Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019813.1 Corchorus olitorius cultivar O-4 contig19846, 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: 43933
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35


Found at i:8561 original size:2 final size:2

Alignment explanation


    Indices: 8554--8583  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       8544 TTATTTAGGA

                                                        
       8554 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

       8584 GCCTCGATGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AG

Found at i:37384 original size:21 final size:24

Alignment explanation


    Indices: 37358--37407  Score: 61
    Period size: 22  Copynumber: 2.2  Consensus size: 24

      37348 TTTTTAACTC

                                    
      37358 ATTATT-TGTATTTA-AAATATAT
          1 ATTATTATGTATTTATAAATATAT

                    *       *       
      37380 -TTATTATTTATTTATTAATATAT
          1 ATTATTATGTATTTATAAATATAT

                 
      37403 ATTAT
          1 ATTAT

      37408 ATCTAATATA


Statistics
Matches: 23,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  21    5  0.22
  22    7  0.30
  23    7  0.30
  24    4  0.17

ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60


Consensus pattern (24 bp):   
ATTATTATGTATTTATAAATATAT

Found at i:42104 original size:14 final size:14

Alignment explanation


    Indices: 42085--42115  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

      42075 TGTTGTTCTA

                          
      42085 TTCCACTATTGTTG
          1 TTCCACTATTGTTG

                          
      42099 TTCCACTATTGTTG
          1 TTCCACTATTGTTG

               
      42113 TTC
          1 TTC

      42116 TGTTCTGTTA


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

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.13, C:0.23, G:0.13, T:0.52


Consensus pattern (14 bp):   
TTCCACTATTGTTG

Found at i:42119 original size:19 final size:19

Alignment explanation


    Indices: 42074--42120  Score: 50
    Period size: 14  Copynumber: 2.7  Consensus size: 19

      42064 TGTTGTTCTG

                      *        
      42074 TTGTTGTTCTATTCCACTA
          1 TTGTTGTTCTGTTCCACTA

                               
      42093 ---TTG-T-TGTTCCACTA
          1 TTGTTGTTCTGTTCCACTA

                          
      42107 TTGTTGTTCTGTTC
          1 TTGTTGTTCTGTTC

      42121 TGTTATGTTC


Statistics
Matches: 22,  Mismatches: 1, Indels: 10
        0.67            0.03        0.30

Matches are distributed among these distances:
  14    9  0.41
  15    1  0.05
  16    3  0.14
  17    3  0.14
  18    1  0.05
  19    5  0.23

ACGTcount: A:0.11, C:0.19, G:0.15, T:0.55


Consensus pattern (19 bp):   
TTGTTGTTCTGTTCCACTA
Done.