Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000305.1 Corchorus capsularis cultivar CVL-1 contig00305, 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: 8953
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35


Found at i:788 original size:8 final size:8

Alignment explanation


    Indices: 760--790  Score: 53
    Period size: 8  Copynumber: 3.8  Consensus size: 8

        750 AGGCCAAAAG

                     
        760 AAAGAAAGA
          1 AAAG-AAGA

                    
        769 AAAGAAGA
          1 AAAGAAGA

                    
        777 AAAGAAGA
          1 AAAGAAGA

                  
        785 AAAGAA
          1 AAAGAA

        791 ACTGCAATCG


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   8   18  0.82
   9    4  0.18

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (8 bp):   
AAAGAAGA

Found at i:3702 original size:25 final size:26

Alignment explanation


    Indices: 3657--3708  Score: 63
    Period size: 25  Copynumber: 2.0  Consensus size: 26

       3647 CTCTAATAAT

                                      
       3657 ACATTATCACGATCTCAAAAAA-AAA
          1 ACATTATCACGATCTCAAAAAAGAAA

                       *     *         
       3682 ACATTATCACTTAT-TCTAAAAAGAAA
          1 ACATTATCAC-GATCTCAAAAAAGAAA

             
       3708 A
          1 A

       3709 AAGAAAAAAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  25   17  0.74
  26    6  0.26

ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25


Consensus pattern (26 bp):   
ACATTATCACGATCTCAAAAAAGAAA

Found at i:4533 original size:16 final size:15

Alignment explanation


    Indices: 4508--4552  Score: 56
    Period size: 16  Copynumber: 2.9  Consensus size: 15

       4498 TTGAATTTTT

                            
       4508 ATTTAA-TAAATTGTC
          1 ATTTAATTAAATT-TC

                           
       4523 ATTTAATTAAATTTC
          1 ATTTAATTAAATTTC

               *           
       4538 ACTGTAATTAAATTT
          1 A-TTTAATTAAATTT

       4553 TTTATTCCAT


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  15    9  0.33
  16   18  0.67

ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49


Consensus pattern (15 bp):   
ATTTAATTAAATTTC

Found at i:5339 original size:21 final size:21

Alignment explanation


    Indices: 5313--5353  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5303 CAGAAGAGTT

                                 
       5313 CGCCTTCCTCAACAAGTAAAA
          1 CGCCTTCCTCAACAAGTAAAA

                       *        
       5334 CGCCTTCCTCAGCAAGTAAA
          1 CGCCTTCCTCAACAAGTAAA

       5354 GCCCACCAGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.34, C:0.34, G:0.12, T:0.20


Consensus pattern (21 bp):   
CGCCTTCCTCAACAAGTAAAA

Found at i:7599 original size:23 final size:23

Alignment explanation


    Indices: 7533--7657  Score: 93
    Period size: 23  Copynumber: 5.6  Consensus size: 23

       7523 ATCGCACTCC

                             *      
       7533 GAAATTTTGAT-AATC-ACACTAT
          1 GAAATTTTGATAAATCTTC-CTAT

                                *    
       7555 G-AATTTGTGATAACATC--GCTAT
          1 GAAATTT-TGATAA-ATCTTCCTAT

                                   
       7577 GAAATTTTGATAAATCTTCCTAT
          1 GAAATTTTGATAAATCTTCCTAT

            *             *  *     
       7600 AAAATTTTGATAAACCTCCCTAT
          1 GAAATTTTGATAAATCTTCCTAT

            *            *     *   
       7623 AAAATTTTGATAACT-TTCTTAT
          1 GAAATTTTGATAAATCTTCCTAT

                          
       7645 GAAATATTT-ATAA
          1 GAAAT-TTTGATAA

       7658 CTACAAATTT


Statistics
Matches: 86,  Mismatches: 10, Indels: 14
        0.78            0.09        0.13

Matches are distributed among these distances:
  21    8  0.09
  22   29  0.34
  23   46  0.53
  24    3  0.03

ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40


Consensus pattern (23 bp):   
GAAATTTTGATAAATCTTCCTAT

Found at i:8402 original size:37 final size:37

Alignment explanation


    Indices: 8314--8405  Score: 121
    Period size: 38  Copynumber: 2.5  Consensus size: 37

       8304 ATCTAAGCCC

                           *  *                  
       8314 AAATAGGACGTTGGAGATTAAGACAAAAAGCAAAATT
          1 AAATAGGACGTTGGAAATAAAGACAAAAAGCAAAATT

                 **                      *        
       8351 AAATACAACGGTTGGAAATAAAGACAAAAGGCAAAATT
          1 AAATAGGAC-GTTGGAAATAAAGACAAAAAGCAAAATT

              *              
       8389 AAGTAGGACGTTGGAAA
          1 AAATAGGACGTTGGAAA

       8406 CAAAAAGTCA


Statistics
Matches: 46,  Mismatches: 8, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  37   15  0.33
  38   31  0.67

ACGTcount: A:0.51, C:0.09, G:0.23, T:0.17


Consensus pattern (37 bp):   
AAATAGGACGTTGGAAATAAAGACAAAAAGCAAAATT
Done.