Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024676.1 Corchorus olitorius cultivar O-4 contig24709, 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: 18523
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30


Found at i:1597 original size:3 final size:3

Alignment explanation


    Indices: 1589--1623  Score: 70
    Period size: 3  Copynumber: 11.7  Consensus size: 3

       1579 CAGAGAGGTG

                                                          
       1589 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
          1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA

       1624 GAAAGCAAAG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31


Consensus pattern (3 bp):   
GAT

Found at i:5847 original size:30 final size:29

Alignment explanation


    Indices: 5808--5887  Score: 92
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       5798 AGCTGCAAAA

                                        * 
       5808 TTTTATTGCAAT-AAATAAGACCC-TGAGC
          1 TTTTATTGCAATCAAATAAG-CCCTTGAAC

                  *                        
       5836 TATTTGTTTGCAATCAAATAAGCCCTTGAAC
          1 T-TTT-ATTGCAATCAAATAAGCCCTTGAAC

                        *        
       5867 TTTTATTGCAATGAAATAAGC
          1 TTTTATTGCAATCAAATAAGC

       5888 TTTAAATTTT


Statistics
Matches: 44,  Mismatches: 4, Indels: 7
        0.80            0.07        0.13

Matches are distributed among these distances:
  28    1  0.02
  29   18  0.41
  30   13  0.30
  31   12  0.27

ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Consensus pattern (29 bp):   
TTTTATTGCAATCAAATAAGCCCTTGAAC

Found at i:17154 original size:5 final size:5

Alignment explanation


    Indices: 17140--17169  Score: 51
    Period size: 5  Copynumber: 6.0  Consensus size: 5

      17130 TCAAGTAATT

                        *                      
      17140 AAAGG AAAGG GAAGG AAAGG AAAGG AAAGG
          1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG

      17170 GGAGGGAAGT


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   5   23  1.00

ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00


Consensus pattern (5 bp):   
AAAGG

Done.