Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023308.1 Corchorus olitorius cultivar O-4 contig23341, 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: 3091
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30


Found at i:2062 original size:16 final size:16

Alignment explanation


    Indices: 2041--2071  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       2031 ACAATTCAGA

                            
       2041 AAGCAGAAAAGCTCTC
          1 AAGCAGAAAAGCTCTC

                           
       2057 AAGCAGAAAAGCTCT
          1 AAGCAGAAAAGCTCT

       2072 GAAGTATTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13


Consensus pattern (16 bp):   
AAGCAGAAAAGCTCTC

Found at i:2228 original size:41 final size:41

Alignment explanation


    Indices: 2171--2385  Score: 277
    Period size: 41  Copynumber: 5.2  Consensus size: 41

       2161 TTTTCGTTTG

                                                     
       2171 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
          1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA

                                                     
       2212 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
          1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA

                                                     
       2253 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
          1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA

                   ***      *              *   *        
       2294 TTCAAGAACAAGTCATTGAGACCCTTGAATCGAGTTATTATCAA
          1 TTCAAGATTGAGTCATCGAGACCCTTGAAT-TA--AATTATCAA

                 * ***    *  *              *   *    
       2338 TTCAAAACCAAGTCGTCAAGACCCTTGAATTAGATTGTCAA
          1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA

                   
       2379 TTCAAGA
          1 TTCAAGA

       2386 CCAAGTCATT


Statistics
Matches: 156,  Mismatches: 15, Indels: 6
        0.88            0.08        0.03

Matches are distributed among these distances:
  41  121  0.78
  42    1  0.01
  43    1  0.01
  44   33  0.21

ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30


Consensus pattern (41 bp):   
TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA

Found at i:2308 original size:82 final size:82

Alignment explanation


    Indices: 2171--2412  Score: 299
    Period size: 82  Copynumber: 2.9  Consensus size: 82

       2161 TTTTCGTTTG

                                                            ***              
       2171 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCATCGAGACCC
          1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGAACAAGTCATCGAGACCC

                  *          
       2236 TTGAATTAAATTATCAA
         66 TTGAATCAAATTATCAA

                                                                     *       
       2253 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGAACAAGTCATTGAGACCC
          1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGAACAAGTCATCGAGACCC

                       *        
       2318 TTGAATCGAGTTATTATCAA
         66 TTGAATC-A--AATTATCAA

                 * ***    *  *              *   *           *                
       2338 TTCAAAACCAAGTCGTCAAGACCCTTGAATTAGATTGTCAATTCAAGACCAAGTCATTC--GACC
          1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGAACAAGTCA-TCGAGACC

                        
       2401 CTTGAATCAAAT
         65 CTTGAATCAAAT

       2413 CAAATCAAAC


Statistics
Matches: 139,  Mismatches: 17, Indels: 9
        0.84            0.10        0.05

Matches are distributed among these distances:
  81    2  0.01
  82   67  0.48
  83    2  0.01
  84   12  0.09
  85   55  0.40
  86    1  0.01

ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30


Consensus pattern (82 bp):   
TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGAACAAGTCATCGAGACCC
TTGAATCAAATTATCAA

Found at i:2391 original size:41 final size:41

Alignment explanation


    Indices: 2181--2412  Score: 270
    Period size: 41  Copynumber: 5.6  Consensus size: 41

       2171 TTCAAGATTG

                                                  ***
       2181 AGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGATTG
          1 AGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGACCA

                                                  ***
       2222 AGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGATTG
          1 AGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGACCA

                                                  *  
       2263 AGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGAACA
          1 AGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGACCA

                  *              *   *             *    
       2304 AGTCATTGAGACCCTTGAATCGAGTTATTATCAATTCAAAACCA
          1 AGTCATCGAGACCCTTGAAT-TA--AATTATCAATTCAAGACCA

                *  *              *   *              
       2348 AGTCGTCAAGACCCTTGAATTAGATTGTCAATTCAAGACCA
          1 AGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGACCA

                                 *    
       2389 AGTCATTC--GACCCTTGAATCAAAT
          1 AGTCA-TCGAGACCCTTGAATTAAAT

       2413 CAAATCAAAC


Statistics
Matches: 169,  Mismatches: 18, Indels: 9
        0.86            0.09        0.05

Matches are distributed among these distances:
  40   14  0.08
  41  118  0.70
  42    3  0.02
  43    1  0.01
  44   33  0.20

ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29


Consensus pattern (41 bp):   
AGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGACCA
Done.