Locus 862

Sequence ID	3R_DroMel_CAF1
Location	2,914,276 – 2,914,416
Length	140
Max. P	0.986951

overview

Window 3

Location	2,914,276 – 2,914,385
Length	109
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.10
Mean single sequence MFE	-44.45
Consensus MFE	-23.44
Energy contribution	-24.20
Covariance contribution	0.76
Combinations/Pair	1.26
Mean z-score	-2.42
Structure conservation index	0.53
SVM decision value	1.46
SVM RNA-class probability	0.956242
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2914276 109 + 27905053
GCGAGGGUGAGGGCGCUGAGGAGUACUAAGCGUCACGCCA--C-UUCAA--CGCUCGAUGGGAGCGUCAUUGGUGGGCGGGGU-AACCGUCGAAAUCAGUGUUUACGC-----UUCCAAU
(((((((((..((((((.((.....)).)))))).)))).--)-)....--)))....((((((((((((((((.(((((...-..)))))...)))))))...))))-----))))).. ( -48.20)
>DroVir_CAF1 5115 118 + 1
GUGAGGGCGAGGGUGCCGAGGAGUACUAAACACG-CUCCACACUUCCAGCCCGCACAGAGCAAGCGUCAUUGGUGGGCGUUGA-GCACGUCGAAACCAAUGCCCACGCAUUGCCUUCGUU
(((.(((((..((((....(((((.........)-)))).))))..).)))).)))((.(((((((((((((((.(((((...-..)))))...)))))))...)))).))))))..... ( -46.00)
>DroSec_CAF1 5098 109 + 1
GCGAGGGAGAGGGUGCUGAGGAGUACUAAGCGUCGCGCCA--C-UCCAA--CGCUCGAUGGGAGCGUCAUUGGUGGGCGGGGA-AACCGUCGAAAUCAUUGUUUACGC-----UUCCAAU
(((..((((..(((((.((.(.........).))))))).--)-)))..--)))....(((((((((((.((((.(((((...-..)))))...)))).))...))))-----))))).. ( -46.50)
>DroEre_CAF1 5171 109 + 1
GCGAGGGCGAGGGUGCUGAGGAGUACUAAGCGUGCCGCCA--C-UCCAA--CGCUCGACUGGAGCGUCAUUGGUGGGCGGGAA-AACCGUCGAAAUCAGUGUUUACGC-----UUCCAAU
..(..((((..((..((((...((((.....))))(((((--.-....(--(((((.....))))))...)))))(((((...-..)))))....))))..))..)))-----)..)... ( -42.20)
>DroWil_CAF1 6097 108 + 1
GCGAGGGUGAGGGAGCUGAGGAGUACUAGAGAUCC--CCA--C-AACAU--AAAUGGGAUGAAGCGUCACUAGUGGGCGUCUAAAGACGUCGAAACUAAUGAUUACGC-----UUCAUUU
......(((.((((.((.((.....))..)).)))--)))--)-.....--.....(((((((((((((.((((.((((((....))))))...)))).)))...)))-----))))))) ( -37.70)
>DroYak_CAF1 4974 109 + 1
GUGAGGGCGAGGGUGCUGAGGAGUACUAAGCGUGCCGCCA--C-UCCAA--CGCUCGAUGGGAGCGUCAUUGGUGGGCGGGAA-AACCGUCGAAAUCAGUGUUUACGC-----UUCCAAU
(.(((((((.(.(((((.((.....)).))))).))))).--)-)))..--.......((((((((((((((((.(((((...-..)))))...)))))))...))))-----))))).. ( -46.10)
>consensus
GCGAGGGCGAGGGUGCUGAGGAGUACUAAGCGUCCCGCCA__C_UCCAA__CGCUCGAUGGGAGCGUCAUUGGUGGGCGGGGA_AACCGUCGAAAUCAGUGUUUACGC_____UUCCAAU
(((.(((((..((((((....))))))...)))....))............(((((.....))))).(((((((.(((((......)))))...)))))))....)))............ (-23.44 = -24.20 +   0.76)

alignment

secondary structure

dotplot

Window 4

Location	2,914,316 – 2,914,416
Length	100
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	83.74
Mean single sequence MFE	-29.84
Consensus MFE	-27.86
Energy contribution	-27.45
Covariance contribution	-0.41
Combinations/Pair	1.29
Mean z-score	-2.58
Structure conservation index	0.93
SVM decision value	2.06
SVM RNA-class probability	0.986951
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2914316 100 + 27905053
CUUCAACGCUCGAUGGGAGCGUCAUUGGUGGGCGGGGU-AACCGUCGAAAUCAGUGUUUACGCUUCCAAUCGCAACAAAAAA------UUCACUG---CAACACUGAAAA
.((((......((((((((((((((((((.(((((...-..)))))...)))))))...)))))))).)))(((........------.....))---).....)))).. ( -32.42)
>DroSec_CAF1 5138 100 + 1
CUCCAACGCUCGAUGGGAGCGUCAUUGGUGGGCGGGGA-AACCGUCGAAAUCAUUGUUUACGCUUCCAAUCGCAACAAAAAA------UUCACUA---CAACACUGAAAA
..........((((((((((((((.((((.(((((...-..)))))...)))).))...)))))))).))))..........------.......---............ ( -27.30)
>DroSim_CAF1 5174 100 + 1
CUCCAACGCUCGAUGGGAGCGUCAUUGGUGGGCGGGGA-AACCGUCGAAAUCAGUGUUUACGCUUCCAAUCGCAACAAAAAA------UUCACUA---CAACACUGAAAA
..........(((((((((((((((((((.(((((...-..)))))...)))))))...)))))))).))))..........------.......---............ ( -30.50)
>DroEre_CAF1 5211 100 + 1
CUCCAACGCUCGACUGGAGCGUCAUUGGUGGGCGGGAA-AACCGUCGAAAUCAGUGUUUACGCUUCCAAUCGCAACAAAAAA------UUCACUG---CAACACUGUAAA
..........(((.(((((((((((((((.(((((...-..)))))...)))))))...)))).)))).)))..........------.....((---((....)))).. ( -28.20)
>DroWil_CAF1 6135 108 + 1
CAACAUAAAUGGGAUGAAGCGUCACUAGUGGGCGUCUAAAGACGUCGAAACUAAUGAUUACGCUUCAUUUAAAAAAAAAAAACAAAUGUUCACUGUUUCUACACUGAA--
...........(((((((((((((.((((.((((((....))))))...)))).)))...))))))))))..................((((.(((....))).))))-- ( -29.20)
>DroYak_CAF1 5014 100 + 1
CUCCAACGCUCGAUGGGAGCGUCAUUGGUGGGCGGGAA-AACCGUCGAAAUCAGUGUUUACGCUUCCAAUCGCAACAAAAAA------UUCACUG---CAACACUGUAAA
..........(((((((((((((((((((.(((((...-..)))))...)))))))...)))))))).))))..........------.....((---((....)))).. ( -31.40)
>consensus
CUCCAACGCUCGAUGGGAGCGUCAUUGGUGGGCGGGGA_AACCGUCGAAAUCAGUGUUUACGCUUCCAAUCGCAACAAAAAA______UUCACUG___CAACACUGAAAA
..........(((((((((((((((((((.(((((......)))))...)))))))...)))))))).))))...................................... (-27.86 = -27.45 +  -0.41)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:04 2006