File formats
Structure files
Dot-bracket
>RNA#1
GGGAUAUAGCGUAUAGCGCGCGCGAUAUUAUAUCGGAUCGCGCCAUUCGCGCCC
(((.....(((.((.(((((..(((((...)))))...))))).)).))).)))
Multiple structures within the same file are allowed.
Connectivity table (CT)
54 RNA#1
1 G 0 2 54 1
2 G 1 3 53 2
3 G 2 4 52 3
4 A 3 5 0 4
5 U 4 6 0 5
6 A 5 7 0 6
7 U 6 8 0 7
8 A 7 9 0 8
9 G 8 10 50 9
10 C 9 11 49 10
11 G 10 12 48 11
12 U 11 13 0 12
13 A 12 14 46 13
14 U 13 15 45 14
15 A 14 16 0 15
16 G 15 17 43 16
17 C 16 18 42 17
18 G 17 19 41 18
19 C 18 20 40 19
20 G 19 21 39 20
21 C 20 22 0 21
22 G 21 23 0 22
23 C 22 24 35 23
24 G 23 25 34 24
25 A 24 26 33 25
26 U 25 27 32 26
27 A 26 28 31 27
28 U 27 29 0 28
29 U 28 30 0 29
30 A 29 31 0 30
31 U 30 32 27 31
32 A 31 33 26 32
33 U 32 34 25 33
34 C 33 35 24 34
35 G 34 36 23 35
36 G 35 37 0 36
37 A 36 38 0 37
38 U 37 39 0 38
39 C 38 40 20 39
40 G 39 41 19 40
41 C 40 42 18 41
42 G 41 43 17 42
43 C 42 44 16 43
44 C 43 45 0 44
45 A 44 46 14 45
46 U 45 47 13 46
47 U 46 48 0 47
48 C 47 49 11 48
49 G 48 50 10 49
50 C 49 51 9 50
51 G 50 52 0 51
52 C 51 53 3 52
53 C 52 54 2 53
54 C 53 0 1 54
Multiple structures within the same file are allowed.
Stockholm
# STOCKHOLM 1.0
#=GF ID Glycine
#=GF AC RF00504
#=GF DE Glycine riboswitch aptamer
#=GF AU Moxon SJ; 0000-0003-4644-1816
#=GF GA 32.0
#=GF NC 31.9
#=GF TC 32.0
#=GF PI gcvT
#=GF SE Barrick JE, Breaker RR
#=GF SS Predicted; Barrick JE, Breaker RR
#=GF TP Cis-reg; riboswitch;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
#=GF CL CL00125
#=GF DR SO; 0000035; riboswitch;
#=GF DR GO; 0006545; glycine biosynthetic process;
#=GF RN [1]
#=GF RM 15472076
#=GF RT A glycine-dependent riboswitch that uses cooperative binding to control
#=GF RT gene expression.
#=GF RA Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR
#=GF RL Science 2004;306:275-279.
#=GF RN [2]
#=GF RM 29089431
#=GF RT In Vivo Behavior of the Tandem Glycine Riboswitch in Bacillus subtilis.
