Locus 3739

Sequence ID	X_DroMel_CAF1
Location	9,953,100 – 9,953,245
Length	145
Max. P	0.999171

overview

Window 3

Location	9,953,100 – 9,953,206
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.94
Mean single sequence MFE	-24.44
Consensus MFE	-20.46
Energy contribution	-20.86
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.74
Structure conservation index	0.84
SVM decision value	3.06
SVM RNA-class probability	0.998312
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9953100 106 + 22224390
GGCUCAUGGAGUCACAAACUCAA-----------AACUUAAACUCGAGCUCU---GGCAUCGACAACAAUGCAAGCCAUUGCAUAAAUUAUUGGAAAUUUAUGCGAAAAUUACAGCAACA
(((((((.((((.....))))..-----------.........((((((...---.)).)))).....)))..)))).(((((((((((......))))))))))).............. ( -24.60)
>DroSec_CAF1 15717 106 + 1
GGCUCAUGGAGUCACAAACUCAA-----------AACUUAAACUCGAGCUCU---GGCAUCGACAACAAUGCAAGCCAUUGCAUAAAUUAUUGGAAAUUUAUGCGAAAAUUACAGCAACA
(((((((.((((.....))))..-----------.........((((((...---.)).)))).....)))..)))).(((((((((((......))))))))))).............. ( -24.60)
>DroSim_CAF1 1868 106 + 1
GGCUCAUGGAGUCACAAACUCAA-----------AACUUAAACUCGAGCUCU---GGCAUCGACAACAAUGCAAGCCAUUGCAUAAAUUAUUGGAAAUUUAUGCGAAAAUUACAGCAACA
(((((((.((((.....))))..-----------.........((((((...---.)).)))).....)))..)))).(((((((((((......))))))))))).............. ( -24.60)
>DroEre_CAF1 15694 120 + 1
AGCUCAUGGAGUCACAAACUCAAACUCAAACUCAAACUUAAACUCGAGCUCUCGUGGCAUCGUCAACAAUGCAAGCCAUUGCAUAAAUUAUUGGAAAUUUAUGCGAAAAUUACAGCAACA
.(((((((((((.....)))).........(((............)))....))))((((.(....).))))......(((((((((((......))))))))))).......))).... ( -22.20)
>DroYak_CAF1 15476 105 + 1
AGCUCAUGGAGUCACAAACUC------------CAACUUAAACUCGAGCUCU---GGCAUCGUCAACAAUGCAAGCCAUUGCAUAAAUUAUUGGAAAUUUAUGCGAAAAUUACAGCAACA
.(((..((((((.....))))------------))..........(.(((..---.((((.(....).)))).)))).(((((((((((......))))))))))).......))).... ( -26.20)
>consensus
GGCUCAUGGAGUCACAAACUCAA___________AACUUAAACUCGAGCUCU___GGCAUCGACAACAAUGCAAGCCAUUGCAUAAAUUAUUGGAAAUUUAUGCGAAAAUUACAGCAACA
(((((((.((((.....)))).......................((((((.....))).)))......)))..)))).(((((((((((......))))))))))).............. (-20.46 = -20.86 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	9,953,100 – 9,953,206
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.94
Mean single sequence MFE	-30.40
Consensus MFE	-25.12
Energy contribution	-25.12
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.34
Structure conservation index	0.83
SVM decision value	2.25
SVM RNA-class probability	0.991041
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9953100 106 - 22224390
UGUUGCUGUAAUUUUCGCAUAAAUUUCCAAUAAUUUAUGCAAUGGCUUGCAUUGUUGUCGAUGCC---AGAGCUCGAGUUUAAGUU-----------UUGAGUUUGUGACUCCAUGAGCC
................(((((((((......)))))))))...(((((((((((....)))))).---.(((((((((.......)-----------))))))))..........))))) ( -28.90)
>DroSec_CAF1 15717 106 - 1
UGUUGCUGUAAUUUUCGCAUAAAUUUCCAAUAAUUUAUGCAAUGGCUUGCAUUGUUGUCGAUGCC---AGAGCUCGAGUUUAAGUU-----------UUGAGUUUGUGACUCCAUGAGCC
................(((((((((......)))))))))...(((((((((((....)))))).---.(((((((((.......)-----------))))))))..........))))) ( -28.90)
>DroSim_CAF1 1868 106 - 1
