Locus 2633

Sequence ID	2R_DroMel_CAF1
Location	9,302,525 – 9,302,654
Length	129
Max. P	0.955973

overview

Window 0

Location	9,302,525 – 9,302,617
Length	92
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	76.53
Mean single sequence MFE	-28.02
Consensus MFE	-11.27
Energy contribution	-11.88
Covariance contribution	0.61
Combinations/Pair	1.19
Mean z-score	-2.74
Structure conservation index	0.40
SVM decision value	1.46
SVM RNA-class probability	0.955973
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9302525 92 - 20766785
UGCAAUUGGGAAAUUCGUGCGCAUGCUAAAAA--GUAUGCG--AUGCAA-AAUGCAUUAAGCAGACUGUCAUGUACAGUGAGGACUG---GGCGCGACAA
..............((.((((((((((....)--))))))(--((((..-...)))))..))))).((((.((..((((....))))---..)).)))). ( -28.20)
>DroPse_CAF1 151923 87 - 1
ACCC-----CCAAUUCGUGGGCAUGCUGAAAA--AUAUGCA--GUGGAA-AAUGUAUUAAGCACGCUGUCAUGUACAGUGAAGACAG---CGAGCAGCGA
...(-----(((.....))))..((((.....--..(((((--.(....-).)))))...((.(((((((............)))))---)).)))))). ( -23.90)
>DroYak_CAF1 171789 92 - 1
UGCAAUUGGGGAAUUCGUGCGCAUGCUGAAAA--GUAUGCG--AUGCAA-AAUGCAUUAAGCACACUGUCAUGUACAGUGAAGACUG---GGCGCGACAA
................(((((((((((....)--))))))(--((((..-...)))))..))))..((((.((..((((....))))---..)).)))). ( -33.90)
>DroMoj_CAF1 279980 94 - 1
CGCAGU-UGACAAUUCGUGCGCAUGCCGAAAAGAGUAUGCAAAAUGCAAAAAUAUAUUAGGGCAGCUGUCGUCUACAGUGAGGACUG---GCA--AACAA
.((..(-(((..(((..((((((((((.....).)))))).....)))..)))...)))).)).((((((.((......)).))).)---)).--..... ( -21.20)
>DroAna_CAF1 178690 91 - 1
CGC----CGAGAAUUCGUGCGCAUGCUGAAAA--GUAUGCG--UUGCAA-AAUGCAUUAAGCACACUGUCAUGUACAGUGAAGACAGAAGGCGGCGACAA
(((----((....((((((((((((((....)--)))))).--.(((..-...)))....))))(((((.....))))).......)))..))))).... ( -35.70)
>DroPer_CAF1 152395 87 - 1
UGCC-----ACAAUUCGUGCGCAAGCUGAAAA--AUAUGCA--GUGGAA-AAUGUAUUAAGCACGCUGUCAUGUACAGUGAAGACAG---CGAGCAGCGA
((((-----((.....))).))).(((.....--..(((((--.(....-).)))))...((.(((((((............)))))---)).))))).. ( -25.20)
>consensus
UGCA____GACAAUUCGUGCGCAUGCUGAAAA__GUAUGCA__AUGCAA_AAUGCAUUAAGCACACUGUCAUGUACAGUGAAGACAG___GGAGCAACAA
.............(((((((((((((........))))))...(((........)))...))))(((((.....)))))))).................. (-11.27 = -11.88 +   0.61)

alignment

secondary structure

dotplot

Window 1

Location	9,302,542 – 9,302,654
Length	112
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	78.25
Mean single sequence MFE	-29.07
Consensus MFE	-19.86
Energy contribution	-20.62
Covariance contribution	0.75
Combinations/Pair	1.14
Mean z-score	-1.98
Structure conservation index	0.68
SVM decision value	1.27
SVM RNA-class probability	0.938032
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9302542 112 - 20766785
CACGCCUCCAACGAUAUGCACAUUCCACACACAGUGCUGCAAUUGGGAAAUUCGUGCGCAUGCUAAAAAGUAUGCGAUGCAAAAUGCAUUAAGCAGACUGUCAUGUACAGUG
.(((..(((..((((.((((((((........)))).)))))))))))....)))(((((((((....)))))))(((((.....)))))..))..(((((.....))))). ( -29.50)
>DroSim_CAF1 173429 103 - 1
-------ACAACGAUAUGCACAUUCCACACAC--UGCUGCAAUUGGGGAAUUCGUGCGCAUGCUGAAAAGUAUGCGAUGCAAAAUGCAUUAAGCAGACUGUCAUGUACAGUG
-------..........(((((((((...((.--(......).)).)))))..))))(((((((....)))))))(((((.....)))))......(((((.....))))). ( -29.40)
>DroEre_CAF1 173050 99 - 1
-------CCCACGA--UGCACAUUGCAC--AC--UGUUGCAGUUGGGGAAUUCGUGCGCAUGCUGAAAAGUAUGCGAUGCAAAAUGCAUUAAGUACACUGUCAUGUACAGUG
-------((((...--((((((......--..--)).))))..))))......(((((((((((....)))))))(((((.....)))))..))))(((((.....))))). ( -34.80)
>DroWil_CAF1 238805 89 - 1
----------------UGCAGA---CACACAG--UAUUG-AAU-UGACAAUUCGUGCGGAUGCCGAAAAGUAUGCAAGGCAAAAUGUAUUAAGCUCACUGUCAUGUACAGUU
----------------((((((---((...((--(...(-(((-.....))))(((((..((((.............))))...)))))...)))...)))).))))..... ( -16.32)
>DroYak_CAF1 171806 101 - 1
-------CCAACGAUAUGCACAUUGCAC--AC--UGCUGCAAUUGGGGAAUUCGUGCGCAUGCUGAAAAGUAUGCGAUGCAAAAUGCAUUAAGCACACUGUCAUGUACAGUG
-------.(..((((.((((....((..--..--.))))))))))..).....(((((((((((....)))))))(((((.....)))))..))))(((((.....))))). ( -33.60)
>DroAna_CAF1 178710 101 - 1
CACUCCCCCGCCCAUAUGCAUAUUUU-----C--UGGCGC----CGAGAAUUCGUGCGCAUGCUGAAAAGUAUGCGUUGCAAAAUGCAUUAAGCACACUGUCAUGUACAGUG
.........((....(((((((((((-----(--.(....----)))))))..(((((((((((....)))))))).)))...))))))...)).((((((.....)))))) ( -30.80)
>consensus
_______CCAACGAUAUGCACAUUCCAC__AC__UGCUGCAAUUGGGGAAUUCGUGCGCAUGCUGAAAAGUAUGCGAUGCAAAAUGCAUUAAGCACACUGUCAUGUACAGUG
.....................................................(((((((((((....)))))))(((((.....)))))..))))(((((.....))))). (-19.86 = -20.62 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:03 2006