Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012048.1 Corchorus capsularis cultivar CVL-1 contig12069, 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, 931

Length: 1552
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34


Found at i:739 original size:29 final size:30

Alignment explanation


    Indices: 700--760  Score: 88
    Period size: 29  Copynumber: 2.1  Consensus size: 30

        690 TATAAATAAT

                  *                 *     
        700 ATAATATAATTAAATAA-TTATATTTATAC
          1 ATAATAAAATTAAATAATTTATATGTATAC

                       *                  
        729 ATAATAAAATTGAATAATTTATATGTATAC
          1 ATAATAAAATTAAATAATTTATATGTATAC

              
        759 AT
          1 AT

        761 TAATTAGATC


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  29   15  0.54
  30   13  0.46

ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43


Consensus pattern (30 bp):   
ATAATAAAATTAAATAATTTATATGTATAC

Found at i:892 original size:25 final size:24

Alignment explanation


    Indices: 858--905  Score: 62
    Period size: 26  Copynumber: 1.9  Consensus size: 24

        848 TTAATGTTTA

                                     
        858 AATTTTATTT-TTATTAAAAAATGT
          1 AATTTTATTTATT-TTAAAAAATGT

                                    
        882 AATTATTATTTCATTTTAAAAAAT
          1 AATT-TTATTT-ATTTTAAAAAAT

        906 AAATATGGGC


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24    4  0.19
  25    6  0.29
  26    9  0.43
  27    2  0.10

ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52


Consensus pattern (24 bp):   
AATTTTATTTATTTTAAAAAATGT

Found at i:1248 original size:20 final size:20

Alignment explanation


    Indices: 1211--1248  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1201 AATTGCTAAA

                        **      
       1211 CACCGCCCCCTTTTACTAGG
          1 CACCGCCCCCTTGGACTAGG

                              
       1231 CACCGCCCCCTTGGACTA
          1 CACCGCCCCCTTGGACTA

       1249 TTTTGCCCTT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.16, C:0.47, G:0.16, T:0.21


Consensus pattern (20 bp):   
CACCGCCCCCTTGGACTAGG
Done.