Locus 766

Sequence ID	2R_DroMel_CAF1
Location	3,706,219 – 3,706,343
Length	124
Max. P	0.999251

overview

Window 4

Location	3,706,219 – 3,706,312
Length	93
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	70.67
Mean single sequence MFE	-25.16
Consensus MFE	-9.88
Energy contribution	-10.48
Covariance contribution	0.60
Combinations/Pair	1.24
Mean z-score	-2.06
Structure conservation index	0.39
SVM decision value	1.29
SVM RNA-class probability	0.938480
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3706219 93 + 20766785
UUCAUUGUUUCCCAAG---CUUAAUGUGGGAAAGU--UGGCUGCAAUUAACAGACUGCA-ACGAGUGCAGGAGUGCAGGAGCUUCAGGAGCUCCUGAAA
(((.((((((((((..---.......))))))(((--((....))))).)))).(((((-.....))))))))..(((((((((...)))))))))... ( -28.80)
>DroSec_CAF1 29663 93 + 1
UUCAUUGUUUCCCAAG---CUUAAUGUGGGAAACU--UGGCUGCAAUUAACAGACUGCA-GCGAGUGCAAGAGUGCAGGAGCUGCAGGAGCUCCUGAAA
..((((((((((((..---.......))))))))(--(.((((((.((....)).))))-)).))......))))((((((((.....))))))))... ( -34.10)
>DroEre_CAF1 26319 79 + 1
UUCAUUGUUUCGCAAG---CUUAAUGUGGGAAACU--UGGCUGCAAUUAACAGACUGCA-GCGAGUGCAGG--------------AGGAGCUCCUGAAA
.......(..((((..---.....))))..).(((--((.(((((.((....)).))))-)))))).((((--------------((...))))))... ( -23.30)
>DroWil_CAF1 57421 82 + 1
UUCCCCCUUCCUUUCUGCAUUUAAUGUGGGAAACGAAGGA---AAAUUACAAGACUGCAAACAAAUGCAAGAAGACA--------------CCAGGAGA
((((.(((((.((((..(((...)))..))))..))))).---............((((......))))........--------------...)))). ( -18.10)
>DroYak_CAF1 27254 79 + 1
UUCAUUGUUUCUCAAG---CUUAAUGUGGGAAACU--UUGCUGCAAUUAACAGACUGCA-GCGAGUGCAGA--------------AGGAGCUCCUGAAA
.......((((...((---(((..(((((....))--((((((((.((....)).))))-))))..)))..--------------..)))))...)))) ( -21.50)
>consensus
UUCAUUGUUUCCCAAG___CUUAAUGUGGGAAACU__UGGCUGCAAUUAACAGACUGCA_GCGAGUGCAGGA___CA________AGGAGCUCCUGAAA
((((..((((((((............))))))))....................(((((......)))))........................)))). ( -9.88 = -10.48 +   0.60)

alignment

secondary structure

dotplot

Window 5

Location	3,706,219 – 3,706,312
Length	93
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	70.67
Mean single sequence MFE	-25.10
Consensus MFE	-8.86
Energy contribution	-8.90
Covariance contribution	0.04
Combinations/Pair	1.38
Mean z-score	-2.88
Structure conservation index	0.35
SVM decision value	3.46
SVM RNA-class probability	0.999251
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3706219 93 - 20766785
UUUCAGGAGCUCCUGAAGCUCCUGCACUCCUGCACUCGU-UGCAGUCUGUUAAUUGCAGCCA--ACUUUCCCACAUUAAG---CUUGGGAAACAAUGAA
...((((((((.....)))))))).............((-((((((......))))))))..--..(((((((.......---..)))))))....... ( -28.00)
>DroSec_CAF1 29663 93 - 1
UUUCAGGAGCUCCUGCAGCUCCUGCACUCUUGCACUCGC-UGCAGUCUGUUAAUUGCAGCCA--AGUUUCCCACAUUAAG---CUUGGGAAACAAUGAA
...((((((((.....)))))))).............((-((((((......))))))))..--.((((((((.......---..))))))))...... ( -34.30)
>DroEre_CAF1 26319 79 - 1
UUUCAGGAGCUCCU--------------CCUGCACUCGC-UGCAGUCUGUUAAUUGCAGCCA--AGUUUCCCACAUUAAG---CUUGCGAAACAAUGAA
...((((((...))--------------))))...((((-((((((......))))))))((--(((((........)))---)))).))......... ( -22.20)
>DroWil_CAF1 57421 82 - 1
UCUCCUGG--------------UGUCUUCUUGCAUUUGUUUGCAGUCUUGUAAUUU---UCCUUCGUUUCCCACAUUAAAUGCAGAAAGGAAGGGGGAA
((((((..--------------..((((..((((((((.((((......))))...---......((.....))..))))))))..))))..)))))). ( -20.10)
>DroYak_CAF1 27254 79 - 1
UUUCAGGAGCUCCU--------------UCUGCACUCGC-UGCAGUCUGUUAAUUGCAGCAA--AGUUUCCCACAUUAAG---CUUGAGAAACAAUGAA
...((((((...))--------------))))..(((((-((((((......)))))))).(--(((((........)))---)))))).......... ( -20.90)
>consensus
UUUCAGGAGCUCCU________UG___UCCUGCACUCGC_UGCAGUCUGUUAAUUGCAGCCA__AGUUUCCCACAUUAAG___CUUGAGAAACAAUGAA
(((((((......................(((((......))))).((((.....))))........................)))))))......... ( -8.86 =  -8.90 +   0.04)

