Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006916.1 Corchorus capsularis cultivar CVL-1 contig06937, 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: 13420
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:6489 original size:16 final size:16

Alignment explanation


    Indices: 6448--6492  Score: 56
    Period size: 15  Copynumber: 2.9  Consensus size: 16

       6438 TCGGATTTTG

                          **
       6448 TCGGTTTCGGGTTATC
          1 TCGGTTTCGGGTTAAA

                *           
       6464 TC-GATTCGGGTTAAA
          1 TCGGTTTCGGGTTAAA

                          
       6479 TCGGTTTCGGGTTA
          1 TCGGTTTCGGGTTA

       6493 TAGTACTTAT


Statistics
Matches: 24,  Mismatches: 4, Indels: 2
        0.80            0.13        0.07

Matches are distributed among these distances:
  15   12  0.50
  16   12  0.50

ACGTcount: A:0.13, C:0.16, G:0.31, T:0.40


Consensus pattern (16 bp):   
TCGGTTTCGGGTTAAA

Found at i:10359 original size:31 final size:29

Alignment explanation


    Indices: 10321--10431  Score: 101
    Period size: 31  Copynumber: 3.9  Consensus size: 29

      10311 GTCCGACGTA

                     *                     
      10321 GCACGCCACGTGTACCAAAAAGTGACATGTG
          1 GCACGCCACATGTACCAAAAAGTGACA--TG

                    *                    
      10352 GCACGCCATATGTACCAAAAAGT--CAT-
          1 GCACGCCACATGTACCAAAAAGTGACATG

                                           
      10378 ----GCCACATGTACCAAAAAGTGACACATG
          1 GCACGCCACATGTACCAAAAAGTG--ACATG

            *        *                 
      10405 CCACGCCACGTGTACCAAAAAGTGACA
          1 GCACGCCACATGTACCAAAAAGTGACA

      10432 CGTGATATGC


Statistics
Matches: 67,  Mismatches: 4, Indels: 20
        0.74            0.04        0.22

Matches are distributed among these distances:
  22   18  0.27
  26    3  0.04
  27    1  0.01
  29    5  0.07
  31   40  0.60

ACGTcount: A:0.37, C:0.28, G:0.20, T:0.15


Consensus pattern (29 bp):   
GCACGCCACATGTACCAAAAAGTGACATG

Found at i:10404 original size:19 final size:20

Alignment explanation


    Indices: 10361--10404  Score: 54
    Period size: 22  Copynumber: 2.1  Consensus size: 20

      10351 GGCACGCCAT

                              *   
      10361 ATGTACCAAAAAGTCATGCCAC
          1 ATGTACCAAAAAG--ATGACAC

                                
      10383 ATGTACCAAAAAG-TGACAC
          1 ATGTACCAAAAAGATGACAC

               
      10402 ATG
          1 ATG

      10405 CCACGCCACG


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  19    8  0.38
  22   13  0.62

ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18


Consensus pattern (20 bp):   
ATGTACCAAAAAGATGACAC

Found at i:10410 original size:53 final size:53

Alignment explanation


    Indices: 10325--10427  Score: 152
    Period size: 53  Copynumber: 1.9  Consensus size: 53

      10315 GACGTAGCAC

                 *                 **  *       *                 
      10325 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCATATGTACCAAAAAGTCAT
          1 GCCACATGTACCAAAAAGTGACACATGCCACGCCACATGTACCAAAAAGTCAT

                                                *             
      10378 GCCACATGTACCAAAAAGTGACACATGCCACGCCACGTGTACCAAAAAGT
          1 GCCACATGTACCAAAAAGTGACACATGCCACGCCACATGTACCAAAAAGT

      10428 GACACGTGAT


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  53   44  1.00

ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17


Consensus pattern (53 bp):   
GCCACATGTACCAAAAAGTGACACATGCCACGCCACATGTACCAAAAAGTCAT

Found at i:10444 original size:31 final size:31

Alignment explanation


    Indices: 10375--10475  Score: 112
    Period size: 31  Copynumber: 3.3  Consensus size: 31

      10365 ACCAAAAAGT

                                       *  *
      10375 CATGCCACATGTACCAAAAAGTGACACATGC
          1 CATGCCACATGTACCAAAAAGTGACACGTGA

              *     *                      
      10406 CACGCCACGTGTACCAAAAAGTGACACGTGA
          1 CATGCCACATGTACCAAAAAGTGACACGTGA

            *           **      *  *      *
      10437 TATGCCACATGTTTCAAAAAATGGCACGTGG
          1 CATGCCACATGTACCAAAAAGTGACACGTGA

                    
      10468 CATGCCAC
          1 CATGCCAC

      10476 GTGCACAAAA


Statistics
Matches: 57,  Mismatches: 13, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  31   57  1.00

ACGTcount: A:0.35, C:0.28, G:0.20, T:0.18


Consensus pattern (31 bp):   
CATGCCACATGTACCAAAAAGTGACACGTGA
Done.