Locus 5292

Sequence ID	3R_DroMel_CAF1
Location	13,820,251 – 13,820,394
Length	143
Max. P	0.987305

overview

Window 2

Location	13,820,251 – 13,820,360
Length	109
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	87.05
Mean single sequence MFE	-29.48
Consensus MFE	-27.21
Energy contribution	-27.60
Covariance contribution	0.39
Combinations/Pair	1.07
Mean z-score	-2.30
Structure conservation index	0.92
SVM decision value	2.07
SVM RNA-class probability	0.987305
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13820251 109 + 27905053
AAAAGCCCCAUGCCCCAUC-CUGGUGGCAGCAUUUGUUAUUCGGGGCAUUUUAAGUGCUCUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCGCCAC
....((.(((((...(((.-...)))((((((..(((....((((((((.....))))))))(((..(((....)))..))))))..))))))......))))).))... ( -34.60)
>DroSec_CAF1 92144 95 + 1
--------------CCAGC-CUGGUGGCAGCAUUAGUUAUUCGGGGCAUUUUAAGUGCUCUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCGCCAC
--------------.....-...(((((..(((.((((((.((((((((.....))))))))(((...(((((.......))))).....))))))))).)))..))))) ( -29.80)
>DroSim_CAF1 94202 95 + 1
--------------CCAGC-CUGGUGGCAGCAUUAGUUAUUCGGGGCAUUUUAAGUGCUCUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCGCCAC
--------------.....-...(((((..(((.((((((.((((((((.....))))))))(((...(((((.......))))).....))))))))).)))..))))) ( -29.80)
>DroEre_CAF1 90062 104 + 1
AAAACCCC------ACUACCCUGGUGGCAGCAUUAGUUAUUCGGGGCAUUUUAAGUGCUCUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCGCCAC
........------.........(((((..(((.((((((.((((((((.....))))))))(((...(((((.......))))).....))))))))).)))..))))) ( -29.80)
>DroYak_CAF1 99383 103 + 1
AAAACCCC------CCGACCC-GGUGGCAGCAUUAGUUAUUCGGGGCAUUUUAAGUGCUCUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCGCCAC
........------.......-.(((((..(((.((((((.((((((((.....))))))))(((...(((((.......))))).....))))))))).)))..))))) ( -29.80)
>DroAna_CAF1 91437 92 + 1
--------------UCACU-CCGGUU---GCAUUAGUUAUUCGGAGCAUUUUAAGUGCUUUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCACUAC
--------------...((-((((..---((....))...)))))).......((((((.(((((...(((((.......))))).....)))......)).)))))).. ( -23.10)
>consensus
______________CCAAC_CUGGUGGCAGCAUUAGUUAUUCGGGGCAUUUUAAGUGCUCUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCGCCAC
.......................(((((..(((.((((((.((((((((.....))))))))(((...(((((.......))))).....))))))))).)))..))))) (-27.21 = -27.60 +   0.39)

alignment

secondary structure

dotplot

Window 3

Location	13,820,289 – 13,820,394
Length	105
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	96.44
Mean single sequence MFE	-26.23
Consensus MFE	-22.79
Energy contribution	-22.85
Covariance contribution	0.06
Combinations/Pair	1.07
Mean z-score	-1.37
Structure conservation index	0.87
SVM decision value	0.06
SVM RNA-class probability	0.564400
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13820289 105 + 27905053
UUCGGGGCAUUUUAAGUGCUCUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCGCCACGUCGCAAACUGAAACAGAAAUUGCAACUGAAACU
..((((((((.....))))))))(((.(((.(((((....(((((....).)))).........(((......)))......))))).))).))).......... ( -25.70)
>DroSec_CAF1 92168 105 + 1
UUCGGGGCAUUUUAAGUGCUCUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCGCCACGUCGCAAACUGAAACAAAAAUUGCCACUGAAACU
(((((((((.(((..((((...((((...(((((.......)))))..))))))))..((((..(((......)))....))))....))).)))).)))))... ( -26.50)
>DroSim_CAF1 94226 105 + 1
UUCGGGGCAUUUUAAGUGCUCUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCGCCACGUCGCAAACUGAAACAGAAAUUGCCACUGAAACU
..((((((((.....))))))))(((...(((((.......))))).....)))....((((((((((......))...(((...))).....)))).))))... ( -28.30)
>DroEre_CAF1 90095 105 + 1
UUCGGGGCAUUUUAAGUGCUCUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCGCCACGUCGCAAACUGAAACAGAAAUUGCAACUGAAACU
..((((((((.....))))))))(((.(((.(((((....(((((....).)))).........(((......)))......))))).))).))).......... ( -25.70)
>DroYak_CAF1 99415 105 + 1
UUCGGGGCAUUUUAAGUGCUCUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCGCCACGUCGCAAACUGAAACAGAAAUUGCAACUGAAACU
..((((((((.....))))))))(((.(((.(((((....(((((....).)))).........(((......)))......))))).))).))).......... ( -25.70)
>DroAna_CAF1 91458 104 + 1
UUCGGAGCAUUUUAAGUGCUUUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCACUACGUCGCAAACUGCAACUGAAAUUGC-ACUGCCACU
...(((((((.....)))))))((((...(((((.......))))).....((((...((((.(((.....)))((.....))...))))..)))-).))))... ( -25.50)
>consensus
UUCGGGGCAUUUUAAGUGCUCUGGCAUUUUGUGUUUAAUCUGCACAUUUGUUGCAUAAUUCAUGGCGCCACGUCGCAAACUGAAACAGAAAUUGCAACUGAAACU
..((((((((.....))))))))(((.(((.(((((....(((((....).))))........(((.....)))........))))).))).))).......... (-22.79 = -22.85 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:14 2006