#=GF RA Babina AM, Lea NE, Meyer MM
#=GF RL MBio. 2017; [Epub ahead of print]
#=GF CC This family represents the bacterial glycine riboswitch. Glycine
#=GF CC riboswitches usually consist of two metabolite-binding aptamers domains
#=GF CC with similar structures in tandem. The aptamers cooperatively bind glycine
#=GF CC to regulate the expression of downstream genes. In Bacillus subtilis, this
#=GF CC riboswitch is found upstream of the gcvT operon which controls glycine
#=GF CC degradation. It is thought that when glycine is in excess it will bind to
#=GF CC both aptamers to activate these genes and facilitate glycine degradation
#=GF CC [1]. In vivo experiments demonstrated that glycine does not need to bind
#=GF CC both aptamers for regulation. Mutation to the first aptamer caused
#=GF CC greatest reduction in downstream gene expression, while mutation to the
#=GF CC second one had varying effects. Glycine-induced expression of the gcvT
#=GF CC operon is needed for B. subtilise growth, swarming motility and biofilm
#=GF CC formation (in high glycine enviroment).[2]
#=GF WK Glycine_riboswitch
#=GF SQ 44
AL766849.1/65640-65772 AGACGGACUU-CUGGAGAGACCUA----------------UAAGUAGCAACAUCUUUGUAUUGACACCAAGAUGUGCUCUAGG-CGCCGAAGGGGCAA-GAAGAGUAAAACAA----------------------CUCC-------------------------UCCAAUCUCUCAGGC---------------AAAAG-
AL766849.1/65560-65639 UGACGUCAUU-CAGGAGAAGAAAG----------------UUAGA----------------------------------CUUU-CGCCGAAGGAAUUA----------------------------------------------------------------------CACUCUCAGGU--------GUCUUAAGACAG-
CR522870.1/1448610-1448703 AUGAACAUAG-CAGGAGAGAUUUU----------------UCCCAUGGCAGUACGGAUGG-----------------GGAAGG-CACCGAAGAAGUAA----------------------------------------------------------------------AUCUUUCAGGU---------------CAAAG-
CR522870.1/1448704-1448793 -----AGCCU-CUGGAGAGUCUC-----------------AUUAU-----------------------------------GGG-CACCGAAGGAGCAA-GCCAGCGUGUA-------------------------GCUG-------------------------GUGAACCUCUCAGGU---------------ACAAGG
BX842577.1/344356-344453 CGCUCUAGUG-CGGGAGAGUUCUGUGGCUG----------CCAGC--------------------------------UACGGA-CGCCGAAGGAGCAAUACCUC-------------------------------UCC--------------------------GUCAACCUCUCAGGC---------------ACCCG-
BX842577.1/344457-344587 -----UGCCU-CUGGAAAGCGGUGGC--------------GACCCCUGGCGGUC-----------------------CUCACC-CGCCGAUGGGGAAA-GGCGAUU-----------------------------CACC-------UGACGGUGGACAGAGUCGCCGAAUCUCUCAGGCGCCUGGCGUGCAGGU--GAA-
AL939108.1/255539-255444 UGACCCCGCG-CGGGAGAGUCCUCCGGAC-----------AUCAC--------------------------------CGGAGG-CGCCGAAGGAGCAA-AUCCU-------------------------------CCCC-------------------------GG-AAUCUCUCAGGC---------------UCACG-
AL939108.1/255442-255325 -----UCACU-CUGGAAAGCAGGGCGGGU-----------GUCGACGGCUUC-------------------------CGCUCU-CACCGACGGUGAAA-GCCGGGCAGAGC------------------------UCCA--------------GGGCUCGCCCGGUGAAGCUCUCAGGU--------------UGAGAU-
AE000516.2/79275-79185 UGACGCGAUG-UGGGAGAA-CCUCC---------------AUGUC----------------------------------GAGG-CGCCGUAGGAGCAA-UCUCCU------------------------------CCCC-------------------------GAGAAUCUCUCAGGC---------------CCAAG-
