Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001038.1 Corchorus capsularis cultivar CVL-1 contig01038, 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: 10035
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:1919 original size:27 final size:26

Alignment explanation


    Indices: 1889--1955  Score: 98
    Period size: 27  Copynumber: 2.5  Consensus size: 26

       1879 AAATCATAAG

                    *                  
       1889 AATATCATGTATTTAAAAATTATAGAT
          1 AATATCA-ATATTTAAAAATTATAGAT

                                       
       1916 AATATTCAATATTTAAAAATTATAGAT
          1 AATA-TCAATATTTAAAAATTATAGAT

                         
       1943 AATATTCAATATT
          1 AATA-TCAATATT

       1956 ATGCAAATGT


Statistics
Matches: 38,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  27   35  0.92
  28    3  0.08

ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42


Consensus pattern (26 bp):   
AATATCAATATTTAAAAATTATAGAT

Found at i:6791 original size:19 final size:19

Alignment explanation


    Indices: 6754--6791  Score: 51
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       6744 ACTATTAGAA

                          *    
       6754 ATATAGTTATATACTAAAT
          1 ATATAGTTATATACAAAAT

                                
       6773 ATATAGTTTATATA-AAAAT
          1 ATATAG-TTATATACAAAAT

       6792 CTCTATAAGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19   10  0.59
  20    7  0.41

ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42


Consensus pattern (19 bp):   
ATATAGTTATATACAAAAT

Found at i:9147 original size:19 final size:18

Alignment explanation


    Indices: 9119--9154  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       9109 TACCTACCTA

                 *             
       9119 ACAAATAAACAAACAAATT
          1 ACAAACAAAC-AACAAATT

                             
       9138 ACAAACAAACAACAAAT
          1 ACAAACAAACAACAAAT

       9155 AAATAAACAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.69, C:0.19, G:0.00, T:0.11


Consensus pattern (18 bp):   
ACAAACAAACAACAAATT
Done.