Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012025.1 Corchorus capsularis cultivar CVL-1 contig12046, 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: 18823
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:10445 original size:15 final size:16

Alignment explanation


    Indices: 10413--10446  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      10403 AAAGAAGAAT

                 *          
      10413 TAAAATTAAATCTAAC
          1 TAAAAGTAAATCTAAC

                            
      10429 TAAAAGTAAAT-TAAC
          1 TAAAAGTAAATCTAAC

               
      10444 TAA
          1 TAA

      10447 GAAAGCAATC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29


Consensus pattern (16 bp):   
TAAAAGTAAATCTAAC

Found at i:14375 original size:14 final size:14

Alignment explanation


    Indices: 14356--14383  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      14346 CTCCTTGTAA

                          
      14356 AGTCGACTTCTCCT
          1 AGTCGACTTCTCCT

                          
      14370 AGTCGACTTCTCCT
          1 AGTCGACTTCTCCT

      14384 CTAATCGGCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

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


Consensus pattern (14 bp):   
AGTCGACTTCTCCT

Found at i:14383 original size:33 final size:33

Alignment explanation


    Indices: 14321--14383  Score: 83
    Period size: 33  Copynumber: 1.9  Consensus size: 33

      14311 TTTGCTTCCA

                       * *       *           
      14321 AAAGTCGACTTGTGTAGTCGATTTGCTCCTTGT
          1 AAAGTCGACTTCTCTAGTCGACTTGCTCCTTGT

                                           
      14354 AAAGTCGACTTCTCCTAGTCGACTT-CTCCT
          1 AAAGTCGACTTCT-CTAGTCGACTTGCTCCT

      14384 CTAATCGGCA


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  33   17  0.65
  34    9  0.35

ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37


Consensus pattern (33 bp):   
AAAGTCGACTTCTCTAGTCGACTTGCTCCTTGT
Done.