AE017355.1/2242861-2242742 GGACGAAUCU-CUGGAGAGACUCCCUCUCGCU--------UUAAAUAGCGUAGAGGAA-------------------AACGAG-CACCGAAGGAGCAAAUCCGC-------------------------------UACU-------------------AUAGCGGAUAAUCUCUCAGGU---------------AAAAG-
AE017355.1/2242962-2242862 AUGAACCAUU-CAGGAGAA-GGUC----------------UAUU-----------------------------------GAUC-UACCGACGGGGCAA-AAAGUUGUUAACC-----------------------GACU-------------------------UUGAAACUCUCAGGU--------CUUGUUUACAAG-
AL596168.1/161626-161717 GUGAAUGUAA-ACAGAGAGACUG-----------------UGAAA--------------------------------AG-CAG-CGCCGACGGGGAAA-GCAUAAG-----------------------------UUAU-------------------------GUGAAACUCUCAGGC---------------AAAAG-
BX640445.1/160210-160126 ACGUGCAGUU-CGGGAGAGACCGU----------------CCAGC--------------------------------GGACGG-CGCCGACGGAGCAA-CCA---------------------------------CCCC-------------------------GG-AAACUCUCAGGC---------------AAAAG-
BX640445.1/160122-160016 -----AACAU-CUGGAGAGUGGCGCGCG------------GUAC---------------------------------GGCGCC-CACCGAAGGGGAU--CCCUG-------------------------------GCGC-------GUUUGCAGCGGCGCACGGGUGAAGCUCUCAGGU---------------AAAUG-
D84432.1/169999-170100 AUGACAGCAA-GGGGAGAGACCUGACC-------------GAAAACCUCGGGA------------------------UACAGG-CGCCGAAGGAGCAA-ACU---------------------------------GCGG------------------------AGUGAAUCUCUCAGGC---------------AAAAG-
BX640439.1/206443-206535 ACGCAUGUCG-CGGGAGAGAGCGGCCG-------------AUUGC--------------------------------GGCUGC-CGCCGAAGGCGCAA-UUC---------------------------------GCCC-------------------------GG-AAUCGCUCAGGU--------------AACCCA-
AL591978.1/212840-212931 GUGAAUGUAA-GCAGAGAGACUGC----------------GAAAA----------------------------------GCAG-CGCCGACGGGGAAA-GCAUA-------------------------------UAUU-----------------------AUGUGAAACUCUCAGGC---------------AAAAG-
CR543861.1/1990167-1990077 AUGAUUAUUG-CAGGAGAGAUAUUCU--------------UGCAA--------------------------------AGGAUA-CGCCGAAGGAGCAA-CG----------------------------------ACCC-------------------------CGGAAACUCUCAGGC---------------AGAAG-
CR543861.1/1990073-1989965 -----AUAAU-CUGGAGAGAAGUAUU--------------UCAAA--------------------------------AAUACU-CACCGAAGGGGAUG-GUACG-------------------------------UAGA-----UUUAUGGAAAUCUAUAGCUACCGAAGCUCUCAGGU---------------ACCCU-
CR378670.1/15794-15904 -----AGCCU-CUGGAGAGACCCG----------------UUAAA---------------------------------UCGGG-CGCCGAAGGAGCAA-GCUUU-------------------------------CCUUUUUGCUGUUUUAACAUGCAUGGAAAGUGAAACUCUCAGGC---------------AAAAG-
AJ312125.1/453-315 AGACGAUACU-CUGGAGAGACCA-----------------UAUA------------------------------------AGG-CACCGAAGGAGCAA-AUUUAAUUGAGAUCUUUAUAUAAAUAAAAAAGCUCAUCCC----UUUUUUAGAUCAAGCGAUUAAAUGAAUCUCUCAGGU---------------AAAAG-
AJ312125.1/523-454 AUGAAGGUGG-CAGGAGAGACCC------------------AUGA---------------------------------G-GGG-CGCCGAAGAAGUAA----------------------------------------------------------------------AGCUUUCAGGC--------------U--UAG-
