Locus 2379

Sequence ID	2R_DroMel_CAF1
Location	8,614,054 – 8,614,243
Length	189
Max. P	0.926992

overview

Window 4

Location	8,614,054 – 8,614,169
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.14
Mean single sequence MFE	-34.05
Consensus MFE	-22.56
Energy contribution	-24.38
Covariance contribution	1.81
Combinations/Pair	1.03
Mean z-score	-1.74
Structure conservation index	0.66
SVM decision value	0.27
SVM RNA-class probability	0.661738
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8614054 115 + 20766785
UGGCCGACAUCUCUUUAUCGUGUGAUUCAUUCUGGUU-UGCCUUUGGCAUUGGCUGUGACUCUGGCUCUGGGUCUGGAUUUUCCAGCCCUUUCCCCAACCGAGAUCC----CUGGCCCAC
.(((((..(((((..........((.((((.(..(..-((((...)))))..)..)))).))(((....(((.((((.....))))))).....)))...)))))..----.)))))... ( -35.70)
>DroSec_CAF1 16382 115 + 1
UGGCCGACAUCUCUUUAUCGUGUGAUUCAUUCUGGUU-UGCCUCUGGCAUUGGCUGUGACUCUGGCUCUGGGUCUGGAUUUUCCAGGCCUUACCCAAACCAAGAUCC----CUGGCCCAC
.((((((.(((.(........).)))))((..(((((-((((.........))).........((....((((((((.....))))))))...))))))))..))..----..))))... ( -35.30)
>DroSim_CAF1 12616 109 + 1
UGGCCGACAUCUCUUUAUCGUGUGAUUCAUUCUGGUU-UGCCUCUGGCAUUGGCUGUGACUC------UGGGUCUGGAUUUUCCAGGCCUUACCCAAACCAAGAUCC----CUGGCCCAC
.((((((.(((.(........).)))))((..(((((-((..((((((....)))).))...------.((((((((.....))))))))....)))))))..))..----..))))... ( -33.40)
>DroEre_CAF1 14214 97 + 1
UGGCCGACAUCUCUUUAUCGUGUGAUUCAUUCGGGUUUUGCCUGUGGCAUUGGCUCCGUCCCCGGCUUUG-----------------------CCAUACCGAGAUCCAGAUCUGGCCCAC
.((((((.(((.(........).)))))....((((((((..(((((((..((((........)))).))-----------------------))))).))))))))......))))... ( -31.80)
>consensus
UGGCCGACAUCUCUUUAUCGUGUGAUUCAUUCUGGUU_UGCCUCUGGCAUUGGCUGUGACUCUGGCUCUGGGUCUGGAUUUUCCAGGCCUUACCCAAACCAAGAUCC____CUGGCCCAC
.((((((.(((.(........).)))))(((.(((((..(((.........))).........((....((((((((.....))))))))...)).))))).)))........))))... (-22.56 = -24.38 +   1.81)

alignment

secondary structure

dotplot

Window 5

Location	8,614,054 – 8,614,169
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.14
Mean single sequence MFE	-36.30
Consensus MFE	-23.10
Energy contribution	-23.97
Covariance contribution	0.87
Combinations/Pair	1.04
Mean z-score	-2.23
Structure conservation index	0.64
SVM decision value	1.18
SVM RNA-class probability	0.926992
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8614054 115 - 20766785
GUGGGCCAG----GGAUCUCGGUUGGGGAAAGGGCUGGAAAAUCCAGACCCAGAGCCAGAGUCACAGCCAAUGCCAAAGGCA-AACCAGAAUGAAUCACACGAUAAAGAGAUGUCGGCCA
...((((.(----(.((((((((((.((...(((((((.....)))).)))....)).......)))))..((((...))))-........................))))).)))))). ( -40.50)
>DroSec_CAF1 16382 115 - 1
GUGGGCCAG----GGAUCUUGGUUUGGGUAAGGCCUGGAAAAUCCAGACCCAGAGCCAGAGUCACAGCCAAUGCCAGAGGCA-AACCAGAAUGAAUCACACGAUAAAGAGAUGUCGGCCA
...((((.(----((((..((((((((((.....((((.....))))))))))).)))..)))...(((.........))).-..))..............((((......)))))))). ( -37.60)
>DroSim_CAF1 12616 109 - 1
GUGGGCCAG----GGAUCUUGGUUUGGGUAAGGCCUGGAAAAUCCAGACCCA------GAGUCACAGCCAAUGCCAGAGGCA-AACCAGAAUGAAUCACACGAUAAAGAGAUGUCGGCCA
...((((.(----(.((((((((((((((.....((((.....)))))))).------........(((.........))))-)))).......(((....)))...))))).)))))). ( -33.50)
>DroEre_CAF1 14214 97 - 1
GUGGGCCAGAUCUGGAUCUCGGUAUGG-----------------------CAAAGCCGGGGACGGAGCCAAUGCCACAGGCAAAACCCGAAUGAAUCACACGAUAAAGAGAUGUCGGCCA
...((((.(((....((((((((.(((-----------------------(....(((....))).)))).((((...))))..))).......(((....)))...)))))))))))). ( -33.60)
>consensus
GUGGGCCAG____GGAUCUCGGUUUGGGUAAGGCCUGGAAAAUCCAGACCCAGAGCCAGAGUCACAGCCAAUGCCAGAGGCA_AACCAGAAUGAAUCACACGAUAAAGAGAUGUCGGCCA
...((((.......(((.(((.(((((....((.((((.....)))).))................(((.........)))....))))).))))))....((((......)))))))). (-23.10 = -23.97 +   0.87)

