Locus 4817

Sequence ID	2R_DroMel_CAF1
Location	15,805,836 – 15,805,971
Length	135
Max. P	0.935271

overview

Window 4

Location	15,805,836 – 15,805,949
Length	113
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	94.13
Mean single sequence MFE	-29.83
Consensus MFE	-26.35
Energy contribution	-27.10
Covariance contribution	0.75
Combinations/Pair	1.06
Mean z-score	-1.80
Structure conservation index	0.88
SVM decision value	1.24
SVM RNA-class probability	0.935271
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15805836 113 - 20766785
AAACAGAAGCAACAACAGCUGCCGCUGCUUGGGGUCAUUUUGCAAUGAAUAAAUUAGAGAAA--CUUUAAGUGGCGGAAGAAGAACUACUGGACAUGCCCAAGUAAGGCAGUCUG
...(((.(((.......))).((((..((((((((..((((..(((......))).)))).)--)))))))..))))...........)))(((.((((.......))))))).. ( -32.20)
>DroSec_CAF1 3845 113 - 1
AAACAGAUGCAACAACAGCUGCCGCUGCUUGGGGUCAUUUUGCAAUGAAUAAAUUAGAGAAA--CUUUAAGUGGCGGAAGAAGAACUACUGGACAUGCCCAAGUAAGGCAGUCUG
...............((((((((..((((((((.(((((....))))).....((((((...--))))))(((.(((.((.....)).)))..))).)))))))).))))).))) ( -31.30)
>DroSim_CAF1 3230 113 - 1
AAACAGAAGCAACAACAGCUGCCGCUGCUUGGGGUCAUUUUGCAAUGAAUAAAUUAGAGAAA--CUUUAAGUGGCGGAAGAAGAACUACUGGACAUGCCCAAGUAAGGCAGUCUG
...(((.(((.......))).((((..((((((((..((((..(((......))).)))).)--)))))))..))))...........)))(((.((((.......))))))).. ( -32.20)
>DroEre_CAF1 4163 113 - 1
AAACAGAAGCAACAACAGCUGCCGCUGCUUGGGGUCAUUUUGCAAUGAAUAAAUUAGAGAAA--CUUUAAGUGGCGGAAGAAGAACUACUGGACAUGCCCAAGUAAGGCAGUCUG
...(((.(((.......))).((((..((((((((..((((..(((......))).)))).)--)))))))..))))...........)))(((.((((.......))))))).. ( -32.20)
>DroYak_CAF1 3255 112 - 1
AAACAGAAGCAACAACAGCUGCCGCUGCU-GGGAUCAUUUUGCAAUGAAUAAAUUAGAGAAA--CUUUAAGUGGCGGAAGAAGAACUACUGGACAUGCCCAAGUAAGGCAGUCUG
...(((.(((.......))).((((..((-....(((((....)))))......(((((...--)))))))..))))...........)))(((.((((.......))))))).. ( -27.10)
>DroAna_CAF1 3819 110 - 1
AAACAGAAGCAGA---AGCUG--GCUGCUUGGGGUCAUUUUGCAAUGCAUAAAUUAGACAAAAGUUUUAAGUGGCGGAAGAAGAACAACUGGACAUGCCCAAGUACGGUAGUCGA
...(((.(((...---.))).--((..(((((((.(.(((((((((......))).).)))))))))))))..)).............)))(((.((((.......))))))).. ( -24.00)
>consensus
AAACAGAAGCAACAACAGCUGCCGCUGCUUGGGGUCAUUUUGCAAUGAAUAAAUUAGAGAAA__CUUUAAGUGGCGGAAGAAGAACUACUGGACAUGCCCAAGUAAGGCAGUCUG
...(((.(((.......))).((((..(((((((...((((..(((......)))...))))..)))))))..))))...........)))(((.((((.......))))))).. (-26.35 = -27.10 +   0.75)

alignment

secondary structure

dotplot

Window 5

Location	15,805,871 – 15,805,971
Length	100
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	87.87
Mean single sequence MFE	-20.75
Consensus MFE	-17.42
Energy contribution	-18.28
Covariance contribution	0.86
Combinations/Pair	1.05
Mean z-score	-1.58
Structure conservation index	0.84
SVM decision value	-0.03
SVM RNA-class probability	0.519437
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15805871 100 + 20766785
CUUCCGCCACUUAAAG--UUUCUCUAAUUUAUUCAUUGCAAAAUGACCCCAAGCAGCGGCAGCUGUUGUUGCUUCUGUUUGUU-------ACCCACACCCUAGA-----------AAUGA
...............(--(((((.........(((((....)))))...(((((((.((((((....)))))).)))))))..-------...........)))-----------))).. ( -23.10)
>DroSec_CAF1 3880 100 + 1
CUUCCGCCACUUAAAG--UUUCUCUAAUUUAUUCAUUGCAAAAUGACCCCAAGCAGCGGCAGCUGUUGUUGCAUCUGUUUGUU-------ACCCACACCCUAGA-----------AAUGA
...............(--(((((.........(((((....)))))...(((((((..(((((....)))))..)))))))..-------...........)))-----------))).. ( -20.90)
>DroSim_CAF1 3265 100 + 1
CUUCCGCCACUUAAAG--UUUCUCUAAUUUAUUCAUUGCAAAAUGACCCCAAGCAGCGGCAGCUGUUGUUGCUUCUGUUUGUU-------ACCCACACCCUAGA-----------AAUGA
...............(--(((((.........(((((....)))))...(((((((.((((((....)))))).)))))))..-------...........)))-----------))).. ( -23.10)
>DroEre_CAF1 4198 100 + 1
CUUCCGCCACUUAAAG--UUUCUCUAAUUUAUUCAUUGCAAAAUGACCCCAAGCAGCGGCAGCUGUUGUUGCUUCUGUUUGUU-------ACCCACACCCUAGA-----------AAUGU
...............(--(((((.........(((((....)))))...(((((((.((((((....)))))).)))))))..-------...........)))-----------))).. ( -23.10)
>DroYak_CAF1 3290 101 + 1
CUUCCGCCACUUAAAG--UUUCUCUAAUUUAUUCAUUGCAAAAUGAUCCC-AGCAGCGGCAGCUGUUGUUGCUUCUGUUUGUU-----UUUCCCACACCCUAGA-----------AAUGU
...............(--(((((.........(((((....)))))....-(((((.((((((....)))))).)))))....-----.............)))-----------))).. ( -19.20)
>DroAna_CAF1 3854 115 + 1
CUUCCGCCACUUAAAACUUUUGUCUAAUUUAUGCAUUGCAAAAUGACCCCAAGCAGC--CAGCU---UCUGCUUCUGUUUGUUCGCAGUUACCCACUCCCUAGAACGACCAUUAAAAAGU
...............(((((((((.........((((....))))....(((((((.--.(((.---...))).))))))).........................))).....)))))) ( -15.10)
>consensus
CUUCCGCCACUUAAAG__UUUCUCUAAUUUAUUCAUUGCAAAAUGACCCCAAGCAGCGGCAGCUGUUGUUGCUUCUGUUUGUU_______ACCCACACCCUAGA___________AAUGA
......................((((......(((((....)))))...(((((((.((((((....)))))).)))))))...................))))................ (-17.42 = -18.28 +   0.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:55 2006