AL939123.1/278145-278052 UGAAUCCGCG-CGGGAGAGUCCCCGG---------------CCGCG-------------------------------CCGGGG-CGCCGAAGGAGCAA-GUCCC-------------------------------UCCC-------------------------UUGAAUCUCUCAGGC---------------ACCGU-
AL939123.1/278050-277936 -----CACAU-CUGAAAAGCGGACCGCC------------CCCGACGG-----------------------------CGGUCC-CACCCAAGGUGCAA-GCCCUGA-----------------------------UCGC-------CGUACUCCGGUGGCCGUGGCGAACCUCUCAGGU--------------UCCGAU-
AJ301559.2/6878-7012 UUCGACAACU-CUGGAAAGUGGUGGGA-------------GCACC----------------------------------CACC-CGCCCAAGGGGAAA-GGUGCCGGU---------------------------GCGC--GCAUGUCAGCGCGCCGUGUUCUACCGAAUCUCUCAGGCGCACGCGUCAGCGAGCACAC-
AJ301559.2/6784-6876 CGCCUGCGCG---GGAGAGUUCCGAGGC------------AUCCAGU------------------------------CUCGGA-CGCCGAAGGAGCAAUACCUC-------------------------------CCC--------------------------GUCAAUCUCUCAGGC---------------ACACG-
BX572605.1/160670-160756 CUAAGUCGCGUCGGGAGAGAUCGGCC--------------GCAA---------------------------------GGCCGG-CGCCGAAGGAGCAA-CCG---------------------------------CCCC-------------------------GG-AAACUCUCAGGC---------------AAACG-
BX572605.1/160757-160849 CGACUGACAU-CUGGAAAGAGACCCUGCCGGGC-------GAUCCCGGGA---------------------------CGGGUC-CGCCGACGGGAUAA----------------------------------------------------------------------UGCUCUCAGGC---------------ACAGC-
AE016822.1/1714518-1714420 GAGGCCGAUG-CGGGAGAGCUGCGGG--------------GGAGAACCCG---------------------------CCCGCGGCACCGAAGGAGCAA-UCCUC-------------------------------CCC--------------------------GACAAUCUCUCAGGU---------------ACGCG-
BX897699.1/1435970-1435876 -----UUUUG-CGGGAGAGUGCAGGC--------------UGCAAGUUUUUGG------------------------GUCUGC-CGCCGAAGGGGAAA-AUA---------------------------------GCCC-------------------------GU-AAUCUCUCAGGC------------UCU--AAG-
BX897699.1/1435871-1435783 -----CAGAU-CUGGAAAGUCGG-----------------GAGG---------------------------------GG-CCG-CGCCGAAGGUGUAA-GCGAA-------------------------------AACU-------------------UUUUUCGCGAGUCUCUCAGGU--------------U--UGU-
BX950851.1/2645129-2645034 UUGAAGCCAA-CUGGAGAGAGGUUGC--------------GAUGC----------------------------------AACC-CACCGAAGGGGCAA-GCAGC-------------------------------UCUG---------------------CUGCGU-AAACUCUCAGGU--------------AAAGCG-
BX950851.1/2645260-2645133 CCGCUCCUCG-CAGGAGAGAGGGCGUGUACUCCAGCAUACUUCAAGCUACAUGUACGUUGGCAUAAAGUAUA-----ACGCUC-CGCCGAAGGCGCAA-AC----------------------------------UCCC-------------------------AU-AAUCGCUCAGGC--------------UACCCU-
AE008691.1/313165-313055 AUGAAGAUAG-CGAGAGAUUAUCUUCC-------------AUAAAUG------------------------------GAAGAU-AGCCGAAGGGGAAA-UACAAAG-----------------------------GCCC-------------GCCAAGCCUUUGUAGAAGCUCUCAGGC---------------GGCAG-
AE008691.1/1826306-1826220 -----AUAUC-CCGGAAAG-CCUC----------------UAAA-----------------------------------GAGG-CACCGAAGGAGCAA-UUCUUCUAU---------------------------AAAG-------------------------AAGAAUCUCUCAGGU---------------AAACA-
AE008923.1/1392465-1392356 -----CAACU-CUGGAGAGACCGGCC--------------GAUG-----------------------------------CCGG-CGCCGAAGGGGCAC-GAAACGCAGGCAG-----------------------GCCA---------CGCGCCAGGCCGCGUUUUUAAACUCUCAGGC---------------AAAAG-
