# R-scape :: RNA Structural Covariation Above Phylogenetic Expectation
# R-scape 2.0.5 (September 2024)
# Copyright (C) 2017-2024 Elena Rivas, Harvard University.
# Freely distributed under the GNU General Public License (GPLv3).
#-------------------------------------------------------------------------------------------------------
# MSA seq+RF00026_seed_1 nseq 189 (189) alen 108 (225) avgid 70.90 (69.92) nbpairs 5 (5)
# One-set statistical test (all pairs are tested as equivalent) 
#
#
# Method Target_E-val [cov_min,cov_max] [FP | TP True Found | Sen PPV F] 
# GTp    0.05         [-9.95,272.78]     [0 | 3 5 3 | 60.00 100.00 75.00] 
#
#       left_pos       right_pos        score          E-value           pvalue       substitutions      power
#--------------------------------------------------------------------------------------------------------------
*	       2	      50	272.77949	4.86652e-07	8.42249e-11	49		0.86
*	       3	      49	258.80373	1.66548e-06	2.88245e-10	59		0.89
*	       5	      45	214.78797	8.08633e-05	1.3995e-08	56		0.88

# The given structure

# Power analysis of given structure 
#
# Powertype = SINGLE SUBSTITUTIONS
# covary  left_pos      right_pos    substitutions      power
#----------------------------------------------------------------
          1		51		33		0.77
     *    2		50		49		0.86
     *    3		49		59		0.89
          4		46		51		0.87
     *    5		45		56		0.88
#
# BPAIRS 5
# avg substitutions per BP  49.6
# BPAIRS expected to covary 4.3 +/- 0.8
# BPAIRS observed to covary 3
#
# RMs = 1 L = 225

# RM_HELIX 1-5 45-51, nbp = 5 nbp_cov = 3
# aggregated NONE
NESTED  <<<<<_________>>>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :<<-<_________>->>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NESTED  <<<<<_______________________________________>>-->>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :<<-<_______________________________________>--->>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# Number of covarying pairs = 3

#
# Method Target_E-val [cov_min,cov_max] [FP | TP True Found | Sen PPV F] 
# GTp    0.05         [-9.95,272.78]     [0 | 3 19 3 | 15.79 100.00 27.27] 
#
# in_fold in_given   left_pos       right_pos      score           E-value    pvalue       substitutions      power
#-----------------------------------------------------------------------------------------------------------------------
*	*	         2	        50	272.77949	4.86652e-07	8.42249e-11	49		0.86
*	*	         3	        49	258.80373	1.66548e-06	2.88245e-10	59		0.89
*	*	         5	        45	214.78797	8.08633e-05	1.3995e-08	56		0.88

# The predicted CaCoFold structure

# Power analysis of CaCoFold structure 
#
# Powertype = SINGLE SUBSTITUTIONS
# covary  left_pos      right_pos    substitutions      power
#----------------------------------------------------------------
          1		51		33		0.77
     *    2		50		49		0.86
     *    3		49		59		0.89
          4		46		51		0.87
     *    5		45		56		0.88
          91		190		17		0.52
          92		189		19		0.57
          93		188		16		0.50
          94		187		23		0.64
          152		186		18		0.55
          153		185		18		0.55
          154		181		17		0.52
          155		180		12		0.39
          156		179		12		0.39
          157		178		13		0.42
          158		177		12		0.39
          159		176		6		0.16
          161		173		5		0.11
          162		172		5		0.11
#
# BPAIRS 19
# avg substitutions per BP  23.2
# BPAIRS expected to covary 10.1 +/- 1.9
# BPAIRS observed to covary 3
#
# RMs = 2 L = 225

# RM_HELIX 1-5 45-51, nbp = 5 nbp_cov = 3
# aggregated NONE
NESTED  <<<<<_________>>>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :<<-<_________>->>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NESTED  <<<<<_______________________________________>>-->>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :<<-<_______________________________________>--->>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

# RM_HELIX 91-162 172-190, nbp = 14 nbp_cov = 0
# aggregated NONE
NESTED  ::::::::::::::::::::::::::::::::::::::::::::::::<<<<<<<<<<<<<<________>>-->>>>>>>>>>>>::::::::::::::::::::::
        ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NESTED  ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<<<<---------------------------------------------------------<<<<<<<<-<<_________>>-->>>>>>--->>>>>>:::::::::::::::::::::::::::::::::::
        :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
