Locus 3166

Sequence ID	X_DroMel_CAF1
Location	8,405,130 – 8,405,310
Length	180
Max. P	0.917516

overview

Window 8

Location	8,405,130 – 8,405,235
Length	105
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.42
Mean single sequence MFE	-30.23
Consensus MFE	-23.29
Energy contribution	-24.60
Covariance contribution	1.31
Combinations/Pair	1.07
Mean z-score	-1.68
Structure conservation index	0.77
SVM decision value	0.42
SVM RNA-class probability	0.729848
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8405130 105 - 22224390
CCUGAAAUCAAGAGACUUUGCCUCGCCACCGAGAAUAGUCAUAUCGCAGCCAAUGCCAUGCUGCUAACAAAGAUAGAUGGUAUGUUUGUGACAUAC---------------AUAUCUUAU
.............((((....((((....))))...)))).....(((((.........))))).....((((((....(((((((...)))))))---------------.)))))).. ( -25.30)
>DroSim_CAF1 7450 101 - 1
CCUGAAAUCAAGAGGCUUUGCCUCGCCACCGAGCACAGUCAUAUCGCAGCCAAUGCCAUGCUGCUGACAAAGAUAGAUGGUAUGUUUGUGACA-------------------UAUCUUAU
.........((((((((.(((.(((....)))))).))))...((((((...(((((((.(((((.....)).))))))))))..))))))..-------------------..)))).. ( -28.00)
>DroEre_CAF1 7795 120 - 1
CCUGAAAUAAAAAGGCUUUGCCUCGCCACCGAGCAAAGUCAUAUCGCAGCCAAUGCCAUGAUGCUGACAAAGCUAGAUGGUAGGUUUGUAGCAUUUUGAUGUUUGGUCAUCAUAUCUAAC
..(((........((((((((.(((....)))))))))))........((((((..((.(((((((.((((.(((.....))).))))))))))).))..).)))))..)))........ ( -33.20)
>DroYak_CAF1 7429 120 - 1
CCUGAAAUAAAGAGGCUUUGCCUCGCCACCGAGCAAAGUCAUAUCGCAGCGAAUGCCAUGAUGCUGACAAAGCUAGAUGGUAUGUUUGUGGCAUUUUGAUGUUUUGUCAUCACAUCUAAA
..........(((((((((((.(((....))))))))))).....((.(((((((((((...(((.....)))...)))))..)))))).))....(((((......)))))..)))... ( -34.40)
>consensus
CCUGAAAUAAAGAGGCUUUGCCUCGCCACCGAGCAAAGUCAUAUCGCAGCCAAUGCCAUGAUGCUGACAAAGAUAGAUGGUAUGUUUGUGACAUUU_______________AUAUCUAAU
.............((((((((.(((....)))))))))))...((((((...(((((((...(((.....)))...)))))))..))))))............................. (-23.29 = -24.60 +   1.31)

