Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011984.1 Corchorus olitorius cultivar O-4 contig12017, 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: 27408
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:11336 original size:19 final size:18

Alignment explanation


    Indices: 11312--11347  Score: 63
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      11302 TGAAGATTTA

                               
      11312 TTGAAGATAATTTGAAGAG
          1 TTGAAGATAA-TTGAAGAG

                             
      11331 TTGAAGATAATTGAAGA
          1 TTGAAGATAATTGAAGA

      11348 ATTATATCAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  18    7  0.41
  19   10  0.59

ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAG

Found at i:15857 original size:24 final size:24

Alignment explanation


    Indices: 15830--15878  Score: 98
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      15820 GCACCAAACT

                                    
      15830 TCAAGTGGTATAGAAAGCAAATTC
          1 TCAAGTGGTATAGAAAGCAAATTC

                                    
      15854 TCAAGTGGTATAGAAAGCAAATTC
          1 TCAAGTGGTATAGAAAGCAAATTC

             
      15878 T
          1 T

      15879 TTAAGGTAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27


Consensus pattern (24 bp):   
TCAAGTGGTATAGAAAGCAAATTC

Found at i:16154 original size:31 final size:31

Alignment explanation


    Indices: 16087--16162  Score: 89
    Period size: 31  Copynumber: 2.4  Consensus size: 31

      16077 TCCTTGATCA

                          *     *     *    
      16087 TTTTTATTTTATACGATTTAGTCCTCTAAAT
          1 TTTTTATTTTATACAATTTAATCCTCCAAAT

            *                           ** 
      16118 ATTTTATTTTATACAATTTAATCCTCCACTT
          1 TTTTTATTTTATACAATTTAATCCTCCAAAT

                          
      16149 TTTTTATATTTATA
          1 TTTTTAT-TTTATA

      16163 ATTTTCTTTT


Statistics
Matches: 37,  Mismatches: 7, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  31   31  0.84
  32    6  0.16

ACGTcount: A:0.28, C:0.13, G:0.03, T:0.57


Consensus pattern (31 bp):   
TTTTTATTTTATACAATTTAATCCTCCAAAT

Found at i:18471 original size:13 final size:15

Alignment explanation


    Indices: 18438--18475  Score: 53
    Period size: 13  Copynumber: 2.7  Consensus size: 15

      18428 TATTATTATT

                           
      18438 ATATAATATATAAGA
          1 ATATAATATATAAGA

                        *  
      18453 ATATAATA-ATACG-
          1 ATATAATATATAAGA

                      
      18466 ATATAATATA
          1 ATATAATATA

      18476 ATAATTTTGT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  13    8  0.38
  14    5  0.24
  15    8  0.38

ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34


Consensus pattern (15 bp):   
ATATAATATATAAGA

Found at i:19525 original size:113 final size:112

Alignment explanation


    Indices: 19368--19690  Score: 366
    Period size: 113  Copynumber: 2.9  Consensus size: 112

      19358 ATAACGGCGT

                            *     *         *                         *      
      19368 TAAATGGGGGC-ATTTAAGGTTAAAAACGTCGTCAAATTTAATTTTTTCCCGGGAAATACAAATT
          1 TAAATGGGGGCGA-TTGAGGTTGAAAACGTCGACAAATTTAATTTTTT-CCGGGAAATGCAAATT

                                     *          *            
      19432 GGGTAAAAATGAGACTAAAATATAGAGGCGTTTCTATCCAAAACGCCAC
         64 GGGTAAAAATGAGACTAAAATATAGCGGCGTTTCTAGCCAAAACGCCAC

                                          *   *               **             
      19481 TAAATGGGGGCGATTGAGGTTGAAAACGTCAACATATTTAATTTTTTTCCAAGAAATGCAAATTG
          1 TAAATGGGGGCGATTGAGGTTGAAAACGTCGACAAATTTAA-TTTTTTCCGGGAAATGCAAATTG

                            *                 **           * 
      19546 GGTAAAAATGAAGACTCAAATATAGCGGCGTTT-GGGCCAAAACGCCGC
         65 GGTAAAAATG-AGACTAAAATATAGCGGCGTTTCTAGCCAAAACGCCAC

                                   *    **  * **                *     *      
      19594 TAAATGGGGGCG-TCTGAGGTTGTAAACACCGCCGCATTTAATTTTTTCCGGAAAATGTAAA-TG
          1 TAAATGGGGGCGAT-TGAGGTTGAAAACGTCGACAAATTTAATTTTTTCCGGGAAATGCAAATTG

                     *                        
      19657 GGTAAAAATTAGACTAAAATATAGCGGCGTTTCT
         65 GGTAAAAATGAGACTAAAATATAGCGGCGTTTCT

      19691 GGCTTAAACG


Statistics
Matches: 177,  Mismatches: 28, Indels: 12
        0.82            0.13        0.06

Matches are distributed among these distances:
 110   21  0.12
 111   11  0.06
 112   17  0.10
 113  101  0.57
 114   27  0.15

ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28


Consensus pattern (112 bp):   
TAAATGGGGGCGATTGAGGTTGAAAACGTCGACAAATTTAATTTTTTCCGGGAAATGCAAATTGG
GTAAAAATGAGACTAAAATATAGCGGCGTTTCTAGCCAAAACGCCAC
Done.