Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015058.1 Corchorus capsularis cultivar CVL-1 contig15079, 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: 21496
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:6531 original size:10 final size:10

Alignment explanation


    Indices: 6516--6540  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       6506 GTTCCTGCAC

                      
       6516 AATTCCAGAA
          1 AATTCCAGAA

                      
       6526 AATTCCAGAA
          1 AATTCCAGAA

                 
       6536 AATTC
          1 AATTC

       6541 TAGAGTCCTC


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

Found at i:12381 original size:16 final size:15

Alignment explanation


    Indices: 12349--12378  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      12339 TCCTAATCTC

                  *        
      12349 TATTATTAAAGAAAA
          1 TATTATAAAAGAAAA

                           
      12364 TATTATAAAAGAAAA
          1 TATTATAAAAGAAAA

      12379 ATAAAATCAT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30


Consensus pattern (15 bp):   
TATTATAAAAGAAAA

Found at i:14895 original size:15 final size:15

Alignment explanation


    Indices: 14875--14907  Score: 66
    Period size: 15  Copynumber: 2.2  Consensus size: 15

      14865 AACCATCACT

                           
      14875 AATGCAAATTAATGG
          1 AATGCAAATTAATGG

                           
      14890 AATGCAAATTAATGG
          1 AATGCAAATTAATGG

               
      14905 AAT
          1 AAT

      14908 ACAAGTTATA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27


Consensus pattern (15 bp):   
AATGCAAATTAATGG

Found at i:16056 original size:16 final size:16

Alignment explanation


    Indices: 16034--16110  Score: 86
    Period size: 15  Copynumber: 4.9  Consensus size: 16

      16024 AATAAGTACT

                           *
      16034 ATAACCCGAAACCGAT
          1 ATAACCCGAAACCGAG

            *          *    
      16050 TTAACCCG-AATCGAG
          1 ATAACCCGAAACCGAG

                           *
      16065 ATAACCCGAAACCGAT
          1 ATAACCCGAAACCGAG

            *          *    
      16081 TTAACCCG-AATCGAG
          1 ATAACCCGAAACCGAG

                           
      16096 ATAACCCGAAACCGA
          1 ATAACCCGAAACCGA

      16111 CAAAATCCGA


Statistics
Matches: 48,  Mismatches: 11, Indels: 4
        0.76            0.17        0.06

Matches are distributed among these distances:
  15   24  0.50
  16   24  0.50

ACGTcount: A:0.40, C:0.30, G:0.16, T:0.14


Consensus pattern (16 bp):   
ATAACCCGAAACCGAG

Found at i:16069 original size:31 final size:31

Alignment explanation


    Indices: 16034--16110  Score: 154
    Period size: 31  Copynumber: 2.5  Consensus size: 31

      16024 AATAAGTACT

                                           
      16034 ATAACCCGAAACCGATTTAACCCGAATCGAG
          1 ATAACCCGAAACCGATTTAACCCGAATCGAG

                                           
      16065 ATAACCCGAAACCGATTTAACCCGAATCGAG
          1 ATAACCCGAAACCGATTTAACCCGAATCGAG

                           
      16096 ATAACCCGAAACCGA
          1 ATAACCCGAAACCGA

      16111 CAAAATCCGA


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   46  1.00

ACGTcount: A:0.40, C:0.30, G:0.16, T:0.14


Consensus pattern (31 bp):   
ATAACCCGAAACCGATTTAACCCGAATCGAG

Found at i:18644 original size:30 final size:32

Alignment explanation


    Indices: 18610--18688  Score: 101
    Period size: 32  Copynumber: 2.5  Consensus size: 32

      18600 ATCCTTTTCT

                              *  **         
      18610 AAAAACATTTTTGGGTTTTTTTTC-AA-AAAA
          1 AAAAACATTTTTGGGTTTATTCACAAAGAAAA

                                             
      18640 AAAAACATTTTTGGG-TTATTCACAAAAGAAAA
          1 AAAAACATTTTTGGGTTTATTCAC-AAAGAAAA

                             
      18672 AAAAACATTTTTGGGTT
          1 AAAAACATTTTTGGGTT

      18689 GGACCTGAAT


Statistics
Matches: 42,  Mismatches: 3, Indels: 5
        0.84            0.06        0.10

Matches are distributed among these distances:
  29    5  0.12
  30   15  0.36
  31    2  0.05
  32   19  0.45
  33    1  0.02

ACGTcount: A:0.43, C:0.08, G:0.13, T:0.37


Consensus pattern (32 bp):   
AAAAACATTTTTGGGTTTATTCACAAAGAAAA
Done.