Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016131.1 Corchorus olitorius cultivar O-4 contig16164, 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: 10715
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:4438 original size:38 final size:37

Alignment explanation


    Indices: 4321--4456  Score: 129
    Period size: 37  Copynumber: 3.7  Consensus size: 37

       4311 ACTAAAACCT

                      *           *             *  
       4321 GATGGGAACTCTCCCTAA--TTAAAAACTTTGAAAACTG
          1 GATGGGAACTTTCCC-AATTTTGAAAA-TTTGAAAATTG

            *                         *  *        
       4358 AATGGGAACTTTCCCAA-TTTGAAAACTTAAAAATTTG
          1 GATGGGAACTTTCCCAATTTTGAAAATTTGAAAA-TTG

                       *              *           
       4395 G-TGGGAACTTCCCCAATTTTGACAATTTTGAAAATTG
          1 GATGGGAACTTTCCCAATTTTGA-AAATTTGAAAATTG

                                      
       4432 GATGGGAACTTTCCCAA-TTTGAAAA
          1 GATGGGAACTTTCCCAATTTTGAAAA

       4457 CTGGCTAAAT


Statistics
Matches: 81,  Mismatches: 13, Indels: 11
        0.77            0.12        0.10

Matches are distributed among these distances:
  36   24  0.30
  37   35  0.43
  38   22  0.27

ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31


Consensus pattern (37 bp):   
GATGGGAACTTTCCCAATTTTGAAAATTTGAAAATTG

Found at i:4584 original size:53 final size:53

Alignment explanation


    Indices: 4421--4585  Score: 138
    Period size: 52  Copynumber: 3.1  Consensus size: 53

       4411 TTTTGACAAT

                    * *                    *    **                
       4421 TTTGAAAATTGGATGGGAACTTTCCCAATTTGAAAACTG-GCTAAATCGAATAC
          1 TTTGAAAAATAGATGGGAACTTTCCCAA-TTAAAAAAAGAGCTAAATCGAATAC

                                          **           *  *  *   *
       4474 TTT-AAAAATAGATGGGAACTTTCCCAATTTGAAAAAGAGCTAGATGGAGTATT
          1 TTTGAAAAATAGATGGGAACTTTCCCAATTAAAAAAAGAGCTAAATCGAATA-C

                    *                * *           *       *      
       4527 TTTGAAAACT-GATGGGAACTTTCCGACTTAAAAAAAAGTGCTAAATTGAATAC
          1 TTTGAAAAATAGATGGGAACTTTCCCAATT-AAAAAAAGAGCTAAATCGAATAC

                  
       4580 TTTGAA
          1 TTTGAA

       4586 GTTTTTGAGT


Statistics
Matches: 88,  Mismatches: 20, Indels: 8
        0.76            0.17        0.07

Matches are distributed among these distances:
  51    6  0.07
  52   32  0.36
  53   29  0.33
  54   21  0.24

ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30


Consensus pattern (53 bp):   
TTTGAAAAATAGATGGGAACTTTCCCAATTAAAAAAAGAGCTAAATCGAATAC

Found at i:5323 original size:23 final size:23

Alignment explanation


    Indices: 5284--5348  Score: 85
    Period size: 23  Copynumber: 2.8  Consensus size: 23

       5274 GGAACTAAAT

                  *                 
       5284 CCAAAGTATAAACTAAAATATAAG
          1 CCAAAGCAT-AACTAAAATATAAG

              *               *    
       5308 CCCAAGCATAACTAAAATTTAAG
          1 CCAAAGCATAACTAAAATATAAG

                  *           
       5331 CCAAAGTATAACTAAAAT
          1 CCAAAGCATAACTAAAAT

       5349 CCAAAACCCA


Statistics
Matches: 36,  Mismatches: 5, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  23   29  0.81
  24    7  0.19

ACGTcount: A:0.54, C:0.17, G:0.08, T:0.22


Consensus pattern (23 bp):   
CCAAAGCATAACTAAAATATAAG

Found at i:10406 original size:40 final size:40

Alignment explanation


    Indices: 10351--10430  Score: 142
    Period size: 40  Copynumber: 2.0  Consensus size: 40

      10341 GAGAGGTTAC

                                            *       
      10351 AATTCTAGATAATTAAGGGGGATAGGATTTATTATAACAT
          1 AATTCTAGATAATTAAGGGGGATAGGATTTATCATAACAT

                                   *                
      10391 AATTCTAGATAATTAAGGGGGATTGGATTTATCATAACAT
          1 AATTCTAGATAATTAAGGGGGATAGGATTTATCATAACAT

      10431 TTATGTGAAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  40   38  1.00

ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35


Consensus pattern (40 bp):   
AATTCTAGATAATTAAGGGGGATAGGATTTATCATAACAT

Found at i:10638 original size:2 final size:2

Alignment explanation


    Indices: 10631--10669  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      10621 TACTATTTAG

                                                                      
      10631 TA TA TA TA TA 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 TA TA TA TA TA T

      10670 TACTCATAAG


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.