Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015788.1 Corchorus olitorius cultivar O-4 contig15821, 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: 31322
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:5948 original size:18 final size:19

Alignment explanation


    Indices: 5925--5963  Score: 53
    Period size: 18  Copynumber: 2.1  Consensus size: 19

       5915 CAAGAAGGTT

                               
       5925 TTGCCCCGATTAGACG-GA
          1 TTGCCCCGATTAGACGCGA

                   *   *       
       5943 TTGCCCCTATTTGACGCGA
          1 TTGCCCCGATTAGACGCGA

              
       5962 TT
          1 TT

       5964 TCGGAACGTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  18   14  0.78
  19    4  0.22

ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31


Consensus pattern (19 bp):   
TTGCCCCGATTAGACGCGA

Found at i:8808 original size:2 final size:2

Alignment explanation


    Indices: 8801--8835  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       8791 CTGTGGCTAG

                                                                 
       8801 TA TA TA TA TA -A 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 TA TA TA TA

       8836 ATAAAATATA


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.97

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:10300 original size:12 final size:12

Alignment explanation


    Indices: 10283--10308  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      10273 TTCAATTCAA

                        
      10283 TAGTTTACCTTT
          1 TAGTTTACCTTT

                        
      10295 TAGTTTACCTTT
          1 TAGTTTACCTTT

              
      10307 TA
          1 TA

      10309 ACTTAAATCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58


Consensus pattern (12 bp):   
TAGTTTACCTTT

Found at i:17916 original size:32 final size:32

Alignment explanation


    Indices: 17866--17951  Score: 156
    Period size: 32  Copynumber: 2.7  Consensus size: 32

      17856 TGATAGGAAG

                *                           
      17866 AAAACAAATCTT-AAAGAATAATTTGAACCAA
          1 AAAAAAAATCTTCAAAGAATAATTTGAACCAA

                                            
      17897 AAAAAAAATCTTCAAAGAATAATTTGAACCAA
          1 AAAAAAAATCTTCAAAGAATAATTTGAACCAA

                                   
      17929 AAAAAAAATCTTCAAAGAATAAT
          1 AAAAAAAATCTTCAAAGAATAAT

      17952 ATTAAAAGGG


Statistics
Matches: 53,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  31   11  0.21
  32   42  0.79

ACGTcount: A:0.60, C:0.12, G:0.06, T:0.22


Consensus pattern (32 bp):   
AAAAAAAATCTTCAAAGAATAATTTGAACCAA

Found at i:19848 original size:14 final size:14

Alignment explanation


    Indices: 19815--19849  Score: 63
    Period size: 13  Copynumber: 2.6  Consensus size: 14

      19805 AATTCTCTTA

                          
      19815 AAAATTTCAATGAG
          1 AAAATTTCAATGAG

                          
      19829 -AAATTTCAATGAG
          1 AAAATTTCAATGAG

                    
      19842 AAAATTTC
          1 AAAATTTC

      19850 TCAATACTAG


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  13   13  0.65
  14    7  0.35

ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31


Consensus pattern (14 bp):   
AAAATTTCAATGAG

Found at i:30810 original size:2 final size:2

Alignment explanation


    Indices: 30803--30846  Score: 79
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      30793 TAATTAGAAG

                                                                      *   
      30803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

              
      30845 AT
          1 AT

      30847 GAATATGTAG


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48


Consensus pattern (2 bp):   
AT

Done.