Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015445.1 Corchorus capsularis cultivar CVL-1 contig15466, 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: 35468
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:5939 original size:76 final size:76

Alignment explanation


    Indices: 5813--5965  Score: 288
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       5803 TGGCGGCGGT

                                 *                                           
       5813 GTCAAAAACGCGCCACCAGGGGCTCTTGCGATTTATACAGTTTAAACTGTTTCTGGAAAATTCAC
          1 GTCAAAAACGCGCCACCAGGGACTCTTGCGATTTATACAGTTTAAACTGTTTCTGGAAAATTCAC

                       
       5878 GCTCCCAGGGC
         66 GCTCCCAGGGC

                    *                                                        
       5889 GTCAAAAATGCGCCACCAGGGACTCTTGCGATTTATACAGTTTAAACTGTTTCTGGAAAATTCAC
          1 GTCAAAAACGCGCCACCAGGGACTCTTGCGATTTATACAGTTTAAACTGTTTCTGGAAAATTCAC

                       
       5954 GCTCCCAGGGC
         66 GCTCCCAGGGC

             
       5965 G
          1 G

       5966 GCGCGTGCAA


Statistics
Matches: 75,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  76   75  1.00

ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25


Consensus pattern (76 bp):   
GTCAAAAACGCGCCACCAGGGACTCTTGCGATTTATACAGTTTAAACTGTTTCTGGAAAATTCAC
GCTCCCAGGGC

Found at i:7399 original size:16 final size:16

Alignment explanation


    Indices: 7368--7421  Score: 83
    Period size: 15  Copynumber: 3.3  Consensus size: 16

       7358 CCTGGTTATT

                            
       7368 TATTAATTCT-TTTAA
          1 TATTAATTCTATTTAA

                            
       7383 TATTAATTCTATTTAA
          1 TATTAATTCTATTTAA

                              
       7399 TATTATATTCTATTTATA
          1 TATTA-ATTCTATTTA-A

                 
       7417 TATTA
          1 TATTA

       7422 CATTTTTATT


Statistics
Matches: 36,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  15   10  0.28
  16   10  0.28
  17   10  0.28
  18    6  0.17

ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59


Consensus pattern (16 bp):   
TATTAATTCTATTTAA

Found at i:15612 original size:2 final size:2

Alignment explanation


    Indices: 15605--15648  Score: 70
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      15595 TGCTTAGCCC

                            *                             *               
      15605 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

              
      15647 AT
          1 AT

      15649 GTGTGTGTAT


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   2   38  1.00

ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:33241 original size:7 final size:7

Alignment explanation


    Indices: 33229--33269  Score: 61
    Period size: 7  Copynumber: 6.3  Consensus size: 7

      33219 AAGAGAGTAG

                   
      33229 TTTGTTT
          1 TTTGTTT

                   
      33236 TTTGTTT
          1 TTTGTTT

                   
      33243 TTTGTTT
          1 TTTGTTT

                   
      33250 TTTG--T
          1 TTTGTTT

                   
      33255 TTTGTTT
          1 TTTGTTT

                   
      33262 TTT-TTT
          1 TTTGTTT

              
      33268 TT
          1 TT

      33270 CAAAGGGCCA


Statistics
Matches: 32,  Mismatches: 0, Indels: 5
        0.86            0.00        0.14

Matches are distributed among these distances:
   5    5  0.16
   6    5  0.16
   7   22  0.69

ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88


Consensus pattern (7 bp):   
TTTGTTT

Found at i:33248 original size:14 final size:14

Alignment explanation


    Indices: 33229--33269  Score: 61
    Period size: 12  Copynumber: 3.1  Consensus size: 14

      33219 AAGAGAGTAG

                          
      33229 TTTGTTTTTTGTTT
          1 TTTGTTTTTTGTTT

                          
      33243 TTTGTTTTTTG--T
          1 TTTGTTTTTTGTTT

                          
      33255 TTTGTTTTTT-TTT
          1 TTTGTTTTTTGTTT

              
      33268 TT
          1 TT

      33270 CAAAGGGCCA


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  12   11  0.44
  13    3  0.12
  14   11  0.44

ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88


Consensus pattern (14 bp):   
TTTGTTTTTTGTTT
Done.