Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015757.1 Corchorus capsularis cultivar CVL-1 contig15778, 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: 8281
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:3686 original size:10 final size:10

Alignment explanation


    Indices: 3670--3699  Score: 51
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       3660 GATTGCGCAC

                      
       3670 CAACCGGCCA
          1 CAACCGGCCA

            *         
       3680 TAACCGGCCA
          1 CAACCGGCCA

                      
       3690 CAACCGGCCA
          1 CAACCGGCCA

       3700 ATGGATCCTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  10   18  1.00

ACGTcount: A:0.30, C:0.47, G:0.20, T:0.03


Consensus pattern (10 bp):   
CAACCGGCCA

Found at i:5958 original size:19 final size:18

Alignment explanation


    Indices: 5925--5960  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       5915 TCGAAATAAT

                              
       5925 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       5943 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       5961 GAAATCTTCA


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

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:6162 original size:20 final size:21

Alignment explanation


    Indices: 6124--6162  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 21

       6114 TAGAAAATAA

                          *      
       6124 GGTAAAAATGCATATAAAAGT
          1 GGTAAAAATGCATAGAAAAGT

                      *        
       6145 GGTAAAAA-GTATAGAAAA
          1 GGTAAAAATGCATAGAAAA

       6163 ATAGCTATAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    8  0.50
  21    8  0.50

ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21


Consensus pattern (21 bp):   
GGTAAAAATGCATAGAAAAGT

Found at i:8223 original size:10 final size:10

Alignment explanation


    Indices: 8208--8232  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       8198 GTTGCTGCTT

                      
       8208 AATTCCAGAA
          1 AATTCCAGAA

                      
       8218 AATTCCAGAA
          1 AATTCCAGAA

                 
       8228 AATTC
          1 AATTC

       8233 TAGAGTCCTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24


Consensus pattern (10 bp):   
AATTCCAGAA
Done.