Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021623.1 Corchorus olitorius cultivar O-4 contig21656, 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: 23419
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:5410 original size:20 final size:20

Alignment explanation


    Indices: 5381--5420  Score: 62
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       5371 TCTAACTAGC

                                
       5381 TAACTAGTTGGCGCCACTTT
          1 TAACTAGTTGGCGCCACTTT

                 *     *        
       5401 TAACTTGTTGGTGCCACTTT
          1 TAACTAGTTGGCGCCACTTT

       5421 GCGTTCTTTT


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

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40


Consensus pattern (20 bp):   
TAACTAGTTGGCGCCACTTT

Found at i:12302 original size:15 final size:15

Alignment explanation


    Indices: 12284--12315  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      12274 AATTGCATTT

                           
      12284 CCACTTAGAGAATCA
          1 CCACTTAGAGAATCA

                           
      12299 CCACTTAGAGAATCA
          1 CCACTTAGAGAATCA

              
      12314 CC
          1 CC

      12316 TTTGATGTGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19


Consensus pattern (15 bp):   
CCACTTAGAGAATCA

Found at i:22713 original size:33 final size:34

Alignment explanation


    Indices: 22657--22725  Score: 104
    Period size: 33  Copynumber: 2.0  Consensus size: 34

      22647 ACAGAAAAAA

                                     *          
      22657 AAAAAGTTACTAAGGAGTAGAATTATTGAATTTGTT
          1 AAAAAGTTACT-A-GAGTAGAATTAGTGAATTTGTT

                                              
      22693 AAAAAGTTACT-GAGTAGAATTAGTGAATTTGTT
          1 AAAAAGTTACTAGAGTAGAATTAGTGAATTTGTT

      22726 GATAGGACTA


Statistics
Matches: 32,  Mismatches: 1, Indels: 3
        0.89            0.03        0.08

Matches are distributed among these distances:
  33   21  0.66
  36   11  0.34

ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36


Consensus pattern (34 bp):   
AAAAAGTTACTAGAGTAGAATTAGTGAATTTGTT

Found at i:23052 original size:49 final size:49

Alignment explanation


    Indices: 22951--23080  Score: 169
    Period size: 49  Copynumber: 2.7  Consensus size: 49

      22941 GAGCGTGCCA

                         *         *     *            *      
      22951 ATCAATTTTGTC-AAAAAATTGATAAAAATTGC-AGTGAAAATTAAAAG
          1 ATCAATTTTGTCTTAAAAATTGAGAAAAAGTGCAAGTGAAAAATAAAAG

                                                              
      22998 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGT-AAAAATAAAAG
          1 ATCAATTTTGTCTTAAAAATTGAGAAAAAG-TGCAAGTGAAAAATAAAAG

            *                                  
      23047 TTCAATTTTGT-TGTAAAAATTGAGAAAAAGTGCA
          1 ATCAATTTTGTCT-TAAAAATTGAGAAAAAGTGCA

      23081 GGAAATGTAA


Statistics
Matches: 74,  Mismatches: 5, Indels: 7
        0.86            0.06        0.08

Matches are distributed among these distances:
  47   12  0.16
  48   19  0.26
  49   40  0.54
  50    3  0.04

ACGTcount: A:0.49, C:0.06, G:0.15, T:0.30


Consensus pattern (49 bp):   
ATCAATTTTGTCTTAAAAATTGAGAAAAAGTGCAAGTGAAAAATAAAAG
Done.