AL591688.1/1674990-1674906 CGACCUCGUU--GGGAGAAACCGG----------------UUCGA---------------------------------UCCGG-UGCCGAAGGAGCAA-CCG---------------------------------CCCC-------------------------GG-AAACUCUCAGGC---------------CAAAG-
AE014292.2/713320-713218 UAAGACAACU-CUGGAAAGUCGGGGG---------------CAAC----------------------------------UCCG-CGCCGAAGGUGUAA-GUAUGGCUUUAUAUAUA-------------------GCCA------------------------UGCGAGUCUCUCAGGC--------------C--UGA-
AE004439.1/116056-116172 -----AACCC-UUGGAGAGAGCCG----------------UUAUAUUAAAAAGAGAUAA------------------AACGGC-CGCCGAAGGCGCAA-AAAGA-------------------------------GCGG---------UUAAUUUUUCCGUUUUUUCAAACGCUCAGGC---------------AAAAG-
AE008691.1/1826408-1826312 AUGAAGAAUG-CGGGAGAGACCC-----------------UAACC-----------------------------------GGG-CGCCGAAGGAGCAA-GCGGGUAUAUGGCCUGUAU-----------------ACUC-------------------------GUGAAACUCUCAGGC---------------AAAAG-
BX842572.1/79202-79095 -----CAACU-CUGGAGACAGGGACG--------------GUCGCACCGACC-------------------------GUGCCU-GACCGAAGGUGUAGAGCGGC-------------------------------GCCA-------------UGAUGCGACGCCGC-AGACUCUCAGGU---------------UUCAG-
AE008922.1/1299977-1299896 GUAACACGGU--GGGAGAA-GCGGC---------------ACUG-----------------------------------CCGC-UGCCGAAGGCGCAA-CA----------------------------------GCCC--------------------------GUAAUCGCUCAGGC--------------C--CGA-
CP000919.1/381215-381303 GGACGGAACU-CUGGAGAGACC------------------GUAAA------------------------------------GG-CACCGAAGGGGCAA-GGCAG-------------------------------GCAA----------------------CUGCUCAAACUCUCAGGU---------------AAAAG-
CP000262.1/1070832-1070913 UGAUGUCAUG-CAGGAGA--AGAA----------------UUUA-----------------------------------UUUU-CGCCGAAGGAGUUA----------------------------------------------------------------------UACUCUCAGGU---GUUCAGUUUUUGAACGG-
#=GC SS_cons :::::(((((.(((,,,,,,<<<<__.............._____................................__>>>>.,<<<<<--<<<---.<<___...............................____.........................>>---->>>>>->>>...............,,,,,.
#=GC RF auaaaccccu.CgGGAGAGacccgcg..............uuaaa................................agcggg.CGCCGAAGGaGcAA.gcaua...............................uCcc.........................gcgAAuCuCUCAGGC...............AaaaG.
AL766849.1/65640-65772 GACAGAAGCUAAAAG
AL766849.1/65560-65639 GACUGAUUGAC----
CR522870.1/1448610-1448703 GACUGCUAUGGGACG
CR522870.1/1448704-1448793 GACAGAGUGUAGCAG
BX842577.1/344356-344453 GACCGCGCGAGACUA
BX842577.1/344457-344587 GACAGAGGGAGAGGG
AL939108.1/255539-255444 UACCGCACGGACGAG
AL939108.1/255442-255325 GACAGAGGGGGAGGC
AE000516.2/79275-79185 CACCACACCGCCGAG
AE017355.1/2242861-2242742 GACAGAGACAAGCGA
AE017355.1/2242962-2242862 UA--GAACUGCAUGG
AL596168.1/161626-161717 GAUGUUUACGGGACG
BX640445.1/160210-160126 GACCGACCUGC----
BX640445.1/160122-160016 GACAGAUGGGGUUGC
D84432.1/169999-170100 AACUCUUGCUCGACG
BX640439.1/206443-206535 UACCGCGACUGCAUC
AL591978.1/212840-212931 GAUGUUUACGGGACG
CR543861.1/1990167-1990077 GACUGUAAUAAUCGA
CR543861.1/1990073-1989965 GACAGAUGGGGCAAC
CR378670.1/15794-15904 GACAGAGGAGAUAAG
AJ312125.1/453-315 GACAGAGAACUGAAU
AJ312125.1/523-454 GACUGUCAUCA----
