Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014791.1 Corchorus capsularis cultivar CVL-1 contig14812, 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: 1850
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36


Found at i:1352 original size:26 final size:27

Alignment explanation


    Indices: 1305--1398  Score: 120
    Period size: 27  Copynumber: 3.5  Consensus size: 27

       1295 GTTGACTAAG

                     *  *  *           
       1305 ATGCCCCTAAATATGCAAATGACCAAA
          1 ATGCCCCTAGATGTGAAAATGACCAAA

                  *                     
       1332 ATGCCCTTAG-TGT-AAAGATGACCAAA
          1 ATGCCCCTAGATGTGAAA-ATGACCAAA

                                        
       1358 ATGCCTCCTAGATGTGAAAATGACCAAA
          1 ATGCC-CCTAGATGTGAAAATGACCAAA

                         
       1386 ATGCCCCTAGATG
          1 ATGCCCCTAGATG

       1399 ACCCTAATGC


Statistics
Matches: 58,  Mismatches: 5, Indels: 8
        0.82            0.07        0.11

Matches are distributed among these distances:
  25    2  0.03
  26   16  0.28
  27   20  0.34
  28   17  0.29
  29    3  0.05

ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21


Consensus pattern (27 bp):   
ATGCCCCTAGATGTGAAAATGACCAAA

Found at i:1389 original size:28 final size:26

Alignment explanation


    Indices: 1321--1398  Score: 113
    Period size: 28  Copynumber: 2.9  Consensus size: 26

       1311 CTAAATATGC

                             *        
       1321 AAATGACCAAAATGCCCTTAG-TGTA
          1 AAATGACCAAAATGCCCCTAGATGTA

                                         
       1346 AAGATGACCAAAATGCCTCCTAGATGTGA
          1 AA-ATGACCAAAATGCC-CCTAGATGT-A

                                    
       1375 AAATGACCAAAATGCCCCTAGATG
          1 AAATGACCAAAATGCCCCTAGATG

       1399 ACCCTAATGC


Statistics
Matches: 48,  Mismatches: 1, Indels: 6
        0.87            0.02        0.11

Matches are distributed among these distances:
  25    2  0.04
  26   14  0.29
  27   12  0.25
  28   17  0.35
  29    3  0.06

ACGTcount: A:0.40, C:0.22, G:0.18, T:0.21


Consensus pattern (26 bp):   
AAATGACCAAAATGCCCCTAGATGTA

Found at i:1791 original size:47 final size:47

Alignment explanation


    Indices: 1734--1850  Score: 144
    Period size: 47  Copynumber: 2.5  Consensus size: 47

       1724 AAAACCCGAT

                 *                 * *  *               *  
       1734 GACCAACTTTGGTCACTAAATTGCAGACTCGCATGGAAGCGAGAGAA
          1 GACCATCTTTGGTCACTAAATTGAAAACCCGCATGGAAGCGAGAAAA

                         *                 **      *       
       1781 GACCATCTTTGGTGACTAAATTGAAAACCCGTGTGGAAGTGAGAAAA
          1 GACCATCTTTGGTCACTAAATTGAAAACCCGCATGGAAGCGAGAAAA

                              *    
       1828 GACCATCTTTGGTCACTAGATTG
          1 GACCATCTTTGGTCACTAAATTG


Statistics
Matches: 59,  Mismatches: 11, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  47   59  1.00

ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24


Consensus pattern (47 bp):   
GACCATCTTTGGTCACTAAATTGAAAACCCGCATGGAAGCGAGAAAA
Done.