Locus 3390

Sequence ID	3R_DroMel_CAF1
Location	9,166,917 – 9,167,014
Length	97
Max. P	0.882099

overview

Window 2

Location	9,166,917 – 9,167,014
Length	97
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	78.07
Mean single sequence MFE	-19.40
Consensus MFE	-11.10
Energy contribution	-11.74
Covariance contribution	0.64
Combinations/Pair	1.06
Mean z-score	-2.06
Structure conservation index	0.57
SVM decision value	0.92
SVM RNA-class probability	0.882099
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9166917 97 + 27905053
UCAUUUAUAGACACUAAUUAA-AGUCAGGUCCAUAAAUGAACCAAGUUCAUUACAGACUAUGUAAUUAAGUUC---CAA---UAAAUGCGUUGUAA--------AGAUAGAA
((((((((.(((.((.((...-.)).))))).)))))))).......((.(((((....(((((.(((.....---...---))).))))))))))--------.))..... ( -14.90)
>DroSec_CAF1 4585 84 + 1
UCAUUUAUUGACACUAAUUAAUAGUUAGGUCGAUAAAUGAACCAAGUUCAUUACAGACUAUGUAAUUAAGUUC---CAA---UAAAUGUG----------------------
((((((((((((.(((((.....)))))))))))))))))...((.((.((((((.....)))))).)).)).---...---........---------------------- ( -21.10)
>DroSim_CAF1 3184 98 + 1
UCAUUUAUUGACACUAAUUAAUAGUCAGGUCGAUAAAUGAACCAAGUUCAUUACAGACUAUGUAAUUAAGUUC---CAA---UAAAUGCGUUGUAA--------AGAUAGAA
.(((((((((..((((((((((((((..((.....(((((((...))))))))).)))))).))))).)))..---)))---))))))........--------........ ( -20.80)
>DroEre_CAF1 4499 104 + 1
UCAUUUAUUGACACUAAUUAGUAGUCAGGUCGAUAAAUGUACCAACUUCAUUAUAGACCAUGCACUUAAGUUC---CAU---UAAAUGCGUUGUAGGGGUAUAAAGA--UAA
.(((((((((((((((.....))))...)))))))))))........((.(((((..(((((((.((((....---..)---))).)))))....))..))))).))--... ( -23.40)
>DroYak_CAF1 1059 109 + 1
UCAUUUAUUGGCACUAAUUAAUAGUCACGUCGAUAAAUGUACCAAGUUCAUUAUAGACUACGC---UAAUUUCAUUCAUUCAUAAAUGCGCUGUAAUAAUAUAAAGAUAUAA
.(((((((((((((((.....))))...)))))))))))........((.(((((.((..(((---.....................)))..)).....))))).))..... ( -16.80)
>consensus
UCAUUUAUUGACACUAAUUAAUAGUCAGGUCGAUAAAUGAACCAAGUUCAUUACAGACUAUGUAAUUAAGUUC___CAA___UAAAUGCGUUGUAA________AGAUAGAA
((((((((((((((((.....))))...))))))))))))........................................................................ (-11.10 = -11.74 +   0.64)

alignment

secondary structure

dotplot

Window 3

Location	9,166,917 – 9,167,014
Length	97
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	78.07
Mean single sequence MFE	-20.22
Consensus MFE	-9.30
Energy contribution	-9.38
Covariance contribution	0.08
Combinations/Pair	1.11
Mean z-score	-2.10
Structure conservation index	0.46
SVM decision value	0.64
SVM RNA-class probability	0.807341
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9166917 97 - 27905053
UUCUAUCU--------UUACAACGCAUUUA---UUG---GAACUUAAUUACAUAGUCUGUAAUGAACUUGGUUCAUUUAUGGACCUGACU-UUAAUUAGUGUCUAUAAAUGA
........--------..............---...---(((((..((((((.....))))))......)))))((((((((((((((..-....)))).)))))))))).. ( -19.80)
>DroSec_CAF1 4585 84 - 1
----------------------CACAUUUA---UUG---GAACUUAAUUACAUAGUCUGUAAUGAACUUGGUUCAUUUAUCGACCUAACUAUUAAUUAGUGUCAAUAAAUGA
----------------------..((((((---(((---..(((.(((((.(((((..(((((((((...))))))).....))...)))))))))))))..))))))))). ( -19.80)
>DroSim_CAF1 3184 98 - 1
UUCUAUCU--------UUACAACGCAUUUA---UUG---GAACUUAAUUACAUAGUCUGUAAUGAACUUGGUUCAUUUAUCGACCUGACUAUUAAUUAGUGUCAAUAAAUGA
........--------........((((((---(((---..(((.(((((.((((((.(((((((((...))))))).....))..))))))))))))))..))))))))). ( -23.60)
>DroEre_CAF1 4499 104 - 1
UUA--UCUUUAUACCCCUACAACGCAUUUA---AUG---GAACUUAAGUGCAUGGUCUAUAAUGAAGUUGGUACAUUUAUCGACCUGACUACUAAUUAGUGUCAAUAAAUGA
...--..............(((((((((((---(..---....))))))))....((......)).))))...(((((((.(((((((.......)))).))).))))))). ( -21.90)
>DroYak_CAF1 1059 109 - 1
UUAUAUCUUUAUAUUAUUACAGCGCAUUUAUGAAUGAAUGAAAUUA---GCGUAGUCUAUAAUGAACUUGGUACAUUUAUCGACGUGACUAUUAAUUAGUGCCAAUAAAUGA
...((((....((((((.((.((((.(((((......)))))....---)))).))..)))))).....))))(((((((....((.((((.....))))))..))))))). ( -16.00)
>consensus
UUAUAUCU________UUACAACGCAUUUA___UUG___GAACUUAAUUACAUAGUCUGUAAUGAACUUGGUUCAUUUAUCGACCUGACUAUUAAUUAGUGUCAAUAAAUGA
..................................................((...((......))...))...(((((((.(((((((.......)))).))).))))))). ( -9.30 =  -9.38 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:48 2006