Locus 903

Sequence ID	X_DroMel_CAF1
Location	2,515,395 – 2,515,589
Length	194
Max. P	0.999272

overview

Window 3

Location	2,515,395 – 2,515,509
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.97
Mean single sequence MFE	-23.24
Consensus MFE	-19.36
Energy contribution	-19.16
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-2.06
Structure conservation index	0.83
SVM decision value	1.66
SVM RNA-class probability	0.970275
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2515395 114 + 22224390
AUAUACCCA----A-AACAGAAAAACUGUGCCGCUUUAGACGCUUUAUCAAUUUCAAAGAACCGAAAAGGAAAUACUCUA-ACGCCUAGAGUAUUUAACAGACCAUUAAAAACCUGAUGG
.........----.-..........((((.((((.......))........((((........)))).))((((((((((-.....)))))))))).)))).((((((......)))))) ( -21.10)
>DroSec_CAF1 13619 113 + 1
AU--ACCCA----AAAACAGAAAAACUGUGCCGCUUUAGACGCUUUGUAAGUUUCAAAGAACCGAAAAGGAAAUACUCUA-ACGCCUAGAGUAUUUAACAGACCAUUAAAAACCUGAUGG
..--.....----............((((.((..((..(...(((((.......)))))..)..))..))((((((((((-.....)))))))))).)))).((((((......)))))) ( -24.00)
>DroSim_CAF1 13609 112 + 1
AU--ACCCA----A-AACAGAAAAACUGUGCCGCUUUAGACGCUUUAUACGUUUCAAAGAACCGAAAAGGAAAUACUCUA-ACGCCUAGAGUAUUCAACAGACCAUUAAAAACCUGAUGG
..--.....----.-..........((((....(((((((((.......))))).))))..((.....)).(((((((((-.....)))))))))..)))).((((((......)))))) ( -22.00)
>DroEre_CAF1 14342 118 + 1
GU--AUCCAUACAAAUCCUGAAAAACUGUGCCGCUUAAGACGCUUGAUAAGUUUUUUAAAACCGAAAAGGAAAUACUCUAAACGCCUAGAGUAUUUAACAGACCAUUAAAAACCUGAUGG
..--..............(((((((((...(.((.......))..)...)))))))))...((.....))((((((((((......))))))))))......((((((......)))))) ( -22.70)
>DroYak_CAF1 15595 113 + 1
GU--ACC-AU---CAUACUGAAAAACUGUGCCGCUUAAGACGCUUGAUAAGUUUUAAAGAACCGAAAGGGAAAUACUCUA-ACGCCUAGAGUAUUUAACAGACCAUUGAAAACCUGAUGG
..--.((-((---((..((..((((((...(.((.......))..)...))))))..))..((....)).((((((((((-.....))))))))))..................)))))) ( -26.40)
>consensus
AU__ACCCA____AAAACAGAAAAACUGUGCCGCUUUAGACGCUUUAUAAGUUUCAAAGAACCGAAAAGGAAAUACUCUA_ACGCCUAGAGUAUUUAACAGACCAUUAAAAACCUGAUGG
.........................((((.((((.......))........((((........)))).))((((((((((......)))))))))).)))).((((((......)))))) (-19.36 = -19.16 +  -0.20)

