Locus 8202

Sequence ID	X_DroMel_CAF1
Location	20,382,430 – 20,382,556
Length	126
Max. P	0.968943

overview

Window 9

Location	20,382,430 – 20,382,523
Length	93
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	82.32
Mean single sequence MFE	-31.30
Consensus MFE	-23.16
Energy contribution	-23.18
Covariance contribution	0.03
Combinations/Pair	1.05
Mean z-score	-2.06
Structure conservation index	0.74
SVM decision value	0.60
SVM RNA-class probability	0.794949
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20382430 93 + 22224390
---------------CGAAAGGCAGGUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGA---AAU-ACGCUAGACG
---------------.(((((((..((((....)))).))(((((((...)))))))......)))))...((((((((......))))))))..---...-.......... ( -29.80)
>DroVir_CAF1 52191 108 + 1
CGGCCCCCAAAAACCGAGCAGCCUCAUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACG--AAAAU-ACG-UAAACG
(((..........)))....(((((((.....)))).)))(((((((...)))))))(((((.(((((...((((((((......)))))))))--)))))-)))-)..... ( -34.10)
>DroGri_CAF1 46404 105 + 1
UG-----AAAUAACCGAGCAGCCCCAUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGAUUUUUCGCAAAUACGGAAAACGAGAAAAU-ACG-UAAACG
..-----.............(((...(((....))).)))(((((((...)))))))(((((.(((((.((.(((((((......))))))))).))))))-)))-)..... ( -30.90)
>DroMoj_CAF1 62373 110 + 1
CGUACCCAAAAAACCGAGCAGCCUCAUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGAGAAAAU-ACG-UAAACG
(((.................(((((((.....)))).)))(((((((...)))))))(((((.(((((.((.(((((((......))))))))).))))))-)))-)..))) ( -34.20)
>DroAna_CAF1 56441 94 + 1
---------------AGAAAGGCAGGUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGA---AAUUUCGCUAGACG
---------------.(((((((..((((....)))).))(((((((...)))))))......)))))...((((((((......))))))))..---.............. ( -29.70)
>DroPer_CAF1 51884 93 + 1
---------------GGGAAGGCAGGUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGA---AAU-ACGUUAGACG
---------------(..((.((..((((....)))).))(((((((...)))))))......))..)...((((((((......))))))))..---...-.......... ( -29.10)
>consensus
_______________GAGAAGCCACAUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGA___AAU_ACG_UAAACG
.............................((((..(((..(((((((...))))))).)))....))))..((((((((......))))))))................... (-23.16 = -23.18 +   0.03)

alignment

secondary structure

dotplot

Window 0

Location	20,382,430 – 20,382,523
Length	93
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	82.32
Mean single sequence MFE	-31.77
Consensus MFE	-24.42
Energy contribution	-24.44
Covariance contribution	0.03
Combinations/Pair	1.05
Mean z-score	-2.05
Structure conservation index	0.77
SVM decision value	0.68
SVM RNA-class probability	0.821042
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20382430 93 - 22224390
CGUCUAGCGU-AUU---UCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUUUCG---------------
......((((-(((---(((((((((((....)))))))))...))))..)))..(((((((...))))))))).((((....))))..........--------------- ( -27.50)
>DroVir_CAF1 52191 108 - 1
CGUUUA-CGU-AUUUU--CGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGAUGAGGCUGCUCGGUUUUUGGGGGCCG
......-.((-(((((--((((((((((....)))))))))...))))).)))..(((((((...)))))))..(((((....))))).((((.((........)).)))). ( -36.80)
>DroGri_CAF1 46404 105 - 1
CGUUUA-CGU-AUUUUCUCGUUUUCCGUAUUUGCGAAAAAUCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGAUGGGGCUGCUCGGUUAUUU-----CA
......-.((-((((((.((((((.(((....))).)))).)).))))).)))..(((((....))((((((.((((((....)))))).)))))).))).....-----.. ( -33.70)
>DroMoj_CAF1 62373 110 - 1
CGUUUA-CGU-AUUUUCUCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGAUGAGGCUGCUCGGUUUUUUGGGUACG
......-.((-((((((.((((((((((....)))))))).)).))))).)))..(((((((...)))))))(((.((((....).))))))(((((((....))))))).. ( -37.90)
>DroAna_CAF1 56441 94 - 1
CGUCUAGCGAAAUU---UCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUUUCU---------------
((((.((((.....---..(((((((((....)))))))))((((.......)))).))))))))....((((..((((....)))).)))).....--------------- ( -27.80)
>DroPer_CAF1 51884 93 - 1
CGUCUAACGU-AUU---UCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUUCCC---------------
........((-(((---(((((((((((....)))))))))...))))..)))..(((((((...)))))))((.((((....))))..))......--------------- ( -26.90)
>consensus
CGUCUA_CGU_AUU___UCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUGCCC_______________
...................(((((((((....)))))))))(((((........((((((((...)))))))).......)))))........................... (-24.42 = -24.44 +   0.03)

