Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012397.1 Corchorus olitorius cultivar O-4 contig12430, 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: 14498
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37


Found at i:75 original size:29 final size:29

Alignment explanation


    Indices: 2--68  Score: 91
    Period size: 29  Copynumber: 2.3  Consensus size: 29

          1 A

                 *      *                
          2 GTCATTTTTGCACATCCAAGGGCATTATG
          1 GTCATCTTTGCATATCCAAGGGCATTATG

                              *       *  
         31 GTCATCTTTGCATATCCAGGGGCATTTTG
          1 GTCATCTTTGCATATCCAAGGGCATTATG

                      
         60 GTCAT-TTTG
          1 GTCATCTTTG

         69 GTTTATCTTA


Statistics
Matches: 34,  Mismatches: 4, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  28    4  0.12
  29   30  0.88

ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39


Consensus pattern (29 bp):   
GTCATCTTTGCATATCCAAGGGCATTATG

Found at i:1062 original size:17 final size:17

Alignment explanation


    Indices: 1040--1072  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       1030 AAACTCAGAA

                             
       1040 AGCAGAATTCTAAATGC
          1 AGCAGAATTCTAAATGC

                  *         
       1057 AGCAGAGTTCTAAATG
          1 AGCAGAATTCTAAATG

       1073 GCAAGGCAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24


Consensus pattern (17 bp):   
AGCAGAATTCTAAATGC

Found at i:6715 original size:22 final size:22

Alignment explanation


    Indices: 6689--6742  Score: 81
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       6679 AGTTTTCTTT

                            *     
       6689 TGGTAACCTTGAATAAGAAGAA
          1 TGGTAACCTTGAATAAAAAGAA

                                **
       6711 TGGTAACCTTGAATAAAAAGGT
          1 TGGTAACCTTGAATAAAAAGAA

                      
       6733 TGGTAACCTT
          1 TGGTAACCTT

       6743 CTTCATTTAT


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  22   29  1.00

ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28


Consensus pattern (22 bp):   
TGGTAACCTTGAATAAAAAGAA

Found at i:6843 original size:85 final size:86

Alignment explanation


    Indices: 6749--6923  Score: 334
    Period size: 85  Copynumber: 2.0  Consensus size: 86

       6739 CCTTCTTCAT

                                                                             
       6749 TTATTTTTTTGGTGGAAATAACCTTTTTCATTTAGATGAAAGCTTACAAAAC-TTTTTTTTTTTG
          1 TTATTTTTTTGGTGGAAATAACCTTTTTCATTTAGATGAAAGCTTACAAAACTTTTTTTTTTTTG

                                 
       6813 CTTCTAAGCTTACAAAACTTA
         66 CTTCTAAGCTTACAAAACTTA

                                                                             
       6834 TTATTTTTTTGGTGGAAATAACCTTTTTCATTTAGATGAAAGCTTACAAAACTTTTTTTTTTTTT
          1 TTATTTTTTTGGTGGAAATAACCTTTTTCATTTAGATGAAAGCTTACAAAAC-TTTTTTTTTTTT

                                  
       6899 GCTTCTAAGCTTACAAAACTTA
         65 GCTTCTAAGCTTACAAAACTTA

               
       6921 TTA
          1 TTA

       6924 AGCATGTAAA


Statistics
Matches: 88,  Mismatches: 0, Indels: 2
        0.98            0.00        0.02

Matches are distributed among these distances:
  85   52  0.59
  87   36  0.41

ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48


Consensus pattern (86 bp):   
TTATTTTTTTGGTGGAAATAACCTTTTTCATTTAGATGAAAGCTTACAAAACTTTTTTTTTTTTG
CTTCTAAGCTTACAAAACTTA

Found at i:10445 original size:4 final size:4

Alignment explanation


    Indices: 10436--10474  Score: 69
    Period size: 4  Copynumber: 9.8  Consensus size: 4

      10426 CATTTTACTT

                                        *                   
      10436 TTTC TTTC TTTC TTTC TTTC TTTT TTTC TTTC TTTC TTT
          1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT

      10475 TTTTTTTTTT


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   4   33  1.00

ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79


Consensus pattern (4 bp):   
TTTC

Found at i:10483 original size:8 final size:8

Alignment explanation


    Indices: 10434--10485  Score: 70
    Period size: 8  Copynumber: 6.6  Consensus size: 8

      10424 ATCATTTTAC

                    
      10434 TTTTTCTT
          1 TTTTTCTT

             *      
      10442 TCTTTCTT
          1 TTTTTCTT

             *      
      10450 TCTTTCTT
          1 TTTTTCTT

                    
      10458 TTTTTCTT
          1 TTTTTCTT

             *      
      10466 TCTTTCTT
          1 TTTTTCTT

                    
      10474 TTTTT-TT
          1 TTTTTCTT

                 
      10481 TTTTT
          1 TTTTT

      10486 GACAATTTTT


Statistics
Matches: 40,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
   7    7  0.17
   8   33  0.82

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (8 bp):   
TTTTTCTT
Done.