alignment

secondary structure

dotplot

Window 4

Location	2,515,430 – 2,515,549
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.30
Mean single sequence MFE	-28.38
Consensus MFE	-25.50
Energy contribution	-25.34
Covariance contribution	-0.16
Combinations/Pair	1.10
Mean z-score	-2.34
Structure conservation index	0.90
SVM decision value	3.48
SVM RNA-class probability	0.999272
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2515430 119 + 22224390
CGCUUUAUCAAUUUCAAAGAACCGAAAAGGAAAUACUCUA-ACGCCUAGAGUAUUUAACAGACCAUUAAAAACCUGAUGGCAACAACAACAACUACGCAGGCAGCAGGAGCUGCACCAGC
.(((.......((((........)))).((((((((((((-.....))))))))))....(.((((((......)))))))...................(((((....))))).))))) ( -27.40)
>DroSec_CAF1 13653 119 + 1
CGCUUUGUAAGUUUCAAAGAACCGAAAAGGAAAUACUCUA-ACGCCUAGAGUAUUUAACAGACCAUUAAAAACCUGAUGGCAACAACAACAACCACGCAGGCAGCAGGAGCUGCACCAGC
.(((((((...((((........)))).((((((((((((-.....))))))))))....(.((((((......)))))))...........))..))))(((((....)))))...))) ( -29.30)
>DroSim_CAF1 13642 119 + 1
CGCUUUAUACGUUUCAAAGAACCGAAAAGGAAAUACUCUA-ACGCCUAGAGUAUUCAACAGACCAUUAAAAACCUGAUGGCAACAACAACAACCUCGCAGGGAGCAGGAGCUGCACCAGC
.((........((((........))))(((.(((((((((-.....))))))))).....(.((((((......)))))))...........))).))..((.((((...)))).))... ( -25.30)
>DroEre_CAF1 14380 120 + 1
CGCUUGAUAAGUUUUUUAAAACCGAAAAGGAAAUACUCUAAACGCCUAGAGUAUUUAACAGACCAUUAAAAACCUGAUGGCAACAACAACAACCACGCAGGCAGCAGGAGCUGCACCAGC
.((.((....(((........((.....))((((((((((......))))))))))))).(.((((((......)))))))............)).))..(((((....)))))...... ( -28.90)
>DroYak_CAF1 15629 119 + 1
CGCUUGAUAAGUUUUAAAGAACCGAAAGGGAAAUACUCUA-ACGCCUAGAGUAUUUAACAGACCAUUGAAAACCUGAUGGCAACAACAACAACCACGCAGGCAGCAGGAGCUGCACCAGC
.((.((....(((((......((....)).((((((((((-.....))))))))))............))))).((.((....)).)).....)).))..(((((....)))))...... ( -31.00)
>consensus
CGCUUUAUAAGUUUCAAAGAACCGAAAAGGAAAUACUCUA_ACGCCUAGAGUAUUUAACAGACCAUUAAAAACCUGAUGGCAACAACAACAACCACGCAGGCAGCAGGAGCUGCACCAGC
.((........((((........)))).((((((((((((......))))))))))....(.((((((......)))))))...........))..))..(((((....)))))...... (-25.50 = -25.34 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	2,515,470 – 2,515,589
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.80
Mean single sequence MFE	-24.68
Consensus MFE	-20.60
Energy contribution	-20.88
Covariance contribution	0.28
Combinations/Pair	1.04
Mean z-score	-2.17
Structure conservation index	0.83
SVM decision value	2.05
SVM RNA-class probability	0.986588
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2515470 119 + 22224390
-ACGCCUAGAGUAUUUAACAGACCAUUAAAAACCUGAUGGCAACAACAACAACUACGCAGGCAGCAGGAGCUGCACCAGCUCUCAAUUUAUUGCCCGCCAGCAAUAACAAUAUAAAUAAU
-..((((.((((..........((((((......))))))...........))).)..))))....(((((((...)))))))....(((((((......)))))))............. ( -25.60)
>DroSec_CAF1 13693 119 + 1
-ACGCCUAGAGUAUUUAACAGACCAUUAAAAACCUGAUGGCAACAACAACAACCACGCAGGCAGCAGGAGCUGCACCAGCUCUCAAUUUAUUGCCCGCCAGCAAUAACCACAUAAAUAAU
-..((((...((.....)).(.((((((......))))))).................))))....(((((((...)))))))....(((((((......)))))))............. ( -25.00)
>DroSim_CAF1 13682 119 + 1
-ACGCCUAGAGUAUUCAACAGACCAUUAAAAACCUGAUGGCAACAACAACAACCUCGCAGGGAGCAGGAGCUGCACCAGCUCUCAAUCUAUUGCCCGCCAGCAAUAACAACAUAAAUAAU
-...(((.(((...((....))((((((......)))))).............)))..)))((...(((((((...)))))))...))((((((......)))))).............. ( -24.20)
>DroEre_CAF1 14420 120 + 1
AACGCCUAGAGUAUUUAACAGACCAUUAAAAACCUGAUGGCAACAACAACAACCACGCAGGCAGCAGGAGCUGCACCAGCUCUCAAUUUAUUGCCCGCCAGCAAUAAUAACACAAAUAAU
...((((...((.....)).(.((((((......))))))).................))))....(((((((...)))))))....(((((((......)))))))............. ( -25.10)
>DroYak_CAF1 15669 116 + 1
-ACGCCUAGAGUAUUUAACAGACCAUUGAAAACCUGAUGGCAACAACAACAACCACGCAGGCAGCAGGAGCUGCACCAGCUCUCAACCUAUUGCCCGCCA---UUGAUAACACAAAUAAU
-..((((((.((.(((((.......))))).)))))..)))...............((.(((((.((((((((...))))).....))).))))).))..---................. ( -23.50)
>consensus
_ACGCCUAGAGUAUUUAACAGACCAUUAAAAACCUGAUGGCAACAACAACAACCACGCAGGCAGCAGGAGCUGCACCAGCUCUCAAUUUAUUGCCCGCCAGCAAUAACAACAUAAAUAAU
...((((((.((.(((((.......))))).)))))..)))...............((.(((((..(((((((...))))))).......))))).))...................... (-20.60 = -20.88 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:41 2006