Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001238.1 Corchorus capsularis cultivar CVL-1 contig01238, 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, 681

Length: 1136
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32


Found at i:94 original size:27 final size:27

Alignment explanation


    Indices: 9--87  Score: 140
    Period size: 27  Copynumber: 2.9  Consensus size: 27

          1 AATCGAGC

                              *        
          9 AAAGATAGTGATAGAAATGCCAATAGA
          1 AAAGATAGTGATAGAAATACCAATAGA

                                       
         36 AAAGATAGTGATAGAAATACCAATAGA
          1 AAAGATAGTGATAGAAATACCAATAGA

                         *           
         63 AAAGATAGTGATAAAAATACCAATA
          1 AAAGATAGTGATAGAAATACCAATA

         88 ACGAAGAAAA


Statistics
Matches: 50,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   50  1.00

ACGTcount: A:0.56, C:0.08, G:0.18, T:0.19


Consensus pattern (27 bp):   
AAAGATAGTGATAGAAATACCAATAGA

Found at i:351 original size:33 final size:32

Alignment explanation


    Indices: 330--459  Score: 134
    Period size: 33  Copynumber: 3.8  Consensus size: 32

        320 TGCAAATGGT

                                       *  *       
        330 AATGATTTAGAAAGTTCTAATGATAATGATTTCGACGA
          1 AATGATTTAGAAAGTTCTAATGAT--TCA-AT-GA--A

                                        * *   
        368 AAATGATTTAGAAAGTTCTAATGATTTCGACGAA
          1 AA-TGATTTAGAAAGTTCTAATGA-TTCAATGAA

                                       *     
        402 AATGATTTAGAAAGTTCTAATGATTTCGATGAA
          1 AATGATTTAGAAAGTTCTAATGA-TTCAATGAA

                                     
        435 AATGATTTAGAAAGTTCTAATGATT
          1 AATGATTTAGAAAGTTCTAATGATT

        460 TCGACGAAAA


Statistics
Matches: 85,  Mismatches: 5, Indels: 10
        0.85            0.05        0.10

Matches are distributed among these distances:
  32    2  0.02
  33   53  0.62
  34    3  0.04
  36    2  0.02
  38    3  0.04
  39   21  0.25
  40    1  0.01

ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35


Consensus pattern (32 bp):   
AATGATTTAGAAAGTTCTAATGATTCAATGAA

Found at i:392 original size:18 final size:18

Alignment explanation


    Indices: 369--460  Score: 70
    Period size: 18  Copynumber: 5.4  Consensus size: 18

        359 TTTCGACGAA

                              
        369 AATGATTTAGAAAGTTCT
          1 AATGATTTAGAAAGTTCT

                    *   *   **
        387 AATGATTTCG-ACG--AA
          1 AATGATTTAGAAAGTTCT

                              
        402 AATGATTTAGAAAGTTCT
          1 AATGATTTAGAAAGTTCT

                    *      ***
        420 AATGATTTCG--A-TGAA
          1 AATGATTTAGAAAGTTCT

                              
        435 AATGATTTAGAAAGTTCT
          1 AATGATTTAGAAAGTTCT

                    
        453 AATGATTT
          1 AATGATTT

        461 CGACGAAAAT


Statistics
Matches: 52,  Mismatches: 16, Indels: 12
        0.65            0.20        0.15

Matches are distributed among these distances:
  15   19  0.37
  16    3  0.06
  17    3  0.06
  18   27  0.52

ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37


Consensus pattern (18 bp):   
AATGATTTAGAAAGTTCT

Found at i:460 original size:33 final size:33

Alignment explanation


    Indices: 353--471  Score: 229
    Period size: 33  Copynumber: 3.6  Consensus size: 33

        343 GTTCTAATGA

                                             
        353 TAATGATTTCGACGAAAATGATTTAGAAAGTTC
          1 TAATGATTTCGACGAAAATGATTTAGAAAGTTC

                                             
        386 TAATGATTTCGACGAAAATGATTTAGAAAGTTC
          1 TAATGATTTCGACGAAAATGATTTAGAAAGTTC

                        *                    
        419 TAATGATTTCGATGAAAATGATTTAGAAAGTTC
          1 TAATGATTTCGACGAAAATGATTTAGAAAGTTC

                                
        452 TAATGATTTCGACGAAAATG
          1 TAATGATTTCGACGAAAATG

        472 GTAATGATTT


Statistics
Matches: 84,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  33   84  1.00

ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34


Consensus pattern (33 bp):   
TAATGATTTCGACGAAAATGATTTAGAAAGTTC
Done.