alignment

secondary structure

dotplot

Window 6

Location	8,614,093 – 8,614,209
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	79.80
Mean single sequence MFE	-30.20
Consensus MFE	-19.34
Energy contribution	-21.03
Covariance contribution	1.69
Combinations/Pair	1.00
Mean z-score	-1.78
Structure conservation index	0.64
SVM decision value	0.26
SVM RNA-class probability	0.655775
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8614093 116 + 20766785
CCUUUGGCAUUGGCUGUGACUCUGGCUCUGGGUCUGGAUUUUCCAGCCCUUUCCCCAACCGAGAUCC----CUGGCCCACUUUAUCUCAAGUUUAUCUCAAUUUGAGGAAAGAAACCUCG
.....((....(((((.((((((((....(((.((((.....))))))).....)))...))).)).----).))))..((((.(((((((((......)))))))))))))...))... ( -32.10)
>DroSec_CAF1 16421 114 + 1
CCUCUGGCAUUGGCUGUGACUCUGGCUCUGGGUCUGGAUUUUCCAGGCCUUACCCAAACCAAGAUCC----CUGGCCCACUUUAUCUCAAGUUUAUCUCAAUUUGAGGAAAGAAACCU--
.....(((...((.(.(.....(((....((((((((.....))))))))...))).....).).))----...)))..((((.(((((((((......)))))))))))))......-- ( -32.10)
>DroSim_CAF1 12655 110 + 1
CCUCUGGCAUUGGCUGUGACUC------UGGGUCUGGAUUUUCCAGGCCUUACCCAAACCAAGAUCC----CUGGCCCACUUUAUCUCAAGUUUAUCUCAAUUUGAGGAAAGAAACCUCG
.....(((.((((...((....------.((((((((.....))))))))....))..)))).....----...)))..((((.(((((((((......)))))))))))))........ ( -30.20)
>DroEre_CAF1 14254 97 + 1
CCUGUGGCAUUGGCUCCGUCCCCGGCUUUG-----------------------CCAUACCGAGAUCCAGAUCUGGCCCACUUUAACUCAAGUUUAUCUCAAUUUGAGGAAAGAAACCUCG
..(((((((..((((........)))).))-----------------------))))).((((..(((....)))....((((..((((((((......)))))))).))))....)))) ( -26.40)
>consensus
CCUCUGGCAUUGGCUGUGACUCUGGCUCUGGGUCUGGAUUUUCCAGGCCUUACCCAAACCAAGAUCC____CUGGCCCACUUUAUCUCAAGUUUAUCUCAAUUUGAGGAAAGAAACCUCG
.....((....((((........((....((((((((.....))))))))...))......((........))))))..((((.(((((((((......)))))))))))))...))... (-19.34 = -21.03 +   1.69)

alignment

secondary structure

dotplot

Window 7

Location	8,614,133 – 8,614,243
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.25
Mean single sequence MFE	-31.30
Consensus MFE	-22.66
Energy contribution	-22.86
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.91
Structure conservation index	0.72
SVM decision value	0.66
SVM RNA-class probability	0.815929
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8614133 110 + 20766785
UUCCAGCCCUUUCCCCAACCGAGAUCC----CUGGCCCACUUUAUCUCAAGUUUAUCUCAAUUUGAGGAAAGAAACCUCGGUCUCCG---GAGCAUUUGGCAUGCAGU---GCUCGGGCU
....(((((.........(.((((((.----..((....((((.(((((((((......)))))))))))))...))..)))))).)---(((((((........)))---))))))))) ( -35.20)
>DroSec_CAF1 16461 104 + 1
UUCCAGGCCUUACCCAAACCAAGAUCC----CUGGCCCACUUUAUCUCAAGUUUAUCUCAAUUUGAGGAAAGAAACCU------CCG---GAGCAUUUGGCAUGCAGU---GCUCGGGCU
...((((.(((.........)))...)----)))((((.((((.(((((((((......)))))))))))))......------...---(((((((........)))---)))))))). ( -29.70)
>DroSim_CAF1 12689 110 + 1
UUCCAGGCCUUACCCAAACCAAGAUCC----CUGGCCCACUUUAUCUCAAGUUUAUCUCAAUUUGAGGAAAGAAACCUCGGUCUCCG---GAGCAUUUGGCAUGCAGU---GCUCGGGCU
...((((.(((.........)))...)----)))((((.((((.(((((((((......)))))))))))))......(((...)))---(((((((........)))---)))))))). ( -30.70)
>DroEre_CAF1 14284 104 + 1
-------------CCAUACCGAGAUCCAGAUCUGGCCCACUUUAACUCAAGUUUAUCUCAAUUUGAGGAAAGAAACCUCGGUCUCCG---GAGCAUUGGGCAUGCACUCGGGCUCGGGCU
-------------.....(((((.(((((.....(((((((((..((((((((......)))))))).))))...(..(((...)))---..)...))))).....)).))))))))... ( -32.70)
>DroYak_CAF1 9841 94 + 1
-------------------AGAGAUCC----CUGGCCCACUUUAUCUCAAGUUUAUCUCAAUUUGAGGAAAGAAACCUCGGUCUCCGCAGGAGCAUUUGGCAUGCACU---GCUCGGGCU
-------------------........----..(((((.((((.(((((((((......)))))))))))))..............((((..((((.....)))).))---))..))))) ( -28.20)
>consensus
UUCCAG_CCUU_CCCAAACCGAGAUCC____CUGGCCCACUUUAUCUCAAGUUUAUCUCAAUUUGAGGAAAGAAACCUCGGUCUCCG___GAGCAUUUGGCAUGCAGU___GCUCGGGCU
.................................(((((.((((.(((((((((......)))))))))))))..................((((.....(....)......))))))))) (-22.66 = -22.86 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:36 2006