Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015601.1 Corchorus capsularis cultivar CVL-1 contig15622, 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: 14086
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31


Found at i:885 original size:9 final size:9

Alignment explanation


    Indices: 871--904  Score: 59
    Period size: 9  Copynumber: 3.7  Consensus size: 9

        861 TCTGGTCGAA

                     
        871 ATTTTTTTT
          1 ATTTTTTTT

                     
        880 ATTTTTTTT
          1 ATTTTTTTT

                      
        889 ATTTTTTTAT
          1 ATTTTTTT-T

                  
        899 ATTTTT
          1 ATTTTT

        905 GATATAACTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   9   17  0.71
  10    7  0.29

ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85


Consensus pattern (9 bp):   
ATTTTTTTT

Found at i:887 original size:10 final size:10

Alignment explanation


    Indices: 872--904  Score: 50
    Period size: 10  Copynumber: 3.4  Consensus size: 10

        862 CTGGTCGAAA

                      
        872 TTTTTTTTA-
          1 TTTTTTTTAT

                      
        881 TTTTTTTTAT
          1 TTTTTTTTAT

                  *   
        891 TTTTTTATAT
          1 TTTTTTTTAT

                
        901 TTTT
          1 TTTT

        905 GATATAACTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
   9    9  0.41
  10   13  0.59

ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88


Consensus pattern (10 bp):   
TTTTTTTTAT

Found at i:11702 original size:33 final size:33

Alignment explanation


    Indices: 11665--11746  Score: 146
    Period size: 33  Copynumber: 2.5  Consensus size: 33

      11655 TTCTTTTCAC

                             *               
      11665 CCAAAACAGAATTATTTTCAATGCTATGATCAA
          1 CCAAAACAGAATTATTTGCAATGCTATGATCAA

                                             
      11698 CCAAAACAGAATTATTTGCAATGCTATGATCAA
          1 CCAAAACAGAATTATTTGCAATGCTATGATCAA

                      *     
      11731 CCAAAACAGATTTATT
          1 CCAAAACAGAATTATT

      11747 ATCATCACAA


Statistics
Matches: 47,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  33   47  1.00

ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29


Consensus pattern (33 bp):   
CCAAAACAGAATTATTTGCAATGCTATGATCAA

Found at i:11770 original size:33 final size:33

Alignment explanation


    Indices: 11732--11828  Score: 122
    Period size: 33  Copynumber: 2.9  Consensus size: 33

      11722 TATGATCAAC

                         *       *           
      11732 CAAAACAGATTTATTATCATCACAAACAACACT
          1 CAAAACAGATTTAGTATCATCGCAAACAACACT

            *              *    *            
      11765 TAAAACAGATTTAGTGTCATTGCAAACAACACT
          1 CAAAACAGATTTAGTATCATCGCAAACAACACT

                **  *                      
      11798 CAAATTAGGTTTAGTATCATCGCAAACAACA
          1 CAAAACAGATTTAGTATCATCGCAAACAACA

      11829 TCTAAACCAC


Statistics
Matches: 53,  Mismatches: 11, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  33   53  1.00

ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26


Consensus pattern (33 bp):   
CAAAACAGATTTAGTATCATCGCAAACAACACT

Found at i:13344 original size:33 final size:32

Alignment explanation


    Indices: 13307--13413  Score: 126
    Period size: 33  Copynumber: 3.2  Consensus size: 32

      13297 CGCCAAGCGA

                              *   *           
      13307 TGGCCGGTTG-TGGCCGGACATGTCCATGTCGCG
          1 TGGCCGG-TGATGGCCGGGCATCTCCA-GTCGCG

                                             
      13340 TGGCCGGTGATGGCCGGGCATCTCCGAGTCGCG
          1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCG

                     *         *            *
      13373 TGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGCA
          1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCG

                    
      13406 TGGCCGGT
          1 TGGCCGGT

      13414 CACTCGCGCC


Statistics
Matches: 66,  Mismatches: 6, Indels: 4
        0.87            0.08        0.05

Matches are distributed among these distances:
  32    2  0.03
  33   63  0.95
  34    1  0.02

ACGTcount: A:0.08, C:0.29, G:0.40, T:0.22


Consensus pattern (32 bp):   
TGGCCGGTGATGGCCGGGCATCTCCAGTCGCG
Done.