alignment

secondary structure

dotplot

Window 6

Location	3,706,235 – 3,706,343
Length	108
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	85.29
Mean single sequence MFE	-27.60
Consensus MFE	-17.38
Energy contribution	-18.38
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.63
SVM decision value	0.23
SVM RNA-class probability	0.642713
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3706235 108 + 20766785
CUUAAUGUGGGAAAGUUGGCUGCAAUUAACAGACUGCAACGAGUGCAGGAGUGCAGGAGCUUCAGGAGCUCCUGAAACCCAAAACCAGUUA--AGUUAAAGCCAUUCAAU
..........(((...(((((....(((((...(((((.....))))).....(((((((((...))))))))).............))))--).....))))))))... ( -32.30)
>DroSec_CAF1 29679 110 + 1
CUUAAUGUGGGAAACUUGGCUGCAAUUAACAGACUGCAGCGAGUGCAAGAGUGCAGGAGCUGCAGGAGCUCCUGAAACCCAAAACCAGUAACCAGUUAAAGCCAUUCAAA
.......((((..(((((.(((((.((....)).)))))))))).........((((((((.....))))))))...))))............................. ( -31.40)
>DroEre_CAF1 26335 93 + 1
CUUAAUGUGGGAAACUUGGCUGCAAUUAACAGACUGCAGCGAGUGCAGG--------------AGGAGCUCCUGAAACCCAAAACCAGUA---AGUUAAAGCCAUUCAAA
((((.((((((..(((((.(((((.((....)).)))))))))).((((--------------((...))))))...))))....)).))---))............... ( -25.80)
>DroYak_CAF1 27270 93 + 1
CUUAAUGUGGGAAACUUUGCUGCAAUUAACAGACUGCAGCGAGUGCAGA--------------AGGAGCUCCUGAAACCCAAAACCAGUA---AGUUAAACCCAUUCGAA
......(((((.(((((.((((...........(((((.....))))).--------------(((....)))............)))))---))))...)))))..... ( -20.90)
>consensus
CUUAAUGUGGGAAACUUGGCUGCAAUUAACAGACUGCAGCGAGUGCAGG______________AGGAGCUCCUGAAACCCAAAACCAGUA___AGUUAAAGCCAUUCAAA
.......((((..((((.((((((.((....)).))))))))))..................((((....))))...))))............................. (-17.38 = -18.38 +   1.00)

alignment

secondary structure

dotplot

Window 7

Location	3,706,235 – 3,706,343
Length	108
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	85.29
Mean single sequence MFE	-30.18
Consensus MFE	-19.61
Energy contribution	-19.93
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-2.42
Structure conservation index	0.65
SVM decision value	0.83
SVM RNA-class probability	0.861709
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3706235 108 - 20766785
AUUGAAUGGCUUUAACU--UAACUGGUUUUGGGUUUCAGGAGCUCCUGAAGCUCCUGCACUCCUGCACUCGUUGCAGUCUGUUAAUUGCAGCCAACUUUCCCACAUUAAG
......(((((.(((.(--((((.((....((((..((((((((.....)))))))).))))(((((.....))))))).)))))))).)))))................ ( -32.00)
>DroSec_CAF1 29679 110 - 1
UUUGAAUGGCUUUAACUGGUUACUGGUUUUGGGUUUCAGGAGCUCCUGCAGCUCCUGCACUCUUGCACUCGCUGCAGUCUGUUAAUUGCAGCCAAGUUUCCCACAUUAAG
....((((.....((((........((...((((..((((((((.....)))))))).))))..))....((((((((......))))))))..)))).....))))... ( -32.80)
>DroEre_CAF1 26335 93 - 1
UUUGAAUGGCUUUAACU---UACUGGUUUUGGGUUUCAGGAGCUCCU--------------CCUGCACUCGCUGCAGUCUGUUAAUUGCAGCCAAGUUUCCCACAUUAAG
....((((.....((((---(.........((((..((((((...))--------------)))).))))((((((((......)))))))).))))).....))))... ( -27.10)
>DroYak_CAF1 27270 93 - 1
UUCGAAUGGGUUUAACU---UACUGGUUUUGGGUUUCAGGAGCUCCU--------------UCUGCACUCGCUGCAGUCUGUUAAUUGCAGCAAAGUUUCCCACAUUAAG
......((((...((((---(.........((((..((((((...))--------------)))).))))((((((((......)))))))).))))).))))....... ( -28.80)
>consensus
UUUGAAUGGCUUUAACU___UACUGGUUUUGGGUUUCAGGAGCUCCU______________CCUGCACUCGCUGCAGUCUGUUAAUUGCAGCCAAGUUUCCCACAUUAAG
....((((.....((((.......)))).((((...((((....))))......................((((((((......)))))))).......))))))))... (-19.61 = -19.93 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:41 2006