Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015830.1 Corchorus capsularis cultivar CVL-1 contig15851, 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: 13125
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:1473 original size:41 final size:41

Alignment explanation


    Indices: 1326--1512  Score: 245
    Period size: 40  Copynumber: 4.6  Consensus size: 41

       1316 TGACACTAAT

                   *                *        ***   *  
       1326 AACTTCTTGTGTCAACA-GTAATTATAATTTACTGGAGTAAC
          1 AACTTCTGGTGTCAA-AGGTAATTTTAATTTACCAAAGTGAC

                    *                                
       1367 -ACTTCTGATGTCAAAGGTAATTTTAATTTACCAAAGTGAC
          1 AACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGAC

                                                     
       1407 AACTTCTGG-GTCAAAGGTAATTTTAATTTACCAAAGTGAC
          1 AACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGAC

                            *  **              *     
       1447 AACTTCTGGTGTCAAAAGTTTTTTTAATTTACCAAGGTGAC
          1 AACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGAC

                                     
       1488 AACTTCTGGTGTCAAAGGTAATTTT
          1 AACTTCTGGTGTCAAAGGTAATTTT

       1513 CAATATTATT


Statistics
Matches: 128,  Mismatches: 15, Indels: 6
        0.86            0.10        0.04

Matches are distributed among these distances:
  39    1  0.01
  40   71  0.55
  41   56  0.44

ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36


Consensus pattern (41 bp):   
AACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGAC

Found at i:9278 original size:16 final size:16

Alignment explanation


    Indices: 9257--9296  Score: 55
    Period size: 16  Copynumber: 2.5  Consensus size: 16

       9247 AACGAGCAAG

                     *       
       9257 TATTTTTT-GTTTTATT
          1 TATTTTTTATTTTTA-T

                            
       9273 TATTTTTTATTTTTAT
          1 TATTTTTTATTTTTAT

                    
       9289 TATTTTTT
          1 TATTTTTT

       9297 TTCAAATGTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  16   17  0.77
  17    5  0.23

ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82


Consensus pattern (16 bp):   
TATTTTTTATTTTTAT

Found at i:12065 original size:19 final size:18

Alignment explanation


    Indices: 12041--12084  Score: 54
    Period size: 17  Copynumber: 2.4  Consensus size: 18

      12031 ATCGACACAC

                        *      
      12041 AAGTCGACTTTTTAAAGCA
          1 AAGTCGAC-TTTGAAAGCA

                          *   
      12060 AAGTCGA-TTTGAAGGCA
          1 AAGTCGACTTTGAAAGCA

                    
      12077 AAGTCGAC
          1 AAGTCGAC

      12085 AAGGAAGTCG


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  17   15  0.68
  19    7  0.32

ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25


Consensus pattern (18 bp):   
AAGTCGACTTTGAAAGCA
Done.