Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007984.1 Corchorus capsularis cultivar CVL-1 contig08005, 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: 7890
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31


Found at i:312 original size:26 final size:28

Alignment explanation


    Indices: 225--303  Score: 122
    Period size: 29  Copynumber: 2.8  Consensus size: 28

        215 ACACTTTAAT

                                         
        225 ATAGCGGCGTCTAGACGCCGCCAATCTAA
          1 ATAGCGGCGTCTAGACGCCGCC-ATCTAA

                         *  *            
        254 ATAGCGGCGTCTATACCCCGCCATTCTAA
          1 ATAGCGGCGTCTAGACGCCGCCA-TCTAA

                                 
        283 ATAGCGGCGTCTAGACGCCGC
          1 ATAGCGGCGTCTAGACGCCGC

        304 TATATATAGT


Statistics
Matches: 45,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  28    1  0.02
  29   44  0.98

ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19


Consensus pattern (28 bp):   
ATAGCGGCGTCTAGACGCCGCCATCTAA

Found at i:755 original size:21 final size:19

Alignment explanation


    Indices: 731--772  Score: 57
    Period size: 21  Copynumber: 2.1  Consensus size: 19

        721 AGGTTTTCCA

                                 
        731 AAAATCCAAAAAAATCAAATC
          1 AAAATCCAAAAAAA--AAATC

                 *             
        752 AAAATTCAAAAAAAAAATC
          1 AAAATCCAAAAAAAAAATC

              
        771 AA
          1 AA

        773 TTTTTTTTCA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  19    7  0.35
  21   13  0.65

ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14


Consensus pattern (19 bp):   
AAAATCCAAAAAAAAAATC

Found at i:3373 original size:35 final size:35

Alignment explanation


    Indices: 3299--3373  Score: 89
    Period size: 35  Copynumber: 2.1  Consensus size: 35

       3289 ATGTCACCTG

                *                   *      *  *
       3299 ACAAAAAGAGAGTTAAGTTGGACATGAACTAGGTG
          1 ACAAGAAGAGAGTTAAGTTGGACAAGAACTAAGTC

                                       *        
       3334 ACAAGAAGAGAGTTAAGTTGGACAAGACCTAAAG-C
          1 ACAAGAAGAGAGTTAAGTTGGACAAGAACT-AAGTC

                 
       3369 ACAAG
          1 ACAAG

       3374 GTTAATGGAC


Statistics
Matches: 34,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  35   32  0.94
  36    2  0.06

ACGTcount: A:0.45, C:0.12, G:0.27, T:0.16


Consensus pattern (35 bp):   
ACAAGAAGAGAGTTAAGTTGGACAAGAACTAAGTC

Found at i:4483 original size:15 final size:16

Alignment explanation


    Indices: 4451--4484  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       4441 AAAGAAGAAT

                 *          
       4451 TAAAATTAAATCTAAC
          1 TAAAAGTAAATCTAAC

                            
       4467 TAAAAGTAAAT-TAAC
          1 TAAAAGTAAATCTAAC

               
       4482 TAA
          1 TAA

       4485 GAAAACAATC


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
Done.