Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014254.1 Corchorus olitorius cultivar O-4 contig14287, 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: 11398
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34


Found at i:2278 original size:15 final size:15

Alignment explanation


    Indices: 2255--2292  Score: 58
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       2245 AGCACATTCT

                *          
       2255 CTGGCTAAGATTGAG
          1 CTGGATAAGATTGAG

                           
       2270 CTGGATAAGATTGAG
          1 CTGGATAAGATTGAG

              *     
       2285 CTAGATAA
          1 CTGGATAA

       2293 TCGTGTGGTG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   21  1.00

ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26


Consensus pattern (15 bp):   
CTGGATAAGATTGAG

Found at i:2312 original size:65 final size:67

Alignment explanation


    Indices: 2179--2350  Score: 242
    Period size: 65  Copynumber: 2.6  Consensus size: 67

       2169 AATGTAGTAA

                     **    *                       *                         
       2179 CACATTCTCCAGCTAGGATTGAGCTGGATAATCGTGTGGTGCTAAATAATCGTGTGGTGCGGGAT
          1 CACATTCTCTGGCTAAGATTGAGCTGGATAA-CGTGTGGAGCTAAATAATCGTGTGGTGCGGGAT

               
       2244 TAG
         65 TAG

                                                        *                    
       2247 CACATTCTCTGGCTAAGATTGAGCTGGATAA-GAT-T-GAGCTAGATAATCGTGTGGTGCGGGAT
          1 CACATTCTCTGGCTAAGATTGAGCTGGATAACG-TGTGGAGCTAAATAATCGTGTGGTGCGGGAT

               
       2309 TAG
         65 TAG

                                *                  
       2312 CACATTCTCTGGCTAAGATTAAGCTGGATAATCGTGTGG
          1 CACATTCTCTGGCTAAGATTGAGCTGGATAA-CGTGTGG

       2351 TGCGGGACTA


Statistics
Matches: 93,  Mismatches: 6, Indels: 10
        0.85            0.06        0.09

Matches are distributed among these distances:
  65   58  0.62
  66    3  0.03
  67    3  0.03
  68   29  0.31

ACGTcount: A:0.25, C:0.16, G:0.30, T:0.30


Consensus pattern (67 bp):   
CACATTCTCTGGCTAAGATTGAGCTGGATAACGTGTGGAGCTAAATAATCGTGTGGTGCGGGATT
AG

Found at i:2838 original size:64 final size:64

Alignment explanation


    Indices: 2759--2955  Score: 256
    Period size: 66  Copynumber: 3.0  Consensus size: 64

       2749 TTCTACCCAA

                    *                  *              *                      
       2759 CCCTAAATTTTTTAAAAACGGAAATT-TATTTTC-TTAATTATTAATAAGGAAAAAATTACTGAA
          1 CCCTAAA-ATTTTAAAAA-GGAAATTAAATTTTCGTTAATTACTAATAAGGAAAAAATTACTGAA

             
       2822 G
         64 G

                                                *                     *      
       2823 CCCTAAAATTCTTAAAAAGGAAATTAAATTTTCGTTGATTACGCTAATAAGGAAAAAAATACT-A
          1 CCCTAAAATT-TTAAAAAGGAAATTAAATTTTCGTTAATTA--CTAATAAGGAAAAAATTACTGA

              
       2887 AG
         63 AG

                                     *                                 *     
       2889 CCCTAAAACTTTTAAAAAGGAAATTCAATTTTCGTTAATTACTAATAAGGAAAAAATTATTGAAG
          1 CCCTAAAA-TTTTAAAAAGGAAATTAAATTTTCGTTAATTACTAATAAGGAAAAAATTACTGAAG

              
       2954 CC
          1 CC

       2956 ACCCTCTCAG


Statistics
Matches: 117,  Mismatches: 9, Indels: 13
        0.84            0.06        0.09

Matches are distributed among these distances:
  63    9  0.08
  64   38  0.32
  65   11  0.09
  66   39  0.33
  67   20  0.17

ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32


Consensus pattern (64 bp):   
CCCTAAAATTTTAAAAAGGAAATTAAATTTTCGTTAATTACTAATAAGGAAAAAATTACTGAAG

Done.