AL939123.1/278145-278052 UACCGCGCGGGCGAG
AL939123.1/278050-277936 GACAGAUGGGGAGGA
AJ301559.2/6878-7012 GACAGAGGGGGAGGA
AJ301559.2/6784-6876 GAC---GCGUGUGGG
BX572605.1/160670-160756 GACCGCGCGGC----
BX572605.1/160757-160849 GACAGAUGGGGCUCG
AE016822.1/1714518-1714420 UACCGCAUCGGACUG
BX897699.1/1435970-1435876 GACCGUAAAAGAAGA
BX897699.1/1435871-1435783 AACAGAGGGGUGCAG
BX950851.1/2645129-2645034 GACAGAGGGAGUGGC
BX950851.1/2645260-2645133 AACUGCGAAUU----
AE008691.1/313165-313055 GAUCGCUAUCGGAUA
AE008691.1/1826306-1826220 GACGGGGGAAUAAAA
AE008923.1/1392465-1392356 GACAGAGGGGCGCGA
AL591688.1/1674990-1674906 GACC-AGCAAGGUG-
AE014292.2/713320-713218 GACAGAGGGGCACGA
AE004439.1/116056-116172 GACAGGGGCAACAAG
AE008691.1/1826408-1826312 GACCGCAUUC-----
BX842572.1/79202-79095 GACAGAGCGGGGAGG
AE008922.1/1299977-1299896 UACC-AUCUUCAACA
CP000919.1/381215-381303 GACAGAGCUAGGAUA
CP000262.1/1070832-1070913 GACUGUUUGAU----
#=GC SS_cons ,,)))))))):::::
#=GC RF GACcGagggggaaag
//
Alignments must contain the #=GC SS_cons line.
Reactivity
Reactivities must be provided as RNA Framework's XML files:
<?xml version="1.0" encoding="UTF-8"?>
<data>
<transcript id="RNA#1" length="&0">
<sequence>
GGAUGGGGAUCUAUCAGAUUCUGGCGAUCUACUGGACUGUCGCCAGUUCACUGGUGCUUU
</sequence>
<reactivity>
0.296,0.283,4.681,4.500,0.134,0.020,0.015,0.017,0.014,0.036,0.036,0.071,0.058,0.060,0.059,0.015,0.017,0.029,0.316,0.246,0.045,0.063,0.102,0.137,0.072,0.030,0.022,0.026,0.057,0.130,0.105,0.099,0.189,0.165,0.133,0.033,0.101,0.093,0.054,0.062,0.080,0.255,0.118,0.226,0.009,0.057,0.196,0.315,0.123,0.149,0.037,0.026,0.016,0.029,0.048,0.077,0.065,0.087,0.073,0.176
</reactivity>
</transcript>
</data>
Base-pair & helix-level annotations
Base-pair annotations can be provided either as R-scape's .cov files:
#
# Method Target_E-val [cov_min,cov_max] [FP | TP True Found | Sen PPV F]
# GTp 0.1 [-9.95,80.38] [0 | 15 22 15 | 68.18 100.00 81.08]
#
# left_pos right_pos score E-value pvalue substitutions power
#--------------------------------------------------------------------------------------------------------------
* 23 81 80.37853 2.15392e-12 9.79054e-14 32 0.78
* 21 83 72.12266 5.45655e-11 2.48025e-12 22 0.66
* 13 204 69.35723 1.60115e-10 7.27796e-12 15 0.51
* 22 82 60.77186 4.6225e-09 2.10114e-10 22 0.66
* 10 206 56.73722 2.24691e-08 1.02132e-09 15 0.51
* 24 80 53.88919 6.82812e-08 3.10369e-09 30 0.76
* 8 208 44.77264 2.35282e-06 1.06947e-07 28 0.74
* 101 165 42.50258 5.62836e-06 2.55834e-07 24 0.69
* 9 207 40.40155 1.26841e-05 5.76552e-07 33 0.79
* 100 166 40.00270 1.48045e-05 6.7293e-07 31 0.77
* 86 179 34.90543 0.000105498 4.79538e-06 15 0.51
* 94 172 23.67098 0.00699781 0.000318082 16 0.54
* 12 205 21.10188 0.0177879 0.000808543 7 0.24
* 6 210 17.99025 0.0503432 0.00228833 36 0.81
* 14 203 17.58020 0.0577269 0.00262395 4 0.10
or as TSV files:
22 80 type#1
20 82 type#1
12 203 type#2
8 206 type#2
In TSV format, the first two fields correspond to i and j base-pair positions (0-based), while the third field (optional) represents the group ID, which, when present, is used to define different colors for the base-pair groups.
