Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022650.1 Corchorus olitorius cultivar O-4 contig22683, 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: 14721
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:4239 original size:29 final size:28

Alignment explanation


    Indices: 4173--4237  Score: 78
    Period size: 29  Copynumber: 2.3  Consensus size: 28

       4163 TATCATTAGG

                                        
       4173 AAATTAAAA-CCTAAATAAAATAGGAAA
          1 AAATTAAAATCCTAAATAAAATAGGAAA

                  *         *    *       
       4200 AAATTTCAAATCCTAATTAAATTAGGAAA
          1 AAA-TTAAAATCCTAAATAAAATAGGAAA

            *        
       4229 TAATTAAAA
          1 AAATTAAAA

       4238 ATAGCAAAGA


Statistics
Matches: 31,  Mismatches: 5, Indels: 3
        0.79            0.13        0.08

Matches are distributed among these distances:
  27    3  0.10
  28   10  0.32
  29   18  0.58

ACGTcount: A:0.60, C:0.08, G:0.06, T:0.26


Consensus pattern (28 bp):   
AAATTAAAATCCTAAATAAAATAGGAAA

Found at i:4289 original size:8 final size:8

Alignment explanation


    Indices: 4276--4304  Score: 58
    Period size: 8  Copynumber: 3.6  Consensus size: 8

       4266 GTGCCACTTT

                    
       4276 CTAACTAG
          1 CTAACTAG

                    
       4284 CTAACTAG
          1 CTAACTAG

                    
       4292 CTAACTAG
          1 CTAACTAG

                 
       4300 CTAAC
          1 CTAAC

       4305 AAACTTGCGC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   21  1.00

ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24


Consensus pattern (8 bp):   
CTAACTAG

Found at i:4630 original size:15 final size:15

Alignment explanation


    Indices: 4612--4653  Score: 57
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       4602 TGGAAACTTC

                           
       4612 TTCGATTGTCTCAAA
          1 TTCGATTGTCTCAAA

                        ** 
       4627 TTCGATTGTCTCGTA
          1 TTCGATTGTCTCAAA

                   *    
       4642 TTCGATTTTCTC
          1 TTCGATTGTCTC

       4654 TTCATTCATG


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   24  1.00

ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48


Consensus pattern (15 bp):   
TTCGATTGTCTCAAA

Found at i:11910 original size:38 final size:36

Alignment explanation


    Indices: 11840--11910  Score: 88
    Period size: 38  Copynumber: 1.9  Consensus size: 36

      11830 ACATTTGGGT

                *                    ***        
      11840 TATTGAATTTATTAATAAAAATAGAGTTTAAAAAAA
          1 TATTAAATTTATTAATAAAAATAGAAAATAAAAAAA

                                               
      11876 TATTAAATTTAATTAAATAAAAATAGAAAATAAAA
          1 TATTAAATTT-ATT-AATAAAAATAGAAAATAAAA

      11911 TATAAAACTG


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  36    9  0.31
  37    3  0.10
  38   17  0.59

ACGTcount: A:0.61, C:0.00, G:0.06, T:0.34


Consensus pattern (36 bp):   
TATTAAATTTATTAATAAAAATAGAAAATAAAAAAA

Found at i:14661 original size:3 final size:3

Alignment explanation


    Indices: 14653--14716  Score: 112
    Period size: 3  Copynumber: 21.7  Consensus size: 3

      14643 CTTTTCATAT

                            *                                              
      14653 TTA TTA TTA TTA CT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                                  
      14700 TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TT

      14717 GGAAT


Statistics
Matches: 58,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
   2    1  0.02
   3   57  0.98

ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Done.