Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020682.1 Corchorus olitorius cultivar O-4 contig20715, 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: 15824
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:317 original size:2 final size:2

Alignment explanation


    Indices: 305--334  Score: 51
    Period size: 2  Copynumber: 14.5  Consensus size: 2

        295 AGTTTAGACT

                                                        
        305 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA T

        335 TAAACTTTTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2   25  0.93
   3    2  0.07

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:2766 original size:6 final size:6

Alignment explanation


    Indices: 2755--2785  Score: 62
    Period size: 6  Copynumber: 5.2  Consensus size: 6

       2745 GCTTCTTCTC

                                                
       2755 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T
          1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T

       2786 TTCCCCTTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84


Consensus pattern (6 bp):   
TCTTTT

Found at i:3802 original size:102 final size:102

Alignment explanation


    Indices: 3626--3830  Score: 401
    Period size: 102  Copynumber: 2.0  Consensus size: 102

       3616 CATTTCATTC

                                                                 *           
       3626 TTTGACTTAGAAGGGGGCTTTTTAGTTATCCTATGATTAAAAGAATAAACTATTGAGAGAAACAC
          1 TTTGACTTAGAAGGGGGCTTTTTAGTTATCCTATGATTAAAAGAATAAACTATGGAGAGAAACAC

                                                 
       3691 CAGAAAGGATATAAAGCAGTTTAAACTTCTCTTTAAA
         66 CAGAAAGGATATAAAGCAGTTTAAACTTCTCTTTAAA

                                                                             
       3728 TTTGACTTAGAAGGGGGCTTTTTAGTTATCCTATGATTAAAAGAATAAACTATGGAGAGAAACAC
          1 TTTGACTTAGAAGGGGGCTTTTTAGTTATCCTATGATTAAAAGAATAAACTATGGAGAGAAACAC

                                                 
       3793 CAGAAAGGATATAAAGCAGTTTAAACTTCTCTTTAAA
         66 CAGAAAGGATATAAAGCAGTTTAAACTTCTCTTTAAA

             
       3830 T
          1 T

       3831 CTAAAGTATT


Statistics
Matches: 102,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 102  102  1.00

ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31


Consensus pattern (102 bp):   
TTTGACTTAGAAGGGGGCTTTTTAGTTATCCTATGATTAAAAGAATAAACTATGGAGAGAAACAC
CAGAAAGGATATAAAGCAGTTTAAACTTCTCTTTAAA

Found at i:4523 original size:2 final size:2

Alignment explanation


    Indices: 4508--4555  Score: 78
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       4498 TTTAAATTAA

                         *                                                 
       4508 AC AC AC TAC CC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
          1 AC AC AC -AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC

                   
       4551 AC AC A
          1 AC AC A

       4556 GAGAGAGAGA


Statistics
Matches: 43,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
   2   41  0.95
   3    2  0.05

ACGTcount: A:0.48, C:0.50, G:0.00, T:0.02


Consensus pattern (2 bp):   
AC

Found at i:4560 original size:2 final size:2

Alignment explanation


    Indices: 4555--4627  Score: 139
    Period size: 2  Copynumber: 37.0  Consensus size: 2

       4545 ACACACACAC

                                                                          
       4555 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                                                           
       4596 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

       4628 TTACTTGAGA


Statistics
Matches: 70,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
   1    1  0.01
   2   69  0.99

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:14080 original size:11 final size:11

Alignment explanation


    Indices: 14064--14088  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

      14054 TATATATGTA

                       
      14064 TATCTATATAC
          1 TATCTATATAC

                       
      14075 TATCTATATAC
          1 TATCTATATAC

               
      14086 TAT
          1 TAT

      14089 ATAAGTCTAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48


Consensus pattern (11 bp):   
TATCTATATAC

Found at i:14165 original size:25 final size:26

Alignment explanation


    Indices: 14128--14179  Score: 97
    Period size: 25  Copynumber: 2.0  Consensus size: 26

      14118 GAAATATCTA

                                      
      14128 AAATACCCTTTTAATTTTAAAATTTT
          1 AAATACCCTTTTAATTTTAAAATTTT

                                      
      14154 AAATA-CCTTTTAATTTTAAAATTTT
          1 AAATACCCTTTTAATTTTAAAATTTT

             
      14179 A
          1 A

      14180 GTTTAAGCAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  25   21  0.81
  26    5  0.19

ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50


Consensus pattern (26 bp):   
AAATACCCTTTTAATTTTAAAATTTT
Done.