Locus 3709

Sequence ID	2R_DroMel_CAF1
Location	12,304,996 – 12,305,100
Length	104
Max. P	0.842350

overview

Window 5

Location	12,304,996 – 12,305,100
Length	104
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	77.72
Mean single sequence MFE	-33.17
Consensus MFE	-26.22
Energy contribution	-25.50
Covariance contribution	-0.72
Combinations/Pair	1.19
Mean z-score	-0.87
Structure conservation index	0.79
SVM decision value	0.12
SVM RNA-class probability	0.590862
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12304996 104 + 20766785
CCUCUGCCCAAAACGAAU---------GAAGAUUUCGCAGCAGCAGCCUGCCGCGAAACUUUGCCGAGAAGUGCCAAUGUUGCAUCGUCAUGAUUGCGCCGGGCAUCGGCACC
.(((.((...........---------((((.((((((.((((....)))).)))))))))))).)))..(((((.((((((((((.....)).))))....)))).))))). ( -32.50)
>DroVir_CAF1 10077 94 + 1
--GCUGC-----------------GCAUUAGAUUUCGCAGCAGCAGCCUGCCGCGCAAUUUCGCACAAAGGUGCCAGUGCUGCAUUGUGAUGAUUGCGCCGGGCAUUGGCACA
--(((((-----------------(.(......).))))))....(((((((((((((((...(((((.((((....))))...)))))..))))))))..))))..)))... ( -38.90)
>DroPse_CAF1 4181 113 + 1
CCGCAACCUAAAAUGAUGCACUGCGCCAUAGAUUUCGCAGCAGCAGCUUGCCGCGCAACUUUGCACAAAAGUGUCAAUGCUGCAUUGUGAUGAUUGCGCCGGGCAUUGGCACC
..............(((((.((((((.((.....(((((((((((((.....))......((((((....))).)))))))))..)))))..)).))).))))))))...... ( -31.80)
>DroGri_CAF1 2305 96 + 1
UGGUGGC-----------------ACACUAGAUUUCGCAGCAGCAGCUUGCCGCGCAACUUUGCACAACGGUGCCAGUGCUGCAUUGUGAUGAUUGCGCCGGGCAUUGGCACA
..(((((-----------------(..((.(....)((....))))..))))))(((....)))......((((((((((((((..........)))....))))))))))). ( -33.10)
>DroMoj_CAF1 2007 95 + 1
CAACUGC------------------AAUUAGAUUUCGCAGCAGCAGCCUGCCGCGCAACUUUGCACAAAGGUGUCAGUGCUGCAUUGUAAUGAUUGCGCCGGGCAUUGGCACA
....(((------------------((..((.((.(((.((((....)))).))).))))))))).....((((((((((((((..........)))....))))))))))). ( -30.90)
>DroPer_CAF1 1943 113 + 1
CCGCAACCUAAAAUGAUGCACUGCGCCAUAGAUUUCGCAGCAGCAGCUUGCCGCGCAACUUUGCACAAAAGUGUCAAUGCUGCAUUGUGAUGAUUGCGCCGGGCAUUGGCACC
..............(((((.((((((.((.....(((((((((((((.....))......((((((....))).)))))))))..)))))..)).))).))))))))...... ( -31.80)
>consensus
CCGCUGC_________________GCAAUAGAUUUCGCAGCAGCAGCCUGCCGCGCAACUUUGCACAAAAGUGCCAAUGCUGCAUUGUGAUGAUUGCGCCGGGCAUUGGCACA
...................................(((.((((....)))).)))...............((((((((((((((..........)))....))))))))))). (-26.22 = -25.50 +  -0.72)

alignment

secondary structure

dotplot

Window 6

Location	12,304,996 – 12,305,100
Length	104
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	77.72
Mean single sequence MFE	-36.53
Consensus MFE	-25.24
Energy contribution	-25.63
Covariance contribution	0.39
Combinations/Pair	1.09
Mean z-score	-1.50
Structure conservation index	0.69
SVM decision value	0.76
SVM RNA-class probability	0.842350
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12304996 104 - 20766785
GGUGCCGAUGCCCGGCGCAAUCAUGACGAUGCAACAUUGGCACUUCUCGGCAAAGUUUCGCGGCAGGCUGCUGCUGCGAAAUCUUC---------AUUCGUUUUGGGCAGAGG
((((((((((....((...(((.....)))))..)))))))))).(((.((...((((((((((((....))))))))))))..((---------(.......))))).))). ( -39.30)
>DroVir_CAF1 10077 94 - 1
UGUGCCAAUGCCCGGCGCAAUCAUCACAAUGCAGCACUGGCACCUUUGUGCGAAAUUGCGCGGCAGGCUGCUGCUGCGAAAUCUAAUGC-----------------GCAGC--
.((((((.(((...(((............))).))).))))))..(((((((......((((((((....))))))))........)))-----------------)))).-- ( -35.14)
>DroPse_CAF1 4181 113 - 1
GGUGCCAAUGCCCGGCGCAAUCAUCACAAUGCAGCAUUGACACUUUUGUGCAAAGUUGCGCGGCAAGCUGCUGCUGCGAAAUCUAUGGCGCAGUGCAUCAUUUUAGGUUGCGG
((.((....))))..(((((((........(((((.(((.(((....)))))).)))))((((....)))).((((((..(....)..))))))...........))))))). ( -38.80)
>DroGri_CAF1 2305 96 - 1
UGUGCCAAUGCCCGGCGCAAUCAUCACAAUGCAGCACUGGCACCGUUGUGCAAAGUUGCGCGGCAAGCUGCUGCUGCGAAAUCUAGUGU-----------------GCCACCA
.............((((((..........(((((((..(((...((((((((....))))))))..)))..)))))))........)))-----------------))).... ( -34.57)
>DroMoj_CAF1 2007 95 - 1
UGUGCCAAUGCCCGGCGCAAUCAUUACAAUGCAGCACUGACACCUUUGUGCAAAGUUGCGCGGCAGGCUGCUGCUGCGAAAUCUAAUU------------------GCAGUUG
((((((.......))))))...........(((((.(((......(((((((....))))))))))))))).(((((((.......))------------------))))).. ( -32.60)
>DroPer_CAF1 1943 113 - 1
GGUGCCAAUGCCCGGCGCAAUCAUCACAAUGCAGCAUUGACACUUUUGUGCAAAGUUGCGCGGCAAGCUGCUGCUGCGAAAUCUAUGGCGCAGUGCAUCAUUUUAGGUUGCGG
((.((....))))..(((((((........(((((.(((.(((....)))))).)))))((((....)))).((((((..(....)..))))))...........))))))). ( -38.80)
>consensus
GGUGCCAAUGCCCGGCGCAAUCAUCACAAUGCAGCACUGACACCUUUGUGCAAAGUUGCGCGGCAAGCUGCUGCUGCGAAAUCUAAUGC_________________GCAGCGG
.(((((.......)))))..((........(((((..((.(((....)))))..)))))((((((......)))))))).................................. (-25.24 = -25.63 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:25 2006