# R-scape :: RNA Structural Covariation Above Phylogenetic Expectation
# R-scape 2.6.4.d (December 2025)
# Copyright (C) 2017-2025 Elena Rivas, Harvard University.
# Freely distributed under the GNU General Public License (GPLv3).
#-------------------------------------------------------------------------------------------------------
# MSA xrRNA nseq 71 (71) alen 178 (201) avgid 60.90 (60.63) nbpairs 0 (0)
# 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         [-9.95,114.10]     [5 | 0 0 5 | 0.00 0.00 0.00] 
#
#       left_pos       right_pos        score          E-value           pvalue       substitutions      power
#--------------------------------------------------------------------------------------------------------------
~	      18	      53	114.10068	5.49344e-08	3.48723e-12	23		0.68
~	      10	      28	85.65505	4.34171e-05	2.75611e-09	30		0.76
~	      19	      52	84.08388	6.31734e-05	4.01025e-09	10		0.36
~	       8	      31	64.14652	0.00675761	4.28973e-07	32		0.78
~	       2	      36	60.09942	0.0174266	1.10624e-06	38		0.82

# The given structure

# Power analysis of given structure 
#
# Powertype = SINGLE SUBSTITUTIONS
# covary  left_pos      right_pos    substitutions      power
#----------------------------------------------------------------
#
# BPAIRS 0
# avg substitutions per BP  0.0
# BPAIRS expected to covary 0.0 +/- 0.0
# BPAIRS observed to covary 0
#
# RMs = 0 L = 201
# Number of covarying pairs = 5

#
# Method Target_E-val [cov_min,cov_max] [FP | TP True Found | Sen PPV F] 
# GTp    0.05         [-9.95,114.10]     [0 | 5 21 5 | 23.81 100.00 38.46] 
#
# in_fold in_given   left_pos       right_pos      score           E-value    pvalue       substitutions      power
#-----------------------------------------------------------------------------------------------------------------------
*	~	        18	        53	114.10068	5.49344e-08	3.48723e-12	23		0.68
*	~	        10	        28	85.65505	4.34171e-05	2.75611e-09	30		0.76
*	~	        19	        52	84.08388	6.31734e-05	4.01025e-09	10		0.36
*	~	         8	        31	64.14652	0.00675761	4.28973e-07	32		0.78
*	~	         2	        36	60.09942	0.0174266	1.10624e-06	38		0.82

# The predicted CaCoFold structure

# Power analysis of CaCoFold structure 
#
# Powertype = SINGLE SUBSTITUTIONS
# covary  left_pos      right_pos    substitutions      power
#----------------------------------------------------------------
          1		43		27		0.73
     *    2		36		38		0.82
          3		35		30		0.76
          5		154		21		0.64
          6		33		3		0.04
          6		153		7		0.24
          7		32		3		0.04
          7		152		5		0.15
     *    8		31		32		0.78
          9		30		33		0.79
     *    10		28		30		0.76
          11		27		18		0.58
          17		55		25		0.70
     *    18		53		23		0.68
     *    19		52		10		0.36
          20		51		1		0.00
          104		141		8		0.28
          105		140		16		0.54
          106		139		43		0.85
          107		138		0		0.00
          108		137		2		0.00
#
# BPAIRS 21
# avg substitutions per BP  17.9
# BPAIRS expected to covary 9.7 +/- 1.8
# BPAIRS observed to covary 5
#
# RMs = 5 L = 201

# RM_HELIX NESTED 17-20 51-55, nbp = 4 nbp_cov = 2
# aggregated NONE
n/a
NESTED  ::::::::::::::::<<<<_______________________>>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :::::::::::::::::<<_________________________>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NESTED  ::::::::::::::::<<<<______________________________>>>->::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :::::::::::::::::<<________________________________>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

# RM_HELIX NESTED 104-108 137-141, nbp = 5 nbp_cov = 0
# aggregated NONE
n/a
NESTED  :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<<<<<____________________________>>>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NESTED  :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<<<<<____________________________>>>>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

# RM_HELIX NESTED 5-7 152-154, nbp = 3 nbp_cov = 0
# aggregated NONE
n/a
NESTED  ::::<<<____________________________________________________________________________________________________________________________>>>::::::::::::::::::::::::::::::::::::::::::::
        ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NESTED  ::::<<<________________________________________________________________________________________________________________________________________________>>>:::::::::::::::::::::::::::::::::::::::::::::::
        :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

# RM_HELIX PK 1-3 35-43, nbp = 3 nbp_cov = 1
# aggregated NONE
n/a
PK      <<<_______________________________>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :<_________________________________>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
PK      <<<_______________________________>>------>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :<_________________________________>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

# RM_HELIX TRIPLET 6-11 27-33, nbp = 6 nbp_cov = 2
# aggregated NONE
n/a
TRIPLET :::::<<<<<<_______________>>->>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :::::::<-<_________________>-->:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
TRIPLET :::::<<<<<<_______________>>->>>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :::::::<-<_________________>-->::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# MSA xrRNA alen=178 nseq=71 time=6.44 secs

