Locus 5285

Sequence ID	2R_DroMel_CAF1
Location	17,169,963 – 17,170,078
Length	115
Max. P	0.991375

overview

Window 6

Location	17,169,963 – 17,170,078
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.28
Mean single sequence MFE	-39.63
Consensus MFE	-23.27
Energy contribution	-25.22
Covariance contribution	1.95
Combinations/Pair	1.20
Mean z-score	-2.56
Structure conservation index	0.59
SVM decision value	2.26
SVM RNA-class probability	0.991375
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17169963 115 + 20766785
CUUAAAGGCAUCUCGCCAUCUGGGGAGACCUUUGAUUGGGUCGCCGAAUUUAUUCGGCAUGAGUAAUGUCCACCUGUUGGUGCCC-UCGCAAUGGGCUCGUCCAUCGACU----UGAGCU
.(((((((..((((.((....)).)))))))))))(..((((((((((....))))))((((((......((((....)))).((-.......)))))))).....))))----..)... ( -42.60)
>DroSec_CAF1 37124 117 + 1
CUUAAAGGCACCUUGCCAGCUGGGGAGACCUUUGAUUGGGUCGCCGAAUUUAUUCGGCAUGAGUAAUAACCACCUGUUGGUGCCC-UCAUAAUGGGCUCGUCCAUCUACUAC--UGAGCU
......(((.....((((((.((((.(((((......)))))((((((....))))))...........)).)).))))))((((-.......))))...............--...))) ( -40.40)
>DroSim_CAF1 38191 115 + 1
CUUAAAGGCACCUUGCCAGCUGGGGAGACCUUUGAUUGGGUCGCCGAAUUUAUUCGGCAUGAGUAAUAACCACCUGUUGGUGCCC-UCAUAAUGGGCUCGUCCAUCUGCU----UGAGCU
.....(((((....((((((.((((.(((((......)))))((((((....))))))...........)).)).))))))((((-.......)))).........))))----)..... ( -42.00)
>DroEre_CAF1 38107 111 + 1
UUUUAAGCCACUUCGCCAACUGGGCAGACCUUUGAUAGGGUCGCCGAAUUUAUUUGGCAUGAAUAAUGCCCACCUGUUGGUGCCC-UCGCCAUGGGCUCGUCCAUCUACUUA--------
...((((.......((((((((((((((((((....))))))((((((....))))))........))))))...))))))((((-.......))))...........))))-------- ( -40.30)
>DroYak_CAF1 37661 118 + 1
UUUUGAGGCACUUCGCCAGCUGGGGAGACCUUUGAUAGGGUCUCUGAAUUUAUUUGGCAUGAAUAAUGCCCACCUGUUGG-GCCC-UCGUAAUGGGCUCGUCCAUUUACUACCGUCUGCU
.....((((......(((((.(((((((((((....)))))))))..........(((((.....)))))..)).)))))-((((-.......))))................))))... ( -41.00)
>DroAna_CAF1 42435 102 + 1
GCUAAA-------------CCGGGGAGCUCUUUGAUAAGGUAAAAGACUUUUUUUCG-AUGAUUAAUUCACACCUGAGGUGGCCCAAUGCAAUGGGCCACGCUAUCUCCU----CUAACU
......-------------..(((((((((.((((.(((((.....)))))...)))-)(((.....))).....)))((((((((......)))))))).....)))))----)..... ( -31.50)
>consensus
CUUAAAGGCACCUCGCCAGCUGGGGAGACCUUUGAUAGGGUCGCCGAAUUUAUUCGGCAUGAGUAAUGCCCACCUGUUGGUGCCC_UCGCAAUGGGCUCGUCCAUCUACU____UGAGCU
..............((((((.((((.(((((......)))))((((((....))))))...........)).)).))))))((((........))))....................... (-23.27 = -25.22 +   1.95)

alignment

secondary structure

dotplot

Window 7

Location	17,169,963 – 17,170,078
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.28
Mean single sequence MFE	-36.68
Consensus MFE	-14.28
Energy contribution	-15.83
Covariance contribution	1.56
Combinations/Pair	1.18
Mean z-score	-2.06
Structure conservation index	0.39
SVM decision value	0.05
SVM RNA-class probability	0.561095
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17169963 115 - 20766785
AGCUCA----AGUCGAUGGACGAGCCCAUUGCGA-GGGCACCAACAGGUGGACAUUACUCAUGCCGAAUAAAUUCGGCGACCCAAUCAAAGGUCUCCCCAGAUGGCGAGAUGCCUUUAAG
.((((.----.(.((((((......)))))))..-)))).......((.(((..........((((((....))))))((((........)))))))))....(((.....)))...... ( -36.40)
>DroSec_CAF1 37124 117 - 1
AGCUCA--GUAGUAGAUGGACGAGCCCAUUAUGA-GGGCACCAACAGGUGGUUAUUACUCAUGCCGAAUAAAUUCGGCGACCCAAUCAAAGGUCUCCCCAGCUGGCAAGGUGCCUUUAAG
......--......(((((......))))).(((-(((((((..(((.(((...........((((((....))))))((((........))))...))).)))....)))))))))).. ( -42.90)
>DroSim_CAF1 38191 115 - 1
AGCUCA----AGCAGAUGGACGAGCCCAUUAUGA-GGGCACCAACAGGUGGUUAUUACUCAUGCCGAAUAAAUUCGGCGACCCAAUCAAAGGUCUCCCCAGCUGGCAAGGUGCCUUUAAG
.((...----.)).(((((......))))).(((-(((((((..(((.(((...........((((((....))))))((((........))))...))).)))....)))))))))).. ( -44.30)
>DroEre_CAF1 38107 111 - 1
--------UAAGUAGAUGGACGAGCCCAUGGCGA-GGGCACCAACAGGUGGGCAUUAUUCAUGCCAAAUAAAUUCGGCGACCCUAUCAAAGGUCUGCCCAGUUGGCGAAGUGGCUUAAAA
--------(((((..((...((.((((.......-)))).(((((...((((((........(((..........)))((((........)))))))))))))))))..)).)))))... ( -34.60)
>DroYak_CAF1 37661 118 - 1
AGCAGACGGUAGUAAAUGGACGAGCCCAUUACGA-GGGC-CCAACAGGUGGGCAUUAUUCAUGCCAAAUAAAUUCAGAGACCCUAUCAAAGGUCUCCCCAGCUGGCGAAGUGCCUCAAAA
(((....((((((((.(((......)))))))((-(.((-(((.....)))))....))).))))...........((((((........))))))....)))(((.....)))...... ( -35.10)
>DroAna_CAF1 42435 102 - 1
AGUUAG----AGGAGAUAGCGUGGCCCAUUGCAUUGGGCCACCUCAGGUGUGAAUUAAUCAU-CGAAAAAAAGUCUUUUACCUUAUCAAAGAGCUCCCCGG-------------UUUAGC
.(((((----(((((.....((((((((......))))))))(((.((((.........)))-)......(((........)))......)))))))....-------------)))))) ( -26.80)
>consensus
AGCUCA____AGUAGAUGGACGAGCCCAUUACGA_GGGCACCAACAGGUGGGCAUUACUCAUGCCAAAUAAAUUCGGCGACCCAAUCAAAGGUCUCCCCAGCUGGCGAGGUGCCUUUAAG
.......................((((........)))).....(((.(((...........(((..........)))((((........))))...))).)))................ (-14.28 = -15.83 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:12 2006