alignment

secondary structure

dotplot

Window 1

Location	20,382,455 – 20,382,556
Length	101
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	79.12
Mean single sequence MFE	-26.15
Consensus MFE	-19.85
Energy contribution	-19.88
Covariance contribution	0.03
Combinations/Pair	1.07
Mean z-score	-2.65
Structure conservation index	0.76
SVM decision value	1.63
SVM RNA-class probability	0.968943
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20382455 101 + 22224390
GCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGA---AAU-ACGCUAGACGAAAAUUCCCUCG------CUCCAAAAACUGCCGAUCCCU
(((((((...)))))))....(((((((...((((((((......))))))))..---...-.(....)..)))))))...(((------(..........).)))..... ( -23.30)
>DroVir_CAF1 52231 86 + 1
GCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACG--AAAAU-ACG-UAAACGAAAACUGGAUG---------CCAA-AAC-----------
(((((((...)))))))(((((.(((((...((((((((......)))))))))--)))))-)))-)..........(((...---------))).-...----------- ( -25.10)
>DroGri_CAF1 46439 89 + 1
GCCGCUGCGUCAGCGGCAUGUAAUUUUCACGAUUUUUCGCAAAUACGGAAAACGAGAAAAU-ACG-UAAACGAAAACUCGCUG---------CCAAAAAC-----------
(((((((...)))))))(((((.(((((.((.(((((((......))))))))).))))))-)))-)...(((....)))...---------........----------- ( -26.50)
>DroMoj_CAF1 62413 89 + 1
GCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGAGAAAAU-ACG-UAAACGAAAACUCGAUG---------CCAAAAAC-----------
(((((((...)))))))(((((.(((((.((.(((((((......))))))))).))))))-)))-)...(((....)))...---------........----------- ( -27.70)
>DroAna_CAF1 56466 100 + 1
GCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGA---AAUUUCGCUAGACGAAAAUUUUAUCG------CUCCAA--GCUGCAGUUUUCC
(((((((...))))))).((((.........((((((((......))))))))..---......(((.(((((........)))------.))..)--))))))....... ( -27.10)
>DroPer_CAF1 51909 107 + 1
GCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGA---AAU-ACGUUAGACGAAAAUUCCCUCGUGCUCGUGCCACAUUCUGCCCAUCUCC
(((((((...)))))))..........((((((((((((......))))))))..---...-.......((((........))))...))))................... ( -27.20)
>consensus
GCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGA___AAU_ACG_UAAACGAAAACUCGAUC_________CCAAAAAC___________
(((((((...)))))))..............((((((((......)))))))).......................................................... (-19.85 = -19.88 +   0.03)

alignment

secondary structure

dotplot

Window 2

Location	20,382,455 – 20,382,556
Length	101
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	79.12
Mean single sequence MFE	-27.59
Consensus MFE	-22.00
Energy contribution	-21.78
Covariance contribution	-0.22
Combinations/Pair	1.08
Mean z-score	-1.62
Structure conservation index	0.80
SVM decision value	0.94
SVM RNA-class probability	0.885625
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20382455 101 - 22224390
AGGGAUCGGCAGUUUUUGGAG------CGAGGGAAUUUUCGUCUAGCGU-AUU---UCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGC
.......((((((..((...(------((..(((((...((.....)).-)))---))(((((((((....))))))))))))...))..)).))))((((...))))... ( -28.40)
>DroVir_CAF1 52231 86 - 1
-----------GUU-UUGG---------CAUCCAGUUUUCGUUUA-CGU-AUUUU--CGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGC
-----------...-..((---------(((..((((((((....-)..-.....--.(((((((((....)))))))))...)))))))..)))))((((...))))... ( -24.30)
>DroGri_CAF1 46439 89 - 1
-----------GUUUUUGG---------CAGCGAGUUUUCGUUUA-CGU-AUUUUCUCGUUUUCCGUAUUUGCGAAAAAUCGUGAAAAUUACAUGCCGCUGACGCAGCGGC
-----------((..((..---------((.(((.(((((((.((-((.-..............))))...))))))).)))))..))..))..(((((((...))))))) ( -26.16)
>DroMoj_CAF1 62413 89 - 1
-----------GUUUUUGG---------CAUCGAGUUUUCGUUUA-CGU-AUUUUCUCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGC
-----------..((((.(---------(...(((....((....-)).-.....)))(((((((((....))))))))).)).))))......(((((((...))))))) ( -26.50)
>DroAna_CAF1 56466 100 - 1
GGAAAACUGCAGC--UUGGAG------CGAUAAAAUUUUCGUCUAGCGAAAUU---UCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGC
.((((......((--(.(((.------(((........)))))))))....))---))(((((((((....))))))))).((((...))))..(((((((...))))))) ( -29.10)
>DroPer_CAF1 51909 107 - 1
GGAGAUGGGCAGAAUGUGGCACGAGCACGAGGGAAUUUUCGUCUAACGU-AUU---UCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGC
.............((((((......((((..(((((...((.....)).-)))---))(((((((((....)))))))))))))....))))))(((((((...))))))) ( -31.10)
>consensus
___________GUUUUUGG_________CAGCGAAUUUUCGUCUA_CGU_AUU___UCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGC
.................................((((((((.....)...........(((((((((....)))))))))...)))))))....(((((((...))))))) (-22.00 = -21.78 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:21 2006