[maker-devel] <MAKER Trac Server> #4: Sequence length growing with MAKER masking

[MAKER]

#4: Sequence length growing with MAKER masking
-------------------------------------------+--------------------------------
 Reporter:  barry.moore at genetics.utah.edu  |       Owner:  Carson                
     Type:  defect                         |      Status:  new                   
 Priority:  minor                          |   Milestone:  Primary Stable Release
Component:  Code                           |     Version:  0.001                 
 Keywords:                                 |  
-------------------------------------------+--------------------------------
 I just noticed that the sequences in a RepeatRunner masked output fasta
 generated by MAKER are sometimes longer than those in the original fasta
 file.  This happens in 111 sequences out of the 714 Phylium scaffolds.

 I'm guessing this is just extra Ns during hard masking, so it wouldn't
 have an effect on MAKER function, but I thought I go ahead and report it
 to the bug tracker just in case this is the symptom of a larger problem.
 The size differences range from 11-99 nts, with a mean/median/mode of
 42/47/50.

 The IDs of the sequences (along with the size difference of the sequences)
 are in the following list:

 >1107000913275  50
 >1107000913276  37
 >1107000913278  21
 >1107000913284  50
 >1107000913289  41
 >1107000913290  42
 >1107000913298  36
 >1107000913309  36
 >1107000913313  50
 >1107000913324  16
 >1107000913326  50
 >1107000913331  48
 >1107000913332  23
 >1107000913339  49
 >1107000913340  18
 >1107000913341  50
 >1107000913342  27
 >1107000913350  49
 >1107000913351  92
 >1107000913364  50
 >1107000913372  50
 >1107000913373  44
 >1107000913374  15
 >1107000913394  42
 >1107000913395  45
 >1107000913416  48
 >1107000913425  27
 >1107000913430  46
 >1107000913433  49
 >1107000913439  47
 >1107000913444  41
 >1107000913461  48
 >1107000913471  48
 >1107000913473  30
 >1107000913476  49
 >1107000913480  48
 >1107000913484  49
 >1107000913494  49
 >1107000913510  29
 >1107000913512  50
 >1107000913524  46
 >1107000913526  86
 >1107000913534  99
 >1107000913550  11
 >1107000913554  18
 >1107000913563  49
 >1107000913566  33
 >1107000913571  37
 >1107000913574  30
 >1107000913575  39
 >1107000913577  49
 >1107000913578  18
 >1107000913592  48
 >1107000913598  49
 >1107000913612  50
 >1107000913614  41
 >1107000913636  48
 >1107000913638  39
 >1107000913639  48
 >1107000913651  16
 >1107000913652  48
 >1107000913653  41
 >1107000913662  48
 >1107000913663  45
 >1107000913668  47
 >1107000913672  48
 >1107000913686  45
 >1107000913696  50
 >1107000913700  48
 >1107000913704  43
 >1107000913707  37
 >1107000913712  50
 >1107000913718  14
 >1107000913719  27
 >1107000913720  49
 >1107000913729  49
 >1107000913744  43
 >1107000913745  38
 >1107000913752  43
 >1107000913753  45
 >1107000913761  18
 >1107000913764  45
 >1107000913768  50
 >1107000913772  29
 >1107000913777  48
 >1107000913782  37
 >1107000913794  50
 >1107000913795  34
 >1107000913799  35
 >1107000913815  47
 >1107000913819  49
 >1107000913828  49
 >1107000913841  50
 >1107000913848  48
 >1107000913855  50
 >1107000913874  50
 >1107000913888  27
 >1107000913895  47
 >1107000913906  49
 >1107000913907  36
 >1107000913937  49
 >1107000913938  28
 >1107000913940  34
 >1107000913943  50
 >1107000913945  50
 >1107000913947  50
 >1107000913950  49
 >1107000913956  26
 >1107000913959  50
 >1107000913962  50
 >1107000913964  47

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