Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018024.1 Corchorus olitorius cultivar O-4 contig18057, 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: 1745
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28


Found at i:1425 original size:66 final size:66

Alignment explanation


    Indices: 1313--1740  Score: 586
    Period size: 66  Copynumber: 6.5  Consensus size: 66

       1303 GATTTCGAAG

                                       *       *                             
       1313 TTCCAGACCTCAGACAGGTCTTTCTCAGTTCAATTCCGACCTCAGACAGGTCTTTCTCAGCTTTT
          1 TTCC-GACCTCAGACAGGTCTTTCTCATTTCAATTTCGACCTCAGACAGGTCTTTCTCAGCTTTT

              
       1378 AA
         65 AA

               *                   *                                         
       1380 TTTTCGACCTCAGACAGGTCTTTAT-ATTTCAATTTCGACCTCAGACAGGTCTTTCTCAGCTTTT
          1 -TTCCGACCTCAGACAGGTCTTTCTCATTTCAATTTCGACCTCAGACAGGTCTTTCTCAGCTTTT

              
       1444 AA
         65 AA

                                           *    *                            
       1446 TTCCGACCTCAGACAGGTCTTTCTCAGCTTTTAATTCCGACCTCAGACAGGTCTTTCTCAG-TTT
          1 TTCCGACCTCAGACAGGTCTTTCTCA--TTTCAATTTCGACCTCAGACAGGTCTTTCTCAGCTTT

             * 
       1510 TTA
         64 TAA

                                           *                            *    
       1513 TTCCGACCTCAGACAGGTCTTTCTCAGTTT-TATTTCGACCTCAGACAGGTCTTTCTCAGTTTTT
          1 TTCCGACCTCAGACAGGTCTTTCTCA-TTTCAATTTCGACCTCAGACAGGTCTTTCTCAGCTTTT

              
       1577 AA
         65 AA

                                    *    *                        *        * 
       1579 TTCCGACCTCAGACAGGTCTTTCTTATTTTAATTTCGACCTCAGACAGGTCTTTAT-A--TTTCA
          1 TTCCGACCTCAGACAGGTCTTTCTCATTTCAATTTCGACCTCAGACAGGTCTTTCTCAGCTTTTA

             
       1641 A
         66 A

                                 *         *                                 
       1642 TTCCGACCTCAGACAGGTCTTCCTCAGTTT-TATTTCGACCTCAGACAGGTCTTTCTCAGCTTTT
          1 TTCCGACCTCAGACAGGTCTTTCTCA-TTTCAATTTCGACCTCAGACAGGTCTTTCTCAGCTTTT

              
       1706 AA
         65 AA

                                   *           
       1708 -TCTCGACCTCAGACAGGTCTTTAT-ATTTCAATT
          1 TTC-CGACCTCAGACAGGTCTTTCTCATTTCAATT

       1741 CCAAC


Statistics
Matches: 324,  Mismatches: 25, Indels: 25
        0.87            0.07        0.07

Matches are distributed among these distances:
  63   53  0.16
  64    7  0.02
  65   59  0.18
  66  121  0.37
  67   50  0.15
  68   34  0.10

ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38


Consensus pattern (66 bp):   
TTCCGACCTCAGACAGGTCTTTCTCATTTCAATTTCGACCTCAGACAGGTCTTTCTCAGCTTTTA
A

Found at i:1458 original size:34 final size:33

Alignment explanation


    Indices: 1313--1729  Score: 582
    Period size: 34  Copynumber: 12.7  Consensus size: 33

       1303 GATTTCGAAG

                                           *  
       1313 TTCCAGACCTCAGACAGGTCTTTCTCAG-TTCAA
          1 TTCC-GACCTCAGACAGGTCTTTCTCAGTTTTAA

                                              
       1346 TTCCGACCTCAGACAGGTCTTTCTCAGCTTTTAA
          1 TTCCGACCTCAGACAGGTCTTTCTCAG-TTTTAA

               *                   *       *  
       1380 TTTTCGACCTCAGACAGGTCTTTAT-A-TTTCAA
          1 -TTCCGACCTCAGACAGGTCTTTCTCAGTTTTAA

              *                               
       1412 TTTCGACCTCAGACAGGTCTTTCTCAGCTTTTAA
          1 TTCCGACCTCAGACAGGTCTTTCTCAG-TTTTAA

                                              
       1446 TTCCGACCTCAGACAGGTCTTTCTCAGCTTTTAA
          1 TTCCGACCTCAGACAGGTCTTTCTCAG-TTTTAA

                                           * 
       1480 TTCCGACCTCAGACAGGTCTTTCTCAGTTTTTA
          1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTTAA

                                             
       1513 TTCCGACCTCAGACAGGTCTTTCTCAGTTTT-A
          1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTTAA

              *                               
       1545 TTTCGACCTCAGACAGGTCTTTCTCAGTTTTTAA
          1 TTCCGACCTCAGACAGGTCTTTCTCAG-TTTTAA

                                    *        
       1579 TTCCGACCTCAGACAGGTCTTTCTTA-TTTTAA
          1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTTAA

              *                   *       *  
       1611 TTTCGACCTCAGACAGGTCTTTAT-A-TTTCAA
          1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTTAA

                                 *           
       1642 TTCCGACCTCAGACAGGTCTTCCTCAGTTTT-A
          1 TTCCGACCTCAGACAGGTCTTTCTCAGTTTTAA

              *                               
       1674 TTTCGACCTCAGACAGGTCTTTCTCAGCTTTTAA
          1 TTCCGACCTCAGACAGGTCTTTCTCAG-TTTTAA

                                   
       1708 -TCTCGACCTCAGACAGGTCTTT
          1 TTC-CGACCTCAGACAGGTCTTT

       1730 ATATTTCAAT


Statistics
Matches: 350,  Mismatches: 21, Indels: 25
        0.88            0.05        0.06

Matches are distributed among these distances:
  31   50  0.14
  32  111  0.32
  33   52  0.15
  34  115  0.33
  35   22  0.06

ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37


Consensus pattern (33 bp):   
TTCCGACCTCAGACAGGTCTTTCTCAGTTTTAA
Done.