Locus 3819

Sequence ID	3R_DroMel_CAF1
Location	10,371,249 – 10,371,343
Length	94
Max. P	0.741191

overview

Window 7

Location	10,371,249 – 10,371,343
Length	94
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	83.46
Mean single sequence MFE	-17.64
Consensus MFE	-12.95
Energy contribution	-13.17
Covariance contribution	0.22
Combinations/Pair	1.12
Mean z-score	-2.24
Structure conservation index	0.73
SVM decision value	0.44
SVM RNA-class probability	0.739179
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10371249 94 + 27905053
UACAAAUGUCGCUUUUCCGUAUCCUCGCACAUGGCGGAUAUUUUACAACUUCCGGCCAU-----------CUUUUAUGGCCGCAC-GCCACCCACUACCACUCACU
.....((((.((..............))))))((((((............)))((((((-----------.....))))))....-)))................. ( -19.64)
>DroSec_CAF1 35167 94 + 1
UACAAAUGUCGCUUUUCCGUAUCCUCGCACAUGGCGGAUAUUUUACAACUUCCGGCCAU-----------CUUUUAUGGCCGCAA-ACCACCCGCUACCACUCACU
.......((.((......((((((..((.....))))))))...........(((((((-----------.....)))))))...-.......)).))........ ( -18.70)
>DroSim_CAF1 30072 94 + 1
UACAAAUGUCGCUUUUCCGUAUCCUCGCACAUGGCGGAUAUUUUACAACUUCCGGCCAU-----------CUUUUAUGGCCGCAA-ACCACCCACUACCACUCACU
...((((((((((....((......)).....))).))))))).........(((((((-----------.....)))))))...-.................... ( -18.00)
>DroEre_CAF1 30498 92 + 1
UACAAAUGUCGCCUUUCCGUAUCCUCGCACAUGGCGGAUAUUUUACAACAUCCGGCCAU-----------CUUUUAUGGCCGCAA-ACCACCCACU-CCACUCAC-
...((((((((((....((......)).....))).))))))).........(((((((-----------.....)))))))...-..........-........- ( -19.90)
>DroWil_CAF1 33988 93 + 1
CACAAAUGUCGACUUUCCGUUUCCUCACACAUGGCGGAUAUUUUACAACUUCCGGACGCCUCCGCAUUGCCUUUUAUGACUCC-------------ACCACAUUCG
.......((((....((((((...........))))))..............((((....))))............))))...-------------.......... ( -12.20)
>DroYak_CAF1 30918 94 + 1
UACAAAUGUCGCUCUUCCGUAUCCUCGUACAUGGCGGAUAUUUUACAACAUCCGGCCAU-----------CUUUUAUGGCCGCAAAACCACCCACUUCCACUCAC-
...((((((((((.....((((....))))..))).))))))).........(((((((-----------.....))))))).......................- ( -17.40)
>consensus
UACAAAUGUCGCUUUUCCGUAUCCUCGCACAUGGCGGAUAUUUUACAACUUCCGGCCAU___________CUUUUAUGGCCGCAA_ACCACCCACUACCACUCACU
......(((......((((...((........))))))......))).....(((((((................)))))))........................ (-12.95 = -13.17 +   0.22)

alignment

secondary structure

dotplot

Window 8

Location	10,371,249 – 10,371,343
Length	94
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	83.46
Mean single sequence MFE	-29.72
Consensus MFE	-18.46
Energy contribution	-19.99
Covariance contribution	1.53
Combinations/Pair	1.15
Mean z-score	-3.01
Structure conservation index	0.62
SVM decision value	0.45
SVM RNA-class probability	0.741191
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10371249 94 - 27905053
AGUGAGUGGUAGUGGGUGGC-GUGCGGCCAUAAAAG-----------AUGGCCGGAAGUUGUAAAAUAUCCGCCAUGUGCGAGGAUACGGAAAAGCGACAUUUGUA
.(..((((...(((.(((((-....((((((.....-----------))))))(((.(((....))).)))))))).))).......((......)).))))..). ( -30.70)
>DroSec_CAF1 35167 94 - 1
AGUGAGUGGUAGCGGGUGGU-UUGCGGCCAUAAAAG-----------AUGGCCGGAAGUUGUAAAAUAUCCGCCAUGUGCGAGGAUACGGAAAAGCGACAUUUGUA
.(..((((...(((.(((((-....((((((.....-----------))))))(((.(((....))).)))))))).))).......((......)).))))..). ( -30.30)
>DroSim_CAF1 30072 94 - 1
AGUGAGUGGUAGUGGGUGGU-UUGCGGCCAUAAAAG-----------AUGGCCGGAAGUUGUAAAAUAUCCGCCAUGUGCGAGGAUACGGAAAAGCGACAUUUGUA
.(..((((...(((.(((((-....((((((.....-----------))))))(((.(((....))).)))))))).))).......((......)).))))..). ( -27.70)
>DroEre_CAF1 30498 92 - 1
-GUGAGUGG-AGUGGGUGGU-UUGCGGCCAUAAAAG-----------AUGGCCGGAUGUUGUAAAAUAUCCGCCAUGUGCGAGGAUACGGAAAGGCGACAUUUGUA
-(..((((.-.(((.(((((-....((((((.....-----------))))))(((((((....)))))))))))).))).......((......)).))))..). ( -31.20)
>DroWil_CAF1 33988 93 - 1
CGAAUGUGGU-------------GGAGUCAUAAAAGGCAAUGCGGAGGCGUCCGGAAGUUGUAAAAUAUCCGCCAUGUGUGAGGAAACGGAAAGUCGACAUUUGