Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010736.1 Corchorus capsularis cultivar CVL-1 contig10757, 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: 10289
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33


Found at i:6366 original size:27 final size:27

Alignment explanation


    Indices: 6328--6402  Score: 105
    Period size: 27  Copynumber: 2.8  Consensus size: 27

       6318 TAGGGTCATC

                 *               **    
       6328 CAAGGCCATTTTGGTCATTTTTGCATT
          1 CAAGGGCATTTTGGTCATTTTCACATT

                                       
       6355 CAAGGGCATTTTGGTCATTTTCACATT
          1 CAAGGGCATTTTGGTCATTTTCACATT

            * *                  
       6382 TAGGGGCATTTTGGTCATTTT
          1 CAAGGGCATTTTGGTCATTTT

       6403 AAGGTCACTT


Statistics
Matches: 43,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  27   43  1.00

ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44


Consensus pattern (27 bp):   
CAAGGGCATTTTGGTCATTTTCACATT

Found at i:6914 original size:15 final size:15

Alignment explanation


    Indices: 6894--6922  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       6884 TAATAAATAC

                           
       6894 AAGGCATTTGATTTT
          1 AAGGCATTTGATTTT

                          
       6909 AAGGCATTTGATTT
          1 AAGGCATTTGATTT

       6923 ACAAATTGGA


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45


Consensus pattern (15 bp):   
AAGGCATTTGATTTT

Found at i:8376 original size:21 final size:21

Alignment explanation


    Indices: 8343--8384  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8333 AGCACAAGTG

                    *            
       8343 ACCGACCATGCGACTTGGAGA
          1 ACCGACCACGCGACTTGGAGA

                *                
       8364 ACCGGCCACGCGACTTGGAGA
          1 ACCGACCACGCGACTTGGAGA

       8385 TGCCCGCGCA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.26, C:0.31, G:0.31, T:0.12


Consensus pattern (21 bp):   
ACCGACCACGCGACTTGGAGA

Found at i:8401 original size:33 final size:32

Alignment explanation


    Indices: 8364--8471  Score: 110
    Period size: 33  Copynumber: 3.3  Consensus size: 32

       8354 GACTTGGAGA

                          *                  
       8364 ACCGGCCACGCGACTTGGAGATGCCCGCGCAAC
          1 ACCGGCCACGCGACATGGAGATGCCCG-GCAAC

                    *                *      * 
       8397 ACCGGCCATGCGACATGGAGAAT-CTCGGTCATC
          1 ACCGGCCACGCGACATGGAG-ATGCCCGG-CAAC

                              **         *  
       8430 ACCGGCCACGCGACATGGCCATGCCCGGCCAC
          1 ACCGGCCACGCGACATGGAGATGCCCGGCAAC

                      
       8462 ACCCGGCCAC
          1 A-CCGGCCAC

       8472 TTGACTCGGC


Statistics
Matches: 61,  Mismatches: 10, Indels: 8
        0.77            0.13        0.10

Matches are distributed among these distances:
  32    6  0.10
  33   53  0.87
  34    2  0.03

ACGTcount: A:0.21, C:0.41, G:0.28, T:0.10


Consensus pattern (32 bp):   
ACCGGCCACGCGACATGGAGATGCCCGGCAAC

Found at i:9527 original size:9 final size:9

Alignment explanation


    Indices: 9509--9543  Score: 52
    Period size: 9  Copynumber: 3.8  Consensus size: 9

       9499 AGTTATATCC

                 *   
       9509 AAAAATATA
          1 AAAAAAATA

                     
       9518 AAAAAAATA
          1 AAAAAAATA

                      
       9527 AAATAAAATA
          1 AAA-AAAATA

                   
       9537 AAAAAAA
          1 AAAAAAA

       9544 ATTTTCGATC


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
   9   15  0.62
  10    9  0.38

ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14


Consensus pattern (9 bp):   
AAAAAAATA

Found at i:9544 original size:10 final size:10

Alignment explanation


    Indices: 9509--9545  Score: 56
    Period size: 10  Copynumber: 3.6  Consensus size: 10

       9499 AGTTATATCC

                       
       9509 AAAAATATAAA
          1 AAAAATA-AAA

                      
       9520 AAAAATAAAA
          1 AAAAATAAAA

            *         
       9530 TAAAATAAAA
          1 AAAAATAAAA

                  
       9540 AAAAAT
          1 AAAAAT

       9546 TTTCGATCAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  10   17  0.71
  11    7  0.29

ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16


Consensus pattern (10 bp):   
AAAAATAAAA
Done.