Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013869.1 Corchorus olitorius cultivar O-4 contig13902, 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: 45064
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:590 original size:17 final size:16

Alignment explanation


    Indices: 556--599  Score: 61
    Period size: 16  Copynumber: 2.7  Consensus size: 16

        546 CGGATTGATC

                 *          
        556 GGGTTCGGGTCATTTT
          1 GGGTTTGGGTCATTTT

                            
        572 GGGTTTGGGTCATTTT
          1 GGGTTTGGGTCATTTT

            *           
        588 TGGTTTCGGGTC
          1 GGGTTT-GGGTC

        600 GTTTGGATTC


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  16   20  0.80
  17    5  0.20

ACGTcount: A:0.05, C:0.11, G:0.39, T:0.45


Consensus pattern (16 bp):   
GGGTTTGGGTCATTTT

Found at i:6249 original size:15 final size:15

Alignment explanation


    Indices: 6229--6257  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       6219 CTTAGTTAGG

                           
       6229 ATTTTGTGGGGAATT
          1 ATTTTGTGGGGAATT

                          
       6244 ATTTTGTGGGGAAT
          1 ATTTTGTGGGGAAT

       6258 CATAAATTTT


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45


Consensus pattern (15 bp):   
ATTTTGTGGGGAATT

Found at i:6442 original size:20 final size:20

Alignment explanation


    Indices: 6417--6456  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       6407 ATTTAAAAAA

                                 
       6417 AATTTTGAT-TTTCCGTTTTT
          1 AATTTTG-TGTTTCCGTTTTT

                        *       
       6437 AATTTTGTGTTTGCGTTTTT
          1 AATTTTGTGTTTCCGTTTTT

       6457 GAAAAAAAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19    1  0.06
  20   17  0.94

ACGTcount: A:0.12, C:0.07, G:0.15, T:0.65


Consensus pattern (20 bp):   
AATTTTGTGTTTCCGTTTTT

Found at i:28356 original size:26 final size:26

Alignment explanation


    Indices: 28325--28414  Score: 92
    Period size: 26  Copynumber: 3.3  Consensus size: 26

      28315 GAATTGACTA

                                      
      28325 AAATGCCCCTGAATGTGCAAATGACC
          1 AAATGCCCCTGAATGTGCAAATGACC

                       *                
      28351 AAATGCCCCTGGATGTGCCAAAATGACC
          1 AAATGCCCCTGAATGTG-C-AAATGACC

                       * *   **         
      28379 AAAATG-CCCTTAGTGTAAAAATGACTC
          1 -AAATGCCCCTGAATGTGCAAATGAC-C

                     
      28406 AAATGCCCC
          1 AAATGCCCC

      28415 CTGGATGACT


Statistics
Matches: 53,  Mismatches: 6, Indels: 9
        0.78            0.09        0.13

Matches are distributed among these distances:
  26   28  0.53
  27    5  0.09
  28   15  0.28
  29    5  0.09

ACGTcount: A:0.36, C:0.27, G:0.18, T:0.20


Consensus pattern (26 bp):   
AAATGCCCCTGAATGTGCAAATGACC

Found at i:28388 original size:28 final size:27

Alignment explanation


    Indices: 28319--28387  Score: 95
    Period size: 26  Copynumber: 2.5  Consensus size: 27

      28309 GATTGAGAAT

                *                      
      28319 TGACTAAAATGCCCCTGAATGTGCAAA
          1 TGACCAAAATGCCCCTGAATGTGCAAA

                             *           
      28346 TGACC-AAATGCCCCTGGATGTGCCAAAA
          1 TGACCAAAATGCCCCTGAATGTG-C-AAA

                          
      28374 TGACCAAAATGCCC
          1 TGACCAAAATGCCC

      28388 TTAGTGTAAA


Statistics
Matches: 37,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
  26   16  0.43
  27    5  0.14
  28    8  0.22
  29    8  0.22

ACGTcount: A:0.35, C:0.28, G:0.19, T:0.19


Consensus pattern (27 bp):   
TGACCAAAATGCCCCTGAATGTGCAAA

Found at i:29698 original size:31 final size:33

Alignment explanation


    Indices: 29662--29724  Score: 87
    Period size: 31  Copynumber: 2.0  Consensus size: 33

      29652 CTAGAAAAAA

                                    *         
      29662 TTTTGGA-AGAAAATTG-CGATAAGA-AAGCAAT
          1 TTTTGGAGA-AAAATTGTCGATAAAAGAAGCAAT

                                            
      29693 TTTTGGAGAAAAATTGTCGATAAAAGAAGCAA
          1 TTTTGGAGAAAAATTGTCGATAAAAGAAGCAA

      29725 GCAAGTCGAC


Statistics
Matches: 28,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  31   14  0.50
  32    8  0.29
  33    6  0.21

ACGTcount: A:0.46, C:0.06, G:0.22, T:0.25


Consensus pattern (33 bp):   
TTTTGGAGAAAAATTGTCGATAAAAGAAGCAAT

Found at i:34219 original size:41 final size:42

Alignment explanation


    Indices: 34170--34249  Score: 144
    Period size: 41  Copynumber: 1.9  Consensus size: 42

      34160 AATCAAAATC

                                   *                  
      34170 AACAAAGTTCCAAATTTCCAACAGAATACTAAAC-AAAATGA
          1 AACAAAGTTCCAAATTTCCAACAAAATACTAAACTAAAATGA

                                                   
      34211 AACAAAGTTCCAAATTTCCAACAAAATACTAAACTAAAA
          1 AACAAAGTTCCAAATTTCCAACAAAATACTAAACTAAAA

      34250 CAAGAAATTA


Statistics
Matches: 37,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  41   33  0.89
  42    4  0.11

ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20


Consensus pattern (42 bp):   
AACAAAGTTCCAAATTTCCAACAAAATACTAAACTAAAATGA
Done.