Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020490.1 Corchorus olitorius cultivar O-4 contig20523, 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: 26568
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33


Found at i:3401 original size:26 final size:26

Alignment explanation


    Indices: 3372--3431  Score: 120
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       3362 CCCCTTCAAG

                                      
       3372 TCCTGTAAGTTTTCTTATGCCTCTTA
          1 TCCTGTAAGTTTTCTTATGCCTCTTA

                                      
       3398 TCCTGTAAGTTTTCTTATGCCTCTTA
          1 TCCTGTAAGTTTTCTTATGCCTCTTA

                    
       3424 TCCTGTAA
          1 TCCTGTAA

       3432 AAATCCATGA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   34  1.00

ACGTcount: A:0.17, C:0.23, G:0.12, T:0.48


Consensus pattern (26 bp):   
TCCTGTAAGTTTTCTTATGCCTCTTA

Found at i:16923 original size:2 final size:2

Alignment explanation


    Indices: 16916--16963  Score: 73
    Period size: 2  Copynumber: 25.0  Consensus size: 2

      16906 ATGATATAAG

                                    *                                     
      16916 TA TA TA TA TA TA TA TA CA TA T- TA TA TA TA TA -A TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                       
      16956 TA TA TA TA
          1 TA TA TA TA

      16964 GTTTGGGTTA


Statistics
Matches: 42,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
   1    2  0.05
   2   40  0.95

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


Consensus pattern (2 bp):   
TA

Found at i:16942 original size:17 final size:16

Alignment explanation


    Indices: 16917--16961  Score: 76
    Period size: 15  Copynumber: 2.9  Consensus size: 16

      16907 TGATATAAGT

                            
      16917 ATATATATATATATAC
          1 ATATATATATATATAC

                            
      16933 ATAT-TATATATATA-
          1 ATATATATATATATAC

                           
      16947 ATATATATATATATA
          1 ATATATATATATATA

      16962 TAGTTTGGGT


Statistics
Matches: 28,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    4  0.14
  15   20  0.71
  16    4  0.14

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (16 bp):   
ATATATATATATATAC

Found at i:17634 original size:15 final size:16

Alignment explanation


    Indices: 17600--17633  Score: 54
    Period size: 14  Copynumber: 2.2  Consensus size: 16

      17590 ATGGTGTTTC

                            
      17600 AAAATCCTAAACTAAA
          1 AAAATCCTAAACTAAA

                            
      17616 AAAATCC-AAA-TAAA
          1 AAAATCCTAAACTAAA

                
      17630 AAAA
          1 AAAA

      17634 AAGAGAAATT


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

Matches are distributed among these distances:
  14    8  0.44
  15    3  0.17
  16    7  0.39

ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15


Consensus pattern (16 bp):   
AAAATCCTAAACTAAA

Found at i:25397 original size:16 final size:17

Alignment explanation


    Indices: 25376--25407  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

      25366 GAGATTGCGT

                             
      25376 TTTATTTTTCT-TTTTC
          1 TTTATTTTTCTATTTTC

                            
      25392 TTTATTTTTCTATTTT
          1 TTTATTTTTCTATTTT

      25408 AATTTGCACT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81


Consensus pattern (17 bp):   
TTTATTTTTCTATTTTC
Done.