UGUUGCUGUAAUUUUCGCAUAAAUUUCCAAUAAUUUAUGCAAUGGCUUGCAUUGUUGUCGAUGCC---AGAGCUCGAGUUUAAGUU-----------UUGAGUUUGUGACUCCAUGAGCC
................(((((((((......)))))))))...(((((((((((....)))))).---.(((((((((.......)-----------))))))))..........))))) ( -28.90)
>DroEre_CAF1 15694 120 - 1
UGUUGCUGUAAUUUUCGCAUAAAUUUCCAAUAAUUUAUGCAAUGGCUUGCAUUGUUGACGAUGCCACGAGAGCUCGAGUUUAAGUUUGAGUUUGAGUUUGAGUUUGUGACUCCAUGAGCU
....(((.........(((((((((......))))))))).((((...((((((....))))))(((((..((((((..(((((......)))))..)))))))))))...)))).))). ( -34.30)
>DroYak_CAF1 15476 105 - 1
UGUUGCUGUAAUUUUCGCAUAAAUUUCCAAUAAUUUAUGCAAUGGCUUGCAUUGUUGACGAUGCC---AGAGCUCGAGUUUAAGUUG------------GAGUUUGUGACUCCAUGAGCU
....(((......((((((((((((......)))))))))...(((((((((((....)))))).---.))))).))).......((------------(((((...)))))))..))). ( -31.00)
>consensus
UGUUGCUGUAAUUUUCGCAUAAAUUUCCAAUAAUUUAUGCAAUGGCUUGCAUUGUUGUCGAUGCC___AGAGCUCGAGUUUAAGUU___________UUGAGUUUGUGACUCCAUGAGCC
....(((......((((((((((((......)))))))))...(((((((((((....)))))).....))))).)))....)))................(((..((....))..))). (-25.12 = -25.12 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	9,953,129 – 9,953,245
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.52
Mean single sequence MFE	-29.50
Consensus MFE	-26.08
Energy contribution	-26.68
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.71
Structure conservation index	0.88
SVM decision value	3.41
SVM RNA-class probability	0.999171
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9953129 116 + 22224390
AACUCGAGCUCU---GGCAUCGACAACAAUGCAAGCCAUUGCAUAAAUUAUUGGAAAUUUAUGCGAAAAUUACAGCAACAACUGCGACGGCAAAACGACC-ACAAUGUCAGCAACGGGAA
..((((.((...---.))...........(((..(((.(((((((((((......)))))))))))........(((.....)))...))).....(((.-.....))).))).)))).. ( -29.90)
>DroSec_CAF1 15746 117 + 1
AACUCGAGCUCU---GGCAUCGACAACAAUGCAAGCCAUUGCAUAAAUUAUUGGAAAUUUAUGCGAAAAUUACAGCAACAACUGCGACGGCAAAACGACCAACAAUGUCAGCAACGGGAA
..((((.((...---.))...........(((..(((.(((((((((((......)))))))))))........(((.....)))...))).....(((.......))).))).)))).. ( -29.40)
>DroSim_CAF1 1897 117 + 1
AACUCGAGCUCU---GGCAUCGACAACAAUGCAAGCCAUUGCAUAAAUUAUUGGAAAUUUAUGCGAAAAUUACAGCAACAACUGCGACGGCAAAACGACCAACAAUGUCAGCAACGGGAA
..((((.((...---.))...........(((..(((.(((((((((((......)))))))))))........(((.....)))...))).....(((.......))).))).)))).. ( -29.40)
>DroEre_CAF1 15734 119 + 1
AACUCGAGCUCUCGUGGCAUCGUCAACAAUGCAAGCCAUUGCAUAAAUUAUUGGAAAUUUAUGCGAAAAUUACAGCAACAACAGCGACAGCAAAACGACC-ACAAUGUCGGCAACGGGAA
..((((.(((.((((.((((.(....).))))......(((((((((((......))))))))))).................)))).)))....((((.-.....))))....)))).. ( -31.30)
>DroYak_CAF1 15504 116 + 1
AACUCGAGCUCU---GGCAUCGUCAACAAUGCAAGCCAUUGCAUAAAUUAUUGGAAAUUUAUGCGAAAAUUACAGCAACAACUGCGACAGCAAAACGACC-ACAAUGUCUGCAACGGGAA
..((((.(((..---.((((.(....).)))).)))..(((((((((((......)))))))))))........(((.....(((....)))....(((.-.....))))))..)))).. ( -27.50)
>consensus
AACUCGAGCUCU___GGCAUCGACAACAAUGCAAGCCAUUGCAUAAAUUAUUGGAAAUUUAUGCGAAAAUUACAGCAACAACUGCGACGGCAAAACGACC_ACAAUGUCAGCAACGGGAA
..((((.(((.....)))...........(((..(((.(((((((((((......)))))))))))........(((.....)))...))).....(((.......))).))).)))).. (-26.08 = -26.68 +   0.60)

