Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005461.1 Corchorus capsularis cultivar CVL-1 contig05479, 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: 5916
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35


Found at i:3756 original size:19 final size:19

Alignment explanation


    Indices: 3732--3770  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       3722 GTTTTTTTAG

                               
       3732 ATAATTAGCATAAATTTCA
          1 ATAATTAGCATAAATTTCA

                               
       3751 ATAATTAGCATAAATTTCA
          1 ATAATTAGCATAAATTTCA

             
       3770 A
          1 A

       3771 GCAACAGTGA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36


Consensus pattern (19 bp):   
ATAATTAGCATAAATTTCA

Found at i:4614 original size:7 final size:7

Alignment explanation


    Indices: 4596--4692  Score: 95
    Period size: 6  Copynumber: 14.9  Consensus size: 7

       4586 GCTTGTTATA

                *  
       4596 ATATGTC
          1 ATATATC

                   
       4603 ATATATC
          1 ATATATC

                   
       4610 -T-TAT-
          1 ATATATC

                   
       4614 ATATAT-
          1 ATATATC

                   
       4620 ATATAT-
          1 ATATATC

                   
       4626 ATATAT-
          1 ATATATC

                  *
       4632 ATATATG
          1 ATATATC

                   
       4639 ATATATC
          1 ATATATC

                   
       4646 ATATATC
          1 ATATATC

                   
       4653 ATATATC
          1 ATATATC

                     
       4660 ATATATATC
          1 --ATATATC

                   
       4669 ATATAT-
          1 ATATATC

                   
       4675 ATATAT-
          1 ATATATC

                   
       4681 ATATAT-
          1 ATATATC

                  
       4687 ATATAT
          1 ATATAT

       4693 TAAAACTGTA


Statistics
Matches: 83,  Mismatches: 2, Indels: 11
        0.86            0.02        0.11

Matches are distributed among these distances:
   5    4  0.05
   6   40  0.48
   7   32  0.39
   9    7  0.08

ACGTcount: A:0.44, C:0.06, G:0.02, T:0.47


Consensus pattern (7 bp):   
ATATATC

Found at i:4616 original size:2 final size:2

Alignment explanation


    Indices: 4611--4692  Score: 119
    Period size: 2  Copynumber: 38.5  Consensus size: 2

       4601 TCATATATCT

                                                                          
       4611 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA TCA TA TA TCA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T-A TA TA T-A

                                                                     
       4654 TA TA TCA TA TA TA TCA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA T-A TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T

       4693 TAAAACTGTA


Statistics
Matches: 75,  Mismatches: 0, Indels: 10
        0.88            0.00        0.12

Matches are distributed among these distances:
   2   65  0.87
   3   10  0.13

ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:5864 original size:2 final size:2

Alignment explanation


    Indices: 5857--5916  Score: 120
    Period size: 2  Copynumber: 30.0  Consensus size: 2

       5847 TATTGCAAAC

                                                                          
       5857 AG AG AG AG AG 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 AG AG AG AG AG

                                      
       5899 AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   58  1.00

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


Consensus pattern (2 bp):   
AG

Done.