Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022688.1 Corchorus olitorius cultivar O-4 contig22721, 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: 21695
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33


Found at i:718 original size:20 final size:20

Alignment explanation


    Indices: 693--730  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        683 CCCACTTACC

                                
        693 CTTTCAAAGTTCCCAATACT
          1 CTTTCAAAGTTCCCAATACT

                       *      
        713 CTTTCAAAGTTTCCAATA
          1 CTTTCAAAGTTCCCAATA

        731 GCAAATATTC


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

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37


Consensus pattern (20 bp):   
CTTTCAAAGTTCCCAATACT

Found at i:3286 original size:20 final size:20

Alignment explanation


    Indices: 3261--3298  Score: 76
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3251 CCCACTTACC

                                
       3261 CTTTCAAAGTTCCCAATACT
          1 CTTTCAAAGTTCCCAATACT

                              
       3281 CTTTCAAAGTTCCCAATA
          1 CTTTCAAAGTTCCCAATA

       3299 GCAAATATTC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34


Consensus pattern (20 bp):   
CTTTCAAAGTTCCCAATACT

Found at i:9662 original size:18 final size:18

Alignment explanation


    Indices: 9618--9664  Score: 60
    Period size: 18  Copynumber: 2.7  Consensus size: 18

       9608 TGTAAACTCA

                             *
       9618 AAAC-AAACTGACTCAAT
          1 AAACTAAACTGACTCAAC

               * *            
       9635 AAAGTGAACTGACTCAAC
          1 AAACTAAACTGACTCAAC

                        
       9653 AAACTAAACTGA
          1 AAACTAAACTGA

       9665 TTTAAACATT


Statistics
Matches: 24,  Mismatches: 5, Indels: 1
        0.80            0.17        0.03

Matches are distributed among these distances:
  17    3  0.12
  18   21  0.88

ACGTcount: A:0.51, C:0.21, G:0.11, T:0.17


Consensus pattern (18 bp):   
AAACTAAACTGACTCAAC

Found at i:15135 original size:2 final size:2

Alignment explanation


    Indices: 15128--15156  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      15118 ATTATGTATT

                                                       
      15128 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      15157 TCTAAAGAAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:20305 original size:30 final size:28

Alignment explanation


    Indices: 20262--20323  Score: 106
    Period size: 30  Copynumber: 2.1  Consensus size: 28

      20252 AACTAAAGAG

                                        
      20262 ATTTGTTTGTGAGTTTTATTTGTAATTT
          1 ATTTGTTTGTGAGTTTTATTTGTAATTT

                                          
      20290 ATTTGTTTGTGTGAGTTTTATTTGTAATTT
          1 ATTTG-TT-TGTGAGTTTTATTTGTAATTT

                
      20320 ATTT
          1 ATTT

      20324 TTTCCTATTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  28    5  0.16
  29    2  0.06
  30   25  0.78

ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65


Consensus pattern (28 bp):   
ATTTGTTTGTGAGTTTTATTTGTAATTT

Found at i:21374 original size:18 final size:18

Alignment explanation


    Indices: 21353--21413  Score: 54
    Period size: 18  Copynumber: 3.2  Consensus size: 18

      21343 ATATAATAAC

                              
      21353 TAAAATACTTACATTAAT
          1 TAAAATACTTACATTAAT

                                   
      21371 TAAATTTAATACTATA-A-TAAT
          1 T-AA---AATACT-TACATTAAT

             *                
      21392 TGAAATACTTACATTAAT
          1 TAAAATACTTACATTAAT

                
      21410 TAAA
          1 TAAA

      21414 TTCTTAGGTA


Statistics
Matches: 34,  Mismatches: 2, Indels: 14
        0.68            0.04        0.28

Matches are distributed among these distances:
  16    2  0.06
  17    7  0.21
  18    8  0.24
  19    2  0.06
  20    1  0.03
  21    5  0.15
  22    7  0.21
  23    2  0.06

ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39


Consensus pattern (18 bp):   
TAAAATACTTACATTAAT

Found at i:21414 original size:17 final size:17

Alignment explanation


    Indices: 21355--21419  Score: 51
    Period size: 17  Copynumber: 3.5  Consensus size: 17

      21345 ATAATAACTA

                             
      21355 AAATACTTACATTAATT
          1 AAATACTTACATTAATT

                    *             
      21372 AAATTTA-ATACTATAATAATT
          1 AAA--TACTTAC-AT--TAATT

                              
      21393 GAAATACTTACATTAATT
          1 -AAATACTTACATTAATT

                *    
      21411 AAATTCTTA
          1 AAATACTTA

      21420 GGTATTTTTT


Statistics
Matches: 38,  Mismatches: 3, Indels: 14
        0.69            0.05        0.25

Matches are distributed among these distances:
  17   11  0.29
  18    8  0.21
  19    4  0.11
  20    4  0.11
  21    8  0.21
  22    3  0.08

ACGTcount: A:0.48, C:0.09, G:0.02, T:0.42


Consensus pattern (17 bp):   
AAATACTTACATTAATT
Done.