Currently, helix-level annotations can only be provided as R-scape's .helixcov files:
# RMs = 7 L = 237
# RM_HELIX NESTED 42-44 53-55, nbp = 3 nbp_cov = 2
# pvals: 0.283613,1.97783e-07,0.000149597
# aggregated LANCASTER E-value: 8.07703e-09 P-value: 1.15386e-09 *
NESTED ::::::::::::::::::::<<<______>>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
:::::::::::::::::::::<<______>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# RM_HELIX NESTED 14-20 65-70, nbp = 5 nbp_cov = 5
# pvals: 2.34551e-10,8.99662e-16,4.00831e-12,6.14824e-12,2.74706e-11
# aggregated LANCASTER E-value: 6.02847e-50 P-value: 8.61209e-51 *
NESTED ::::::::::::<<<<<_____________________>>>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
::::::::::::<<<<<_____________________>>>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# RM_HELIX NESTED 71-83 147-165, nbp = 10 nbp_cov = 6
# pvals: 1.52662e-07,0.00961031,0.445125,0.445125,0.445125,6.56332e-10,3.48256e-10,1.55891e-16,4.47543e-19,3.29459e-12
# aggregated LANCASTER E-value: 2.51331e-78 P-value: 3.59044e-79 *
NESTED :::::::::::::::::::::::::::::::::::::::::::<<<<-<<<<<<___________>>>>-->>>>>>:::::::::::::::::::::::::::::::::::::
:::::::::::::::::::::::::::::::::::::::::::<-----<<<<<___________>>>>-->---->:::::::::::::::::::::::::::::::::::::
# RM_HELIX NESTED 178-183 216-222, nbp = 6 nbp_cov = 6
# pvals: 5.07931e-10,3.26901e-21,6.3265e-23,5.49811e-26,6.45275e-15,1.3215e-08
# aggregated LANCASTER E-value: 3.44693e-91 P-value: 4.92418e-92 *
NESTED :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<<<<<<______>>>>>>:::::::::::
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<<<<<<______>>>>>>:::::::::::
# RM_HELIX NESTED 170-170 227-227, nbp = 1 nbp_cov = 1
# pvals: 1.72192e-09
# aggregated LANCASTER E-value: 1.20534e-08 P-value: 1.72192e-09 *
NESTED ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<________________________>::::::::
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<________________________>::::::::
# RM_HELIX NESTED 1-9 229-114, nbp = 8 nbp_cov = 6
# pvals: 8.97714e-05,1.75872e-06,4.14908e-08,0.00222791,1.23242e-05,0.310495,0.299138,1.54874e-05
# aggregated LANCASTER E-value: 2.53491e-21 P-value: 3.62129e-22 *
NESTED <<<<<<<<__________________________________________________________________________________________________>>>>>>>>
<<<<<--<__________________________________________________________________________________________________>-->>>>>
# RM_HELIX PK 48-51 171-176, nbp = 4 nbp_cov = 4
# pvals: 3.05913e-07,2.8265e-11,0.000139183,6.80035e-05
# aggregated LANCASTER E-value: 4.41785e-21 P-value: 6.31122e-22 *
PK :::::::::::::::::::::::::<<<<____________________________________________________>>>>:::::::::::::::::::::::::::::
:::::::::::::::::::::::::<<<<____________________________________________________>>>>:::::::::::::::::::::::::::::