alignment

secondary structure

dotplot

Window 6

Location	9,953,129 – 9,953,245
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.52
Mean single sequence MFE	-33.36
Consensus MFE	-30.62
Energy contribution	-30.90
Covariance contribution	0.28
Combinations/Pair	1.03
Mean z-score	-1.95
Structure conservation index	0.92
SVM decision value	2.55
SVM RNA-class probability	0.995167
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9953129 116 - 22224390
UUCCCGUUGCUGACAUUGU-GGUCGUUUUGCCGUCGCAGUUGUUGCUGUAAUUUUCGCAUAAAUUUCCAAUAAUUUAUGCAAUGGCUUGCAUUGUUGUCGAUGCC---AGAGCUCGAGUU
....((..((((((.....-.))).....(((((.(((((....))))).......(((((((((......))))))))).)))))..((((((....)))))).---..))).)).... ( -32.00)
>DroSec_CAF1 15746 117 - 1
UUCCCGUUGCUGACAUUGUUGGUCGUUUUGCCGUCGCAGUUGUUGCUGUAAUUUUCGCAUAAAUUUCCAAUAAUUUAUGCAAUGGCUUGCAUUGUUGUCGAUGCC---AGAGCUCGAGUU
...((((((((((.((((((((..(((((((.((..((((....))))..))....))).))))..))))))))))).)))))))((.((((((....)))))).---)).......... ( -34.60)
>DroSim_CAF1 1897 117 - 1
UUCCCGUUGCUGACAUUGUUGGUCGUUUUGCCGUCGCAGUUGUUGCUGUAAUUUUCGCAUAAAUUUCCAAUAAUUUAUGCAAUGGCUUGCAUUGUUGUCGAUGCC---AGAGCUCGAGUU
...((((((((((.((((((((..(((((((.((..((((....))))..))....))).))))..))))))))))).)))))))((.((((((....)))))).---)).......... ( -34.60)
>DroEre_CAF1 15734 119 - 1
UUCCCGUUGCCGACAUUGU-GGUCGUUUUGCUGUCGCUGUUGUUGCUGUAAUUUUCGCAUAAAUUUCCAAUAAUUUAUGCAAUGGCUUGCAUUGUUGACGAUGCCACGAGAGCUCGAGUU
....(((((.(((((.(((-(((((((((((.((.((....)).)).)))).....(((((((((......))))))))))))))).)))).))))).)))))...(((....))).... ( -32.30)
>DroYak_CAF1 15504 116 - 1
UUCCCGUUGCAGACAUUGU-GGUCGUUUUGCUGUCGCAGUUGUUGCUGUAAUUUUCGCAUAAAUUUCCAAUAAUUUAUGCAAUGGCUUGCAUUGUUGACGAUGCC---AGAGCUCGAGUU
.....((((((((((((((-((..(.....)..)))))).)))..))))))).((((((((((((......)))))))))...(((((((((((....)))))).---.))))).))).. ( -33.30)
>consensus
UUCCCGUUGCUGACAUUGU_GGUCGUUUUGCCGUCGCAGUUGUUGCUGUAAUUUUCGCAUAAAUUUCCAAUAAUUUAUGCAAUGGCUUGCAUUGUUGUCGAUGCC___AGAGCUCGAGUU
....(((((.(((((.(((.(((((((........(((((....))))).......(((((((((......)))))))))))))))).))).))))).)))))................. (-30.62 = -30.90 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:07 2006