Locus 520

Sequence ID	X_DroMel_CAF1
Location	1,504,618 – 1,504,772
Length	154
Max. P	0.998856

overview

Window 4

Location	1,504,618 – 1,504,732
Length	114
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	67.71
Mean single sequence MFE	-52.77
Consensus MFE	-31.54
Energy contribution	-34.48
Covariance contribution	2.94
Combinations/Pair	1.31
Mean z-score	-2.30
Structure conservation index	0.60
SVM decision value	3.25
SVM RNA-class probability	0.998856
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1504618 114 + 22224390
CAGCAGCAGCGGCGGCCAACAAUAGCGUUAAUGUGGGCGGUGGAUCGGUAGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAGCUGCCGCGGCGGCCGAACUGC
..((((...((((.(((.....((.((((......)))).))...(((((((((..(((...)))..))).((((((((....))))))))..)))))).))).))))..)))) ( -57.30)
>DroVir_CAF1 48029 96 + 1
CUGCGGCGG---CGGUUAACAAUAGUGUU------GCAGGG---------GGCGGGGCUGGGGGGAAUGCUGUGGCCGCAGCAGCAGCUGCCGCUGCGGCCGCUGCUGAGCUGC
(((((((.(---((((...(..((((.((------((....---------.)))).))))..).....))))).)))))))(((((((.((((...)))).)))))))...... ( -51.20)
>DroSec_CAF1 29326 114 + 1
CAGCAGCAGCGGCGGCCAACAAUAGCGUUAAUGUAGGCGGUGGAUCGGUAGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAGCUGCCGCGGCGGCCGAACUGC
..((((...((((.(((.....((.((((......)))).))...(((((((((..(((...)))..))).((((((((....))))))))..)))))).))).))))..)))) ( -57.20)
>DroWil_CAF1 22074 90 + 1
CUGCUGCUG---------GUAAUAGUG------UUGGCGGCG---------GUGGGGCCAAUGGCAAUGCUGUGGCAGCGGCAGCUGCAGCAGCUGCUGCCGCCGCUGAGUUAU
(..((((((---------.((((...)------))).)))))---------)..).(((...)))(((...(((((.((((((((((...)))))))))).)))))...))).. ( -45.40)
>consensus
CAGCAGCAG___CGGCCAACAAUAGCGUU____U_GGCGGUG________GGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCAGCAGCCGCAGCUGCCGCCGCGGCCGAACUGC
.....((((...(((((..................................(((..(((...)))..))).((((((((((((((....)))))))))))))))))))..)))) (-31.54 = -34.48 +   2.94)

alignment

secondary structure

dotplot

Window 5

Location	1,504,618 – 1,504,732
Length	114
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	67.71
Mean single sequence MFE	-41.98
Consensus MFE	-26.38
Energy contribution	-27.50
Covariance contribution	1.12
Combinations/Pair	1.21
Mean z-score	-1.91
Structure conservation index	0.63
SVM decision value	2.39
SVM RNA-class probability	0.993338
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1504618 114 - 22224390
GCAGUUCGGCCGCCGCGGCAGCUGCGGCUGCAGCAGCAGCCACUGCAUUGCCCCCGGCCCCGCCUACCGAUCCACCGCCCACAUUAACGCUAUUGUUGGCCGCCGCUGCUGCUG
(((((.((((.((((.(((((.(((((((((....))))))...))))))))..))))..................(((.(((.((....)).))).))).))))..))))).. ( -48.00)
>DroVir_CAF1 48029 96 - 1
GCAGCUCAGCAGCGGCCGCAGCGGCAGCUGCUGCUGCGGCCACAGCAUUCCCCCCAGCCCCGCC---------CCCUGC------AACACUAUUGUUAACCG---CCGCCGCAG
((.((...((((.((((((((((((....))))))))))))...((..........))......---------..))))------((((....)))).....---..)).)).. ( -38.80)
>DroSec_CAF1 29326 114 - 1
GCAGUUCGGCCGCCGCGGCAGCUGCGGCUGCAGCAGCAGCCACUGCAUUGCCCCCGGCCCCGCCUACCGAUCCACCGCCUACAUUAACGCUAUUGUUGGCCGCCGCUGCUGCUG
(((((.((((.((((.(((((.(((((((((....))))))...))))))))..))))..................(((.(((.((....)).))).))).))))..))))).. ( -48.00)
>DroWil_CAF1 22074 90 - 1
AUAACUCAGCGGCGGCAGCAGCUGCUGCAGCUGCCGCUGCCACAGCAUUGCCAUUGGCCCCAC---------CGCCGCCAA------CACUAUUAC---------CAGCAGCAG
........((((((((((..((((..(((((....)))))..)))).)))))...((.....)---------))))))...------.........---------......... ( -33.10)
>consensus
GCAGCUCAGCCGCCGCGGCAGCUGCGGCUGCAGCAGCAGCCACAGCAUUGCCCCCGGCCCCGCC________CACCGCC_A____AACACUAUUGUUGGCCG___CUGCUGCAG
......(((((((.((....)).)))))))((((((((((....((...((.....))...)).....................(((((....)))))......)))))))))) (-26.38 = -27.50 +   1.12)

alignment

secondary structure

dotplot

Window 6

Location	1,504,658 – 1,504,772
Length	114
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	77.78
Mean single sequence MFE	-60.63
Consensus MFE	-42.51
Energy contribution	-44.97
Covariance contribution	2.46
Combinations/Pair	1.21
Mean z-score	-1.62
Structure conservation index	0.70
SVM decision value	0.59
SVM RNA-class probability	0.791327
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1504658 114 + 22224390
UGGAUCGGUAGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAGCUGCCGCGGCGGCCGAACUGCUUCUCUCUCCGAUCGUUGGCGCCGCUGCCGUGGCCGGGGG
.((..((((((.(((.((((((((....((((((((((((((.(((((....))))).)))))))))..)))))....)))))(....)..))).)))))))))...))..... ( -63.60)
>DroSec_CAF1 29366 114 + 1
UGGAUCGGUAGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAGCUGCCGCGGCGGCCGAACUGCUUCUCUCUCCGAUCGUUGGCGCCGCUGCCGUGGCCGGGGG
.((..((((((.(((.((((((((....((((((((((((((.(((((....))))).)))))))))..)))))....)))))(....)..))).)))))))))...))..... ( -63.60)
>DroWil_CAF1 22099 105 + 1
CG---------GUGGGGCCAAUGGCAAUGCUGUGGCAGCGGCAGCUGCAGCAGCUGCUGCCGCCGCUGAGUUAUUGCUCUCACCAAUUGUGGGGGCAGCCGCUGUGGCGGGGGG
((---------(((((((....((((..(((((.(((((....))))).)))))))))))).)))))).....((((((((((.....))))))))))((((....)))).... ( -54.70)
>consensus
UGGAUCGGUAGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAGCUGCCGCGGCGGCCGAACUGCUUCUCUCUCCGAUCGUUGGCGCCGCUGCCGUGGCCGGGGG
....(((((.((((((((((((((....((((((((((((((.(((((....))))).)))))))))..))))).....)))))).........))).)))))...)))))... (-42.51 = -44.97 +   2.46)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:36 2006