Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017493.1 Corchorus olitorius cultivar O-4 contig17526, 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: 13582
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:5487 original size:15 final size:15

Alignment explanation


    Indices: 5463--5503  Score: 55
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5453 TGCACCGTTT

                 *         
       5463 CCATTATTGTTCACA
          1 CCATTGTTGTTCACA

                       **  
       5478 CCATTGTTGTTTGCA
          1 CCATTGTTGTTCACA

                       
       5493 CCATTGTTGTT
          1 CCATTGTTGTT

       5504 TGCACCATTC


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.17, C:0.22, G:0.15, T:0.46


Consensus pattern (15 bp):   
CCATTGTTGTTCACA

Found at i:5504 original size:15 final size:15

Alignment explanation


    Indices: 5476--5512  Score: 74
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       5466 TTATTGTTCA

                           
       5476 CACCATTGTTGTTTG
          1 CACCATTGTTGTTTG

                           
       5491 CACCATTGTTGTTTG
          1 CACCATTGTTGTTTG

                   
       5506 CACCATT
          1 CACCATT

       5513 CACCCTAGCA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.16, C:0.24, G:0.16, T:0.43


Consensus pattern (15 bp):   
CACCATTGTTGTTTG

Found at i:6437 original size:50 final size:49

Alignment explanation


    Indices: 6347--6477  Score: 169
    Period size: 50  Copynumber: 2.7  Consensus size: 49

       6337 AATTTTGTCA

                     *                                     ** 
       6347 AAAAATTGATAAAAAGTGCAA-TAAAAAGTTAAAAGATCAATTTTATCTT
          1 AAAAATTGAGAAAAAGTGCAAGTAAAAAG-TAAAAGATCAATTTTATAGT

                                                 *        *    
       6396 AAAAATTGAGAAAAAGGGTGCAAGTAAAAA-TAAAAGTTCAATTTTGTAGT
          1 AAAAATTGAGAAAAA--GTGCAAGTAAAAAGTAAAAGATCAATTTTATAGT

                                             
       6446 AAAAATTGAGAAAAAGTGC-AGTAAAAAGTAAA
          1 AAAAATTGAGAAAAAGTGCAAGTAAAAAGTAAA

       6478 GGATTGCTTG


Statistics
Matches: 73,  Mismatches: 5, Indels: 9
        0.84            0.06        0.10

Matches are distributed among these distances:
  47    8  0.11
  48    8  0.11
  49   14  0.19
  50   31  0.42
  51    6  0.08
  52    6  0.08

ACGTcount: A:0.54, C:0.05, G:0.16, T:0.25


Consensus pattern (49 bp):   
AAAAATTGAGAAAAAGTGCAAGTAAAAAGTAAAAGATCAATTTTATAGT

Found at i:13006 original size:2 final size:2

Alignment explanation


    Indices: 13001--13059  Score: 51
    Period size: 2  Copynumber: 33.0  Consensus size: 2

      12991 TTTTTTTGAG

                                           *                              
      13001 TA TA TA TA TA TA TA TA TA TA TT TA TA TA T- TA T- TA T- TA T-
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                        *                      
      13039 TA -A TA TA AA TA -A TA T- TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA

      13060 ATAAACGAAC


Statistics
Matches: 46,  Mismatches: 4, Indels: 14
        0.72            0.06        0.22

Matches are distributed among these distances:
   1    7  0.15
   2   39  0.85

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:13135 original size:35 final size:35

Alignment explanation


    Indices: 13089--13163  Score: 141
    Period size: 35  Copynumber: 2.1  Consensus size: 35

      13079 TTATATAAAC

                                       *       
      13089 GAACACTTAAATGAACAATAAACGAGCTTGTTCGT
          1 GAACACTTAAATGAACAATAAACGAGCATGTTCGT

                                               
      13124 GAACACTTAAATGAACAATAAACGAGCATGTTCGT
          1 GAACACTTAAATGAACAATAAACGAGCATGTTCGT

                 
      13159 GAACA
          1 GAACA

      13164 TAAACGAACT


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  35   39  1.00

ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23


Consensus pattern (35 bp):   
GAACACTTAAATGAACAATAAACGAGCATGTTCGT
Done.