alignment

secondary structure

dotplot

Window 9

Location	8,405,155 – 8,405,270
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.61
Mean single sequence MFE	-34.90
Consensus MFE	-28.77
Energy contribution	-29.40
Covariance contribution	0.63
Combinations/Pair	1.17
Mean z-score	-2.06
Structure conservation index	0.82
SVM decision value	1.12
SVM RNA-class probability	0.917516
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8405155 115 + 22224390
CCAUCUAUCUUUGUUAGCAGCAUGGCAUUGGCUGCGAUAUGACUAUUCUCGGUGGCGAGGCAAAGUCUCUUGAUUUCAGGCAUUGCUUCGUUAAUUUUUAGCAUUAAAG-----UGAAUA
...((...(((((...(((((.........)))))...(((.(((.......(((((((((((.((((.........)))).))))))))))).....)))))))))))-----.))... ( -29.50)
>DroSim_CAF1 7471 114 + 1
CCAUCUAUCUUUGUCAGCAGCAUGGCAUUGGCUGCGAUAUGACUGUGCUCGGUGGCGAGGCAAAGCCUCUUGAUUUCAGGAGUUGUUUCGUUAAUUUUCAGCAUUAAAG-----UGAAU-
...((...(((((((((((((.........)))))....)))).(((((...(((((((((((...((((((....)))))))))))))))))......))))).))))-----.))..- ( -33.30)
>DroEre_CAF1 7835 119 + 1
CCAUCUAGCUUUGUCAGCAUCAUGGCAUUGGCUGCGAUAUGACUUUGCUCGGUGGCGAGGCAAAGCCUUUUUAUUUCAGGCAUUGCUUCGUUCAUGUUGGACAUUAAAUUAAAGUGACU-
(((((.(((...((((..(((..(((....)))..))).))))...))).))))).(((((((.((((.........)))).)))))))((((.....)))).................- ( -39.20)
>DroYak_CAF1 7469 114 + 1
CCAUCUAGCUUUGUCAGCAUCAUGGCAUUCGCUGCGAUAUGACUUUGCUCGGUGGCGAGGCAAAGCCUCUUUAUUUCAGGUAUUGCUUCGCUUAUGUUGGACAUUAAAC-----UGAAU-
.((((.(((...((((..(((..(((....)))..))).))))...))).))))(((((((((.((((.........)))).)))))))))....(((........)))-----.....- ( -37.60)
>consensus
CCAUCUAGCUUUGUCAGCAGCAUGGCAUUGGCUGCGAUAUGACUUUGCUCGGUGGCGAGGCAAAGCCUCUUGAUUUCAGGCAUUGCUUCGUUAAUGUUGAACAUUAAAG_____UGAAU_
.((((.(((...((((..(((..(((....)))..))).))))...))).))))(((((((((.((((.........)))).)))))))))............................. (-28.77 = -29.40 +   0.63)

alignment

secondary structure

dotplot

Window 0

Location	8,405,195 – 8,405,310
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	78.71
Mean single sequence MFE	-28.60
Consensus MFE	-17.26
Energy contribution	-17.82
Covariance contribution	0.56
Combinations/Pair	1.24
Mean z-score	-1.91
Structure conservation index	0.60
SVM decision value	0.38
SVM RNA-class probability	0.713272
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8405195 115 + 22224390
GACUAUUCUCGGUGGCGAGGCAAAGUCUCUUGAUUUCAGGCAUUGCUUCGUUAAUUUUUAGCAUUAAAG-----UGAAUACAUAUGUAUAUUUAGUUUAUGAAUUGAGGAAAGUCCCUAA
((((.((((((((((((((((((.((((.........)))).)))))))))).........(((.(((.-----((((((........)))))).)))))).)))))))).))))..... ( -32.60)
>DroSim_CAF1 7511 107 + 1
GACUGUGCUCGGUGGCGAGGCAAAGCCUCUUGAUUUCAGGAGUUGUUUCGUUAAUUUUCAGCAUUAAAG-----UGAAU--------AUAUUGAGUUUACGAAUGGAGGAAAAUCCCUAA
....(((((...(((((((((((...((((((....)))))))))))))))))......)))))....(-----(((((--------.......))))))...(((.((.....))))). ( -28.40)
>DroEre_CAF1 7875 112 + 1
GACUUUGCUCGGUGGCGAGGCAAAGCCUUUUUAUUUCAGGCAUUGCUUCGUUCAUGUUGGACAUUAAAUUAAAGUGACU--------AUAUUUAUUUUUUGAAUUGGGAAAAAUCCUUAG
((.(((.((((((.(((((((((.((((.........)))).)))))))((((.....))))...........)).)))--------..(((((.....))))).))).))).))..... ( -25.60)
>DroYak_CAF1 7509 107 + 1
GACUUUGCUCGGUGGCGAGGCAAAGCCUCUUUAUUUCAGGUAUUGCUUCGCUUAUGUUGGACAUUAAAC-----UGAAU--------AUAUUUAAUUUUUGAGUAGGAAAAAAUCCUUAA
.....(((((((.((((((((((.((((.........)))).))))))))))((((((((........)-----).)))--------)))........)))))))(((.....))).... ( -27.80)
>consensus
GACUUUGCUCGGUGGCGAGGCAAAGCCUCUUGAUUUCAGGCAUUGCUUCGUUAAUGUUGAACAUUAAAG_____UGAAU________AUAUUUAGUUUAUGAAUUGAGAAAAAUCCCUAA
.....(((((((.((((((((((.((((.........)))).))))))))))....)))))))......................................................... (-17.26 = -17.82 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:52 2006