Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013629.1 Corchorus olitorius cultivar O-4 contig13662, 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: 11741
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:152 original size:89 final size:89

Alignment explanation


    Indices: 1--184  Score: 341
    Period size: 89  Copynumber: 2.1  Consensus size: 89

                                                          *                  
          1 ATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTTGCTATAGAATGTATACCA
          1 ATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTCGCTATAGAATGTATACCA

                    *               
         66 ACAGCGGGTGGCGTTGGTATAGCC
         66 ACAGCGGGGGGCGTTGGTATAGCC

                                                                  *          
         90 ATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTCGCTATAGCATGTATACCA
          1 ATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTCGCTATAGAATGTATACCA

                                    
        155 ACAGCGGGGGGCGTTGGTATAGCC
         66 ACAGCGGGGGGCGTTGGTATAGCC

                  
        179 ATAAAC
          1 ATAAAC

        185 AGCCAACAGG


Statistics
Matches: 92,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  89   92  1.00

ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24


Consensus pattern (89 bp):   
ATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTCGCTATAGAATGTATACCA
ACAGCGGGGGGCGTTGGTATAGCC

Found at i:209 original size:89 final size:89

Alignment explanation


    Indices: 1--218  Score: 312
    Period size: 89  Copynumber: 2.4  Consensus size: 89

                         *        *                       *                  
          1 ATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTTGCTATAGAATGTATACCA
          1 ATAAACCAAAAAACAGTATGATGGGAGATATACCTACGGCTTCCGTCGCTATAGAATGTATACCA

                    *               
         66 ACAGCGGGTGGCGTTGGTATAGCC
         66 ACAGCGGGGGGCGTTGGTATAGCC

                         *        *                               *          
         90 ATAAACCAAAAAATAGTATGATTGGAGATATACCTACGGCTTCCGTCGCTATAGCATGTATACCA
          1 ATAAACCAAAAAACAGTATGATGGGAGATATACCTACGGCTTCCGTCGCTATAGAATGTATACCA

                                    
        155 ACAGCGGGGGGCGTTGGTATAGCC
         66 ACAGCGGGGGGCGTTGGTATAGCC

                    ***       *       *              
        179 ATAAA-CAGCCAACAGGTTTGATGGGGGATATACCTACGGC
          1 ATAAACCAAAAAACA-GTATGATGGGAGATATACCTACGGC

        219 GAAGAAACTA


Statistics
Matches: 118,  Mismatches: 10, Indels: 2
        0.91            0.08        0.02

Matches are distributed among these distances:
  88    5  0.04
  89  113  0.96

ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24


Consensus pattern (89 bp):   
ATAAACCAAAAAACAGTATGATGGGAGATATACCTACGGCTTCCGTCGCTATAGAATGTATACCA
ACAGCGGGGGGCGTTGGTATAGCC

Found at i:3066 original size:13 final size:13

Alignment explanation


    Indices: 3050--3076  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       3040 ATCATATATA

                         
       3050 ATTTCATTAATGT
          1 ATTTCATTAATGT

                         
       3063 ATTTCATTAATGT
          1 ATTTCATTAATGT

             
       3076 A
          1 A

       3077 CGGAATTATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52


Consensus pattern (13 bp):   
ATTTCATTAATGT

Found at i:5772 original size:49 final size:49

Alignment explanation


    Indices: 5716--5818  Score: 197
    Period size: 49  Copynumber: 2.1  Consensus size: 49

       5706 CCCTTTTGAG

                                                      *      
       5716 TCAAACTAATCTTACCTTTGACCTTTAATTATAGAAAAGATATATGCAA
          1 TCAAACTAATCTTACCTTTGACCTTTAATTATAGAAAAGATAAATGCAA

                                                             
       5765 TCAAACTAATCTTACCTTTGACCTTTAATTATAGAAAAGATAAATGCAA
          1 TCAAACTAATCTTACCTTTGACCTTTAATTATAGAAAAGATAAATGCAA

                 
       5814 TCAAA
          1 TCAAA

       5819 TTCTTGAAAA


Statistics
Matches: 53,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  49   53  1.00

ACGTcount: A:0.43, C:0.17, G:0.08, T:0.33


Consensus pattern (49 bp):   
TCAAACTAATCTTACCTTTGACCTTTAATTATAGAAAAGATAAATGCAA

Found at i:6860 original size:27 final size:27

Alignment explanation


    Indices: 6821--6872  Score: 86
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       6811 GTCTTGTGCA

                          *            
       6821 ACTTCTTTACCACAGTGAGGACAATGC
          1 ACTTCTTTACCACAATGAGGACAATGC

                    *                
       6848 ACTTCTTTTCCACAATGAGGACAAT
          1 ACTTCTTTACCACAATGAGGACAAT

       6873 CCACCAACCT


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

Matches are distributed among these distances:
  27   23  1.00

ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29


Consensus pattern (27 bp):   
ACTTCTTTACCACAATGAGGACAATGC

Found at i:11249 original size:2 final size:2

Alignment explanation


    Indices: 11244--11273  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      11234 TCTCTCTCTC

                                        *               
      11244 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      11274 CTAGTAATTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Done.