Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006480.1 Corchorus capsularis cultivar CVL-1 contig06501, 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: 18666
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:17137 original size:20 final size:21

Alignment explanation


    Indices: 17090--17139  Score: 66
    Period size: 22  Copynumber: 2.4  Consensus size: 21

      17080 AACTTAATTA

                *            *   
      17090 TTTATAAAATATAATTTTATT
          1 TTTAAAAAATATAATTTCATT

                                  
      17111 TTCTAAAAAATATAATTTCA-T
          1 TT-TAAAAAATATAATTTCATT

                    
      17132 TTTAAAAA
          1 TTTAAAAA

      17140 TTAATTATAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  20    6  0.23
  21    5  0.19
  22   15  0.58

ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48


Consensus pattern (21 bp):   
TTTAAAAAATATAATTTCATT

Found at i:18009 original size:22 final size:22

Alignment explanation


    Indices: 17981--18037  Score: 78
    Period size: 22  Copynumber: 2.6  Consensus size: 22

      17971 TGCAGATTAT

                                  
      17981 CAAAATTTCATAGTGTGGCCAC
          1 CAAAATTTCATAGTGTGGCCAC

                        *     ** *
      18003 CAAAATTTCATAATGTGGTTAT
          1 CAAAATTTCATAGTGTGGCCAC

                         
      18025 CAAAATTTCATAG
          1 CAAAATTTCATAG

      18038 AAGGTAATCA


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   30  1.00

ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33


Consensus pattern (22 bp):   
CAAAATTTCATAGTGTGGCCAC

Found at i:18260 original size:36 final size:36

Alignment explanation


    Indices: 18213--18289  Score: 154
    Period size: 36  Copynumber: 2.1  Consensus size: 36

      18203 TCAAAATTAA

                                                
      18213 TTTCATACAGAGGTTATCACAATTTTATAGTGTGGC
          1 TTTCATACAGAGGTTATCACAATTTTATAGTGTGGC

                                                
      18249 TTTCATACAGAGGTTATCACAATTTTATAGTGTGGC
          1 TTTCATACAGAGGTTATCACAATTTTATAGTGTGGC

                 
      18285 TTTCA
          1 TTTCA

      18290 AAATATCATA


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   41  1.00

ACGTcount: A:0.27, C:0.14, G:0.18, T:0.40


Consensus pattern (36 bp):   
TTTCATACAGAGGTTATCACAATTTTATAGTGTGGC

Found at i:18326 original size:21 final size:22

Alignment explanation


    Indices: 18288--18343  Score: 69
    Period size: 21  Copynumber: 2.6  Consensus size: 22

      18278 GTGTGGCTTT

                  *               
      18288 CAAAATATCATAGTGTGGTGAC
          1 CAAAATTTCATAGTGTGGTGAC

                               * *
      18310 CAAAATTTCAT-GTGTGGTTAT
          1 CAAAATTTCATAGTGTGGTGAC

                *        
      18331 CAAAGTTTCATAG
          1 CAAAATTTCATAG

      18344 AGAGGGTATC


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  21   18  0.62
  22   11  0.38

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


Consensus pattern (22 bp):   
CAAAATTTCATAGTGTGGTGAC

Found at i:18360 original size:43 final size:44

Alignment explanation


    Indices: 18249--18361  Score: 106
    Period size: 43  Copynumber: 2.6  Consensus size: 44

      18239 ATAGTGTGGC

                   *     *           *                  
      18249 TTTCATACAGAGGTTATCACAATTTTATAGTGTGGCTTTCAAAA
          1 TTTCATAGAGAGGGTATCACAATTTCATAGTGTGGCTTTCAAAA

             *      *  *     *  *                        *
      18293 TATCATAGTG-TGGTGACCAAAATTTCAT-GTGTGG-TTATCAAAG
          1 TTTCATAGAGAGGGT-ATCACAATTTCATAGTGTGGCTT-TCAAAA

                                      
      18336 TTTCATAGAGAGGGTATCACAATTTC
          1 TTTCATAGAGAGGGTATCACAATTTC

      18362 TTAGGGAGGT


Statistics
Matches: 52,  Mismatches: 14, Indels: 7
        0.71            0.19        0.10

Matches are distributed among these distances:
  42    2  0.04
  43   30  0.58
  44   20  0.38

ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36


Consensus pattern (44 bp):   
TTTCATAGAGAGGGTATCACAATTTCATAGTGTGGCTTTCAAAA

Found at i:18361 original size:22 final size:22

Alignment explanation


    Indices: 18328--18378  Score: 59
    Period size: 22  Copynumber: 2.3  Consensus size: 22

      18318 CATGTGTGGT

                                  
      18328 TATCAAAGTTTCATAGAGAGGG
          1 TATCAAAGTTTCATAGAGAGGG

                         *   *    *
      18350 TATCACAA-TTTCTTAGGGAGGT
          1 TATCA-AAGTTTCATAGAGAGGG

                   
      18372 TATCAAA
          1 TATCAAA

      18379 AAAATATAAC


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  21    2  0.08
  22   21  0.84
  23    2  0.08

ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31


Consensus pattern (22 bp):   
TATCAAAGTTTCATAGAGAGGG
Done.