# 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 infernal_1 nseq 71 (71) alen 178 (197) avgid 60.65 (60.40) nbpairs 11 (11)
# 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         [-9.95,118.96]     [2 | 2 11 4 | 18.18 50.00 26.67] 
#
#       left_pos       right_pos        score          E-value           pvalue       substitutions      power
#--------------------------------------------------------------------------------------------------------------
*	      19	      54	118.96332	1.4461e-10	9.17981e-15	23		0.68
*	      20	      53	84.74503	4.2177e-06	2.67739e-10	10		0.36
~	      11	      29	84.13270	5.04413e-06	3.20201e-10	30		0.76
~	       9	      32	71.80894	0.000194742	1.23622e-08	31		0.77

# The given structure

# Power analysis of given structure 
#
# Powertype = SINGLE SUBSTITUTIONS
# covary  left_pos      right_pos    substitutions      power
#----------------------------------------------------------------
          6		150		22		0.66
          7		149		8		0.28
          8		148		4		0.10
     *    19		54		23		0.68
     *    20		53		10		0.36
          21		52		1		0.00
          100		137		9		0.32
          101		136		19		0.60
          102		135		45		0.85
          103		134		0		0.00
          104		133		1		0.00
#
# BPAIRS 11
# avg substitutions per BP  12.9
# BPAIRS expected to covary 3.8 +/- 1.2
# BPAIRS observed to covary 2
#
# RMs = 3 L = 197

# RM_HELIX NESTED 19-21 52-54, nbp = 3 nbp_cov = 2
# aggregated NONE
n/a
NESTED  :::::::::::::::::<<<_______________________>>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :::::::::::::::::<<_________________________>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NESTED  ::::::::::::::::::<<<______________________________>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        ::::::::::::::::::<<________________________________>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

# RM_HELIX NESTED 100-104 133-137, nbp = 5 nbp_cov = 0
# aggregated NONE
n/a
NESTED  :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<<<<<____________________________>>>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NESTED  :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<<<<<____________________________>>>>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

# RM_HELIX NESTED 6-8 148-150, nbp = 3 nbp_cov = 0
# aggregated NONE
n/a
NESTED  ::::<<<____________________________________________________________________________________________________________________________>>>::::::::::::::::::::::::::::::::::::::::::::
        ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NESTED  :::::<<<___________________________________________________________________________________________________________________________________________>>>:::::::::::::::::::::::::::::::::::::::::::::::
        :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# Number of covarying pairs = 4

#
# Method Target_E-val [cov_min,cov_max] [FP | TP True Found | Sen PPV F] 
# GTp    0.05         [-9.95,118.96]     [0 | 4 18 4 | 22.22 100.00 36.36] 
#
# in_fold in_given   left_pos       right_pos      score           E-value    pvalue       substitutions      power
#-----------------------------------------------------------------------------------------------------------------------
*	*	        19	        54	118.96332	1.4461e-10	9.17981e-15	23		0.68
*	*	        20	        53	84.74503	4.2177e-06	2.67739e-10	10		0.36
*	~	        11	        29	84.13270	5.04413e-06	3.20201e-10	30		0.76
*	~	         9	        32	71.80894	0.000194742	1.23622e-08	31		0.77

# The predicted CaCoFold structure

# Power analysis of CaCoFold structure 
#
# Powertype = SINGLE SUBSTITUTIONS
# covary  left_pos      right_pos    substitutions      power
#----------------------------------------------------------------
          6		150		22		0.66
          7		34		3		0.04
          7		149		8		0.28
          8		33		2		0.00
          8		148		4		0.10
     *    9		32		31		0.77
          10		31		30		0.76
     *    11		29		30		0.76
          12		28		18		0.58
          18		55		24		0.69
     *    19		54		23		0.68
     *    20		53		10		0.36
          21		52		1		0.00
          100		137		9		0.32
          101		136		19		0.60
          102		135		45		0.85
          103		134		0		0.00
          104		133		1		0.00
#
# BPAIRS 18
# avg substitutions per BP  15.6
# BPAIRS expected to covary 7.5 +/- 1.6
# BPAIRS observed to covary 4
#
# RMs = 4 L = 197

# RM_HELIX NESTED 18-21 52-55, nbp = 4 nbp_cov = 2
# aggregated NONE
n/a
NESTED  ::::::::::::::::<<<<_______________________>>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :::::::::::::::::<<_________________________>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NESTED  :::::::::::::::::<<<<______________________________>>>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        ::::::::::::::::::<<________________________________>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

# RM_HELIX NESTED 100-104 133-137, nbp = 5 nbp_cov = 0
# aggregated NONE
n/a
NESTED  :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<<<<<____________________________>>>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NESTED  :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<<<<<____________________________>>>>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

# RM_HELIX NESTED 6-8 148-150, nbp = 3 nbp_cov = 0
# aggregated NONE
n/a
NESTED  ::::<<<____________________________________________________________________________________________________________________________>>>::::::::::::::::::::::::::::::::::::::::::::
        ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NESTED  :::::<<<___________________________________________________________________________________________________________________________________________>>>:::::::::::::::::::::::::::::::::::::::::::::::
        :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

# RM_HELIX TRIPLET 7-12 28-34, nbp = 6 nbp_cov = 2
# aggregated NONE
n/a
TRIPLET :::::<<<<<<_______________>>->>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        :::::::<-<_________________>-->:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
TRIPLET ::::::<<<<<<_______________>>->>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
        ::::::::<-<_________________>-->:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# MSA infernal_1 alen=178 nseq=71 time=6.37 secs

