Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011603.1 Corchorus capsularis cultivar CVL-1 contig11624, 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: 7791
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32


Found at i:6000 original size:21 final size:21

Alignment explanation


    Indices: 5967--6008  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5957 AGCACAAGTG

                    *            
       5967 ACCGACCATGCGACTTGGAGA
          1 ACCGACCACGCGACTTGGAGA

                *                
       5988 ACCGGCCACGCGACTTGGAGA
          1 ACCGACCACGCGACTTGGAGA

       6009 TGCCCGCGCA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.26, C:0.31, G:0.31, T:0.12


Consensus pattern (21 bp):   
ACCGACCACGCGACTTGGAGA

Found at i:6025 original size:33 final size:33

Alignment explanation


    Indices: 5988--6081  Score: 127
    Period size: 33  Copynumber: 2.8  Consensus size: 33

       5978 GACTTGGAGA

                          *                   
       5988 ACCGGCCACGCGACTTGGAGATGCCCGCG-CAAC
          1 ACCGGCCACGCGACATGGAGATGCCCG-GTCAAC

                    *                      * 
       6021 ACCGGCCATGCGACATGGAGATGCCCGGTCATC
          1 ACCGGCCACGCGACATGGAGATGCCCGGTCAAC

                              **        
       6054 ACCGGCCACGCGACATGGCCATGCCCGG
          1 ACCGGCCACGCGACATGGAGATGCCCGG

       6082 CCACACGATC


Statistics
Matches: 54,  Mismatches: 6, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  32    1  0.02
  33   53  0.98

ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11


Consensus pattern (33 bp):   
ACCGGCCACGCGACATGGAGATGCCCGGTCAAC

Found at i:6998 original size:8 final size:8

Alignment explanation


    Indices: 6985--7018  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       6975 CCTTCTTCAA

                    
       6985 AAAAATTC
          1 AAAAATTC

                    
       6993 AAAAATTC
          1 AAAAATTC

                 *   
       7001 AGAAACTTC
          1 A-AAAATTC

                    
       7010 AAAAATTC
          1 AAAAATTC

             
       7018 A
          1 A

       7019 TAGCTGATTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC

Found at i:7107 original size:5 final size:5

Alignment explanation


    Indices: 7097--7128  Score: 64
    Period size: 5  Copynumber: 6.4  Consensus size: 5

       7087 ATCGAAAAAT

                                                  
       7097 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
          1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT

       7129 TTCGACCAGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   27  1.00

ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22


Consensus pattern (5 bp):   
ATAAA

Done.