Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006722.1 Corchorus capsularis cultivar CVL-1 contig06743, 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: 2181
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34


Found at i:1230 original size:28 final size:28

Alignment explanation


    Indices: 1162--1235  Score: 121
    Period size: 28  Copynumber: 2.6  Consensus size: 28

       1152 GTGAACTTAG

                        * *             
       1162 AATGACCAAAATACACCTAAACACAGAA
          1 AATGACCAAAATGCCCCTAAACACAGAA

                                  *     
       1190 AATGACCAAAATGCCCCTAAACGCAGAA
          1 AATGACCAAAATGCCCCTAAACACAGAA

                              
       1218 AATGACCAAAATGCCCCT
          1 AATGACCAAAATGCCCCT

       1236 GGATGACCCT


Statistics
Matches: 43,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   43  1.00

ACGTcount: A:0.49, C:0.28, G:0.11, T:0.12


Consensus pattern (28 bp):   
AATGACCAAAATGCCCCTAAACACAGAA

Found at i:1662 original size:23 final size:22

Alignment explanation


    Indices: 1581--1662  Score: 85
    Period size: 22  Copynumber: 3.7  Consensus size: 22

       1571 AATTCATTGA

                    * *           
       1581 TTGGTAACTTACTTATAAAATT
          1 TTGGTAACCTCCTTATAAAATT

                     *       *     
       1603 TTGGTAACCACAC-TATGAAATT
          1 TTGGTAACCTC-CTTATAAAATT

                    * *            
       1625 TTGGTAACGTTCTTATCAAAATT
          1 TTGGTAACCTCCTTAT-AAAATT

                           
       1648 TTGGTAACCTCCTTA
          1 TTGGTAACCTCCTTA

       1663 ATTATTTTTG


Statistics
Matches: 47,  Mismatches: 10, Indels: 5
        0.76            0.16        0.08

Matches are distributed among these distances:
  21    1  0.02
  22   27  0.57
  23   19  0.40

ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40


Consensus pattern (22 bp):   
TTGGTAACCTCCTTATAAAATT

Found at i:1929 original size:95 final size:95

Alignment explanation


    Indices: 1806--1978  Score: 251
    Period size: 95  Copynumber: 1.8  Consensus size: 95

       1796 GAATGAGGGA

                       * *                        *     *                    
       1806 CATTTTTGGCCTCTGATGGCCGTGATGGATAACATTTGTCTTCCGGA-CAGTTTCTCGCCCCCAA
          1 CATTTTTGGCCCCGGATGGCCGTGATGGATAACATTTGCCTTCCAGATC-GTTTCTCGCCCCCAA

                 *                          
       1870 TGGTCGTGAT-GGTAGCCTTTGGGATCAAGGC
         65 -GGTCATGATAGGTAGCCTTTGGGATCAAGGC

                                            **                               
       1901 CATTTTTGGCCCCGGATGGCCGTGATGGATAATTTTTGCCTTCCAGATCGTTTCTCGCCCCCAAG
          1 CATTTTTGGCCCCGGATGGCCGTGATGGATAACATTTGCCTTCCAGATCGTTTCTCGCCCCCAAG

                         
       1966 GTCATGATAGGTA
         66 GTCATGATAGGTA

       1979 ACGTTGTCTT


Statistics
Matches: 69,  Mismatches: 7, Indels: 4
        0.86            0.09        0.05

Matches are distributed among these distances:
  94    8  0.12
  95   60  0.87
  96    1  0.01

ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32


Consensus pattern (95 bp):   
CATTTTTGGCCCCGGATGGCCGTGATGGATAACATTTGCCTTCCAGATCGTTTCTCGCCCCCAAG
GTCATGATAGGTAGCCTTTGGGATCAAGGC
Done.