Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024375.1 Corchorus olitorius cultivar O-4 contig24408, 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: 14383
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:9259 original size:32 final size:32

Alignment explanation


    Indices: 9214--9285  Score: 85
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       9204 GGTTTCAGGT

                *   *                         
       9214 TCAGTTCATACGGGT-TTCGGGTCATACTGA-TC
          1 TCAGGTCAAACGGGTCTT-GGGTCATAC-GAGTC

                                     *      
       9246 TCAGGTCAAACGGGTCTTGGGTCATTCGAGTC
          1 TCAGGTCAAACGGGTCTTGGGTCATACGAGTC

                    
       9278 TCAGGTCA
          1 TCAGGTCA

       9286 TTCTGATTAT


Statistics
Matches: 35,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  31    2  0.06
  32   31  0.89
  33    2  0.06

ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31


Consensus pattern (32 bp):   
TCAGGTCAAACGGGTCTTGGGTCATACGAGTC

Found at i:10070 original size:23 final size:23

Alignment explanation


    Indices: 10043--10088  Score: 92
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      10033 TTTTTCATAA

                                   
      10043 TAGTAATTTGGGAAAGGCAAGGC
          1 TAGTAATTTGGGAAAGGCAAGGC

                                   
      10066 TAGTAATTTGGGAAAGGCAAGGC
          1 TAGTAATTTGGGAAAGGCAAGGC

      10089 AAATGAGGTG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.35, C:0.09, G:0.35, T:0.22


Consensus pattern (23 bp):   
TAGTAATTTGGGAAAGGCAAGGC

Found at i:11470 original size:2 final size:2

Alignment explanation


    Indices: 11463--11490  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      11453 CTTATAACGT

                                                     
      11463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      11491 AATTGTTGAC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:11789 original size:2 final size:2

Alignment explanation


    Indices: 11776--11814  Score: 69
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      11766 TGTTTGGTGT

                                                                     
      11776 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      11815 CTAGTTAAAG


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   34  0.94
   3    2  0.06

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:13406 original size:58 final size:58

Alignment explanation


    Indices: 13305--13417  Score: 147
    Period size: 58  Copynumber: 1.9  Consensus size: 58

      13295 ATTAATCAAA

                                       *  *               *           
      13305 TATCAAGTGACATGTTCTTTATTAGATGCATTAAAAAAAACGTTTTCGGACCGAGACT
          1 TATCAAGTGACATGTTCTTTATTAGATACACTAAAAAAAACGTTTTAGGACCGAGACT

                *            *                 *   *                
      13363 TATCGAGTGACATGTTTTTTTATTAGATAC-CTAAGAAAGACGTTTTAGGACCGAG
          1 TATCAAGTGACATG-TTCTTTATTAGATACACTAAAAAAAACGTTTTAGGACCGAG

      13418 GCATGATGCT


Statistics
Matches: 47,  Mismatches: 7, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  58   34  0.72
  59   13  0.28

ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34


Consensus pattern (58 bp):   
TATCAAGTGACATGTTCTTTATTAGATACACTAAAAAAAACGTTTTAGGACCGAGACT
Done.