Locus 5866

Sequence ID	3R_DroMel_CAF1
Location	15,374,010 – 15,374,116
Length	106
Max. P	0.741446

overview

Window 2

Location	15,374,010 – 15,374,116
Length	106
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	75.91
Mean single sequence MFE	-33.63
Consensus MFE	-16.66
Energy contribution	-17.41
Covariance contribution	0.75
Combinations/Pair	1.09
Mean z-score	-1.92
Structure conservation index	0.50
SVM decision value	0.45
SVM RNA-class probability	0.741446
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15374010 106 + 27905053
AGCUUGCUG---AGCG-UUGCCAACUUGCCCAAUGU-----GCCAACU--GUGG--AGCCCUUUGUUAGCCCUGCUAAAUAUUCGUUAACGUGGCGAGCAAAUUUCGUUGGCAAACAGA
.((((...)---))).-((((((((..(((((..((-----....)).--.)))--.))..((((((.(((.((.(((.......))).)).))).))))))....))))))))..... ( -28.70)
>DroVir_CAF1 152775 107 + 1
AGCUACGCGAAAAUAG-UUGCCAACUUGGCCAAUGU-----GCCAACU--GGGC--CG-CCUUUGUUGGCAUUGCUAAAUGUUCGUUAACGUGGCGCAUAAAUUU-GUUAGCCAACAAA
.((((((((((..(((-((((((((.(((((...((-----....)).--.)))--))-.....)))))))..))))....))))....)))))).......(((-(((....)))))) ( -34.30)
>DroGri_CAF1 160364 107 + 1
AGCUCCACGAAAAUAG-UUCCCAACUUGGCCAAUGU-----GCCAACU--GGGC--CG-CCUUUGUUAGCGUUGCUAAAUGUUCGUUAACGUGGCGCAUAAAUUU-GUUGGCAAACAAA
.(((..(((((.....-..((((..(((((......-----))))).)--))).--((-((..((((((((..((.....)).)))))))).))))......)))-)).)))....... ( -32.10)
>DroWil_CAF1 166169 109 + 1
-GUUUGUUU---UCCGUUUGCCAACUUGGCCAAUGUGGU--GCCAAAC--GGGGUUGGCUUUGUGUUUGCCUUGCUAAAUAUUCGUUAACGUGGCGCACA-AUUUCGUUGGCACACAU-
-........---...((.(((((((..(((((((.(.((--.....))--.).)))))))((((((..(((.((.(((.......))).)).))))))))-)....))))))).))..- ( -35.10)
>DroMoj_CAF1 151101 107 + 1
AGCUUCGCGAAAAUAG-UUGCCAACUUGGCCAAUGG-----GCCAACU--GGGC--CA-ACUCUGUUAGCAUUGCUAAAUGUUCGUUAACGUGGCGCAUAAAUUU-GUUGGCAAACAAA
................-((((((((((((((....)-----))))).(--(.((--((-....(((((((...((.....))..))))))))))).)).......-))))))))..... ( -34.60)
>DroAna_CAF1 118877 108 + 1
-----GCUC---AGCG-UUGCCAACUUGGCCAAUGGGCUGGGCCAACGAAGCCG--GGUCCUUUGUUAGCCCUGCUAAAUAUUCGUUAACGUGGCGAACAAAUUUCGUUGGCAAACACU
-----((((---(...-..(((.....)))...)))))...(((((((((((.(--(((.........)))).))).....((((((.....))))))......))))))))....... ( -37.00)
>consensus
AGCUUCCCG___AUAG_UUGCCAACUUGGCCAAUGU_____GCCAACU__GGGC__CG_CCUUUGUUAGCCUUGCUAAAUAUUCGUUAACGUGGCGCACAAAUUU_GUUGGCAAACAAA
...............(.(((((((((((((...........)))))..............(..(((((((..............)))))))..)............)))))))).)... (-16.66 = -17.41 +   0.75)

alignment

secondary structure

dotplot

Window 3

Location	15,374,010 – 15,374,116
Length	106
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	75.91
Mean single sequence MFE	-31.58
Consensus MFE	-15.98
Energy contribution	-16.74
Covariance contribution	0.75
Combinations/Pair	1.08
Mean z-score	-1.74
Structure conservation index	0.51
SVM decision value	0.09
SVM RNA-class probability	0.578261
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15374010 106 - 27905053
UCUGUUUGCCAACGAAAUUUGCUCGCCACGUUAACGAAUAUUUAGCAGGGCUAACAAAGGGCU--CCAC--AGUUGGC-----ACAUUGGGCAAGUUGGCAA-CGCU---CAGCAAGCU
.....((((((((.....((((((((((((((((.......))))).(((((.......))).--))..--.).))))-----.....))))))))))))))-.(((---.....))). ( -29.20)
>DroVir_CAF1 152775 107 - 1
UUUGUUGGCUAAC-AAAUUUAUGCGCCACGUUAACGAACAUUUAGCAAUGCCAACAAAGG-CG--GCCC--AGUUGGC-----ACAUUGGCCAAGUUGGCAA-CUAUUUUCGCGUAGCU
((((((....)))-))).(((((((((..(((((.......)))))...(((......))-))--))((--(((((((-----......))))).))))...-........)))))).. ( -28.70)
>DroGri_CAF1 160364 107 - 1
UUUGUUUGCCAAC-AAAUUUAUGCGCCACGUUAACGAACAUUUAGCAACGCUAACAAAGG-CG--GCCC--AGUUGGC-----ACAUUGGCCAAGUUGGGAA-CUAUUUUCGUGGAGCU
((((((....)))-))).....((.(((((..((..............((((......))-))--.(((--(((((((-----......))))).)))))..-...))..))))).)). ( -31.30)
>DroWil_CAF1 166169 109 - 1
-AUGUGUGCCAACGAAAU-UGUGCGCCACGUUAACGAAUAUUUAGCAAGGCAAACACAAAGCCAACCCC--GUUUGGC--ACCACAUUGGCCAAGUUGGCAAACGGA---AAACAAAC-
-.(((.(((((((....(-((((.(((..(((((.......)))))..)))...))))).(((((....--..)))))--..............))))))).)))..---........- ( -30.10)
>DroMoj_CAF1 151101 107 - 1
UUUGUUUGCCAAC-AAAUUUAUGCGCCACGUUAACGAACAUUUAGCAAUGCUAACAGAGU-UG--GCCC--AGUUGGC-----CCAUUGGCCAAGUUGGCAA-CUAUUUUCGCGAAGCU
(((((((((((((-.......((.((((((....)).....(((((...)))))......-))--)).)--).(((((-----(....))))))))))))))-........)))))... ( -30.70)
>DroAna_CAF1 118877 108 - 1
AGUGUUUGCCAACGAAAUUUGUUCGCCACGUUAACGAAUAUUUAGCAGGGCUAACAAAGGACC--CGGCUUCGUUGGCCCAGCCCAUUGGCCAAGUUGGCAA-CGCU---GAGC-----
((((((.(((((((((.....)))((((((....))........((.((((((((.(((....--...))).)))))))).))....))))...))))))))-))))---....----- ( -39.50)
>consensus
UUUGUUUGCCAAC_AAAUUUAUGCGCCACGUUAACGAACAUUUAGCAAGGCUAACAAAGG_CG__CCCC__AGUUGGC_____ACAUUGGCCAAGUUGGCAA_CGAU___CACCAAGCU
...(.((((((((...........((((.(((((.......)))))...((((((.................)))))).........))))...)))))))).)............... (-15.98 = -16.74 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:32 2006