Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009804.1 Corchorus capsularis cultivar CVL-1 contig09825, 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: 11589
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33


Found at i:979 original size:21 final size:20

Alignment explanation


    Indices: 940--984  Score: 54
    Period size: 20  Copynumber: 2.2  Consensus size: 20

        930 AATTATCAAT

                  *       *     
        940 TAAAAAGAAAGCAATTAAAC
          1 TAAAAACAAAGCAAGTAAAC

                                *
        960 TAAAAACAAAGCAAAGTAAAT
          1 TAAAAACAAAGC-AAGTAAAC

                
        981 TAAA
          1 TAAA

        985 TCTAAATCTA


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

Matches are distributed among these distances:
  20   11  0.52
  21   10  0.48

ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16


Consensus pattern (20 bp):   
TAAAAACAAAGCAAGTAAAC

Found at i:2209 original size:10 final size:10

Alignment explanation


    Indices: 2194--2218  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       2184 TAACTCCAAT

                      
       2194 TATGGACTTA
          1 TATGGACTTA

                      
       2204 TATGGACTTA
          1 TATGGACTTA

                 
       2214 TATGG
          1 TATGG

       2219 GCTGAATATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40


Consensus pattern (10 bp):   
TATGGACTTA

Found at i:2371 original size:19 final size:18

Alignment explanation


    Indices: 2338--2373  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       2328 TTGAAATAAT

                              
       2338 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       2356 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       2374 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:2678 original size:38 final size:38

Alignment explanation


    Indices: 2627--2726  Score: 146
    Period size: 38  Copynumber: 2.6  Consensus size: 38

       2617 GAGGATATCT

                            *    *                
       2627 TGTTTCCAGCCAACTTCGATAGCTCCTGAAAGATGACC
          1 TGTTTCCAGCCAACTTTGATAACTCCTGAAAGATGACC

                                    **   *        
       2665 TGTTTCCAGCCAACTTTGATAACTGTTGAGAGATGACC
          1 TGTTTCCAGCCAACTTTGATAACTCCTGAAAGATGACC

                     *              
       2703 TGTTTCCAGTCAACTTTGATAACT
          1 TGTTTCCAGCCAACTTTGATAACT

       2727 TCTTTGAGTT


Statistics
Matches: 56,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  38   56  1.00

ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32


Consensus pattern (38 bp):   
TGTTTCCAGCCAACTTTGATAACTCCTGAAAGATGACC

Found at i:3713 original size:28 final size:28

Alignment explanation


    Indices: 3678--3763  Score: 163
    Period size: 28  Copynumber: 3.1  Consensus size: 28

       3668 CCTTGGGAGG

                                        
       3678 CTCCTTGAGTTCCCATCCTTACTCTAGA
          1 CTCCTTGAGTTCCCATCCTTACTCTAGA

                                 *      
       3706 CTCCTTGAGTTCCCATCCTTAATCTAGA
          1 CTCCTTGAGTTCCCATCCTTACTCTAGA

                                        
       3734 CTCCTTGAGTTCCCATCCTTACTCTAGA
          1 CTCCTTGAGTTCCCATCCTTACTCTAGA

              
       3762 CT
          1 CT

       3764 GCCCTTTCGG


Statistics
Matches: 56,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  28   56  1.00

ACGTcount: A:0.19, C:0.35, G:0.10, T:0.36


Consensus pattern (28 bp):   
CTCCTTGAGTTCCCATCCTTACTCTAGA

Found at i:11301 original size:15 final size:14

Alignment explanation


    Indices: 11283--11331  Score: 53
    Period size: 15  Copynumber: 3.2  Consensus size: 14

      11273 CTTTTTTGGA

                           
      11283 TTTATTTTATTTTAT
          1 TTTATTTT-TTTTAT

                            
      11298 TTTATTTTTTTTAGAT
          1 TTTATTTTTTTT--AT

                        *  
      11314 TTCTATTTTTTTCAT
          1 TT-TATTTTTTTTAT

               
      11329 TTT
          1 TTT

      11332 TTTGAATTTT


Statistics
Matches: 30,  Mismatches: 1, Indels: 7
        0.79            0.03        0.18

Matches are distributed among these distances:
  14    5  0.17
  15   12  0.40
  16    4  0.13
  17    9  0.30

ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78


Consensus pattern (14 bp):   
TTTATTTTTTTTAT
Done.