Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010297.1 Corchorus olitorius cultivar O-4 contig10329, 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: 4070
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:895 original size:17 final size:17

Alignment explanation


    Indices: 873--908  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        863 ATACAAAGAG

                             
        873 CTATCTAGTATAACAAA
          1 CTATCTAGTATAACAAA

                  *  *       
        890 CTATCTGGTGTAACAAA
          1 CTATCTAGTATAACAAA

              
        907 CT
          1 CT

        909 TTACAAATCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31


Consensus pattern (17 bp):   
CTATCTAGTATAACAAA

Found at i:2315 original size:22 final size:22

Alignment explanation


    Indices: 2290--2366  Score: 93
    Period size: 22  Copynumber: 3.5  Consensus size: 22

       2280 TATTTTTGTG

                                 *
       2290 AAATTTTGATAATCACCCTATT
          1 AAATTTTGATAATCACCCTATA

                        *    *    
       2312 AAATTTTGATAACCACCATATA
          1 AAATTTTGATAATCACCCTATA

                   *     *        
       2334 AAATTTTAATAATTA-CCTATA
          1 AAATTTTGATAATCACCCTATA

                 *      
       2355 AAATTGTGATAA
          1 AAATTTTGATAA

       2367 ACTCCATAAG


Statistics
Matches: 46,  Mismatches: 9, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  21   15  0.33
  22   31  0.67

ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38


Consensus pattern (22 bp):   
AAATTTTGATAATCACCCTATA

Found at i:2374 original size:43 final size:44

Alignment explanation


    Indices: 2290--2374  Score: 109
    Period size: 43  Copynumber: 2.0  Consensus size: 44

       2280 TATTTTTGTG

                   *             *     *      *         
       2290 AAATTTTGATAATCACCCTATTAAATTTTGATAACCACCATATA
          1 AAATTTTAATAATCACCCTATAAAATTGTGATAAACACCATATA

                         *                      *     
       2334 AAATTTTAATAATTA-CCTATAAAATTGTGATAAACTCCATA
          1 AAATTTTAATAATCACCCTATAAAATTGTGATAAACACCATA

       2375 AGAAACTAAC


Statistics
Matches: 35,  Mismatches: 6, Indels: 1
        0.83            0.14        0.02

Matches are distributed among these distances:
  43   22  0.63
  44   13  0.37

ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36


Consensus pattern (44 bp):   
AAATTTTAATAATCACCCTATAAAATTGTGATAAACACCATATA

Found at i:2459 original size:21 final size:22

Alignment explanation


    Indices: 2390--2474  Score: 61
    Period size: 22  Copynumber: 4.0  Consensus size: 22

       2380 CTAACCTAAA

                  *     *    *  * 
       2390 CTATGAAATTTTAATAAACTTT
          1 CTATGAGATTTTGATAATCTCT

                              *    
       2412 CATATGA-ATTTTG-TAACCT-T
          1 C-TATGAGATTTTGATAATCTCT

                    *              
       2432 CTTATGA-TTTTTGATAATCTCT
          1 C-TATGAGATTTTGATAATCTCT

                         *       
       2454 CTATGAGATTTTGTTAATCTC
          1 CTATGAGATTTTGATAATCTC

       2475 CCTACAATTT


Statistics
Matches: 52,  Mismatches: 7, Indels: 8
        0.78            0.10        0.12

Matches are distributed among these distances:
  20   12  0.23
  21   15  0.29
  22   20  0.38
  23    5  0.10

ACGTcount: A:0.29, C:0.13, G:0.09, T:0.48


Consensus pattern (22 bp):   
CTATGAGATTTTGATAATCTCT
Done.