAGATCCAAAGGTATTAACCGGGTAAAAGGAGCTCTTCCAACAAGATGTACCTAACATGCAGTCT

                   *                             
        240 GACAGCAGTACTGACTCTTCTGGAAACTGACGATAGA
        131 GACAGCAATACTGACTCTTCTGGAAACTGACGATAGA

                               *          *                *                *
        277 AAGTACAATCCAA-CTGGTGCCAAATATCAGCATTTCTAGAACCTTCTGCTACAGTCAAATATTT
          1 AAGTACAAT-CAAGCTGGTACCAAATATCAACATTTCTAGAACCTTCCGCTACAGTCAAATA-TC

                *      *                            *  * * *       *         
        341 AGCATATCCAAGGGTATTAACCGGGTAAAAGGAGCTCTTCTAATAGGTTGTACCTGACATGCAGT
         64 AGCAGATCCAAAGGTATTAACCGGGTAAAAGGAGCTCTTCCAACAAGATGTACCTAACATGCAGT

                           
        406 CTGACAGCAATACTG
        129 CTGACAGCAATACTG

        421 GCTTTGCTAA


Statistics
Matches: 122,  Mismatches: 20, Indels: 3
        0.84            0.14        0.02

Matches are distributed among these distances:
 167   50  0.41
 168   72  0.59

ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26


Consensus pattern (167 bp):   
AAGTACAATCAAGCTGGTACCAAATATCAACATTTCTAGAACCTTCCGCTACAGTCAAATATCAG
CAGATCCAAAGGTATTAACCGGGTAAAAGGAGCTCTTCCAACAAGATGTACCTAACATGCAGTCT
GACAGCAATACTGACTCTTCTGGAAACTGACGATAGA

Found at i:1177 original size:9 final size:10

Alignment explanation


    Indices: 1152--1180  Score: 51
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       1142 CTGCAAGGAA

                      
       1152 GCATGGAGAT
          1 GCATGGAGAT

                      
       1162 GCATGGAGAT
          1 GCATGGAGAT

                      
       1172 -CATGGAGAT
          1 GCATGGAGAT

       1181 ATCGATAAGC


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
   9    9  0.47
  10   10  0.53

ACGTcount: A:0.31, C:0.10, G:0.38, T:0.21


Consensus pattern (10 bp):   
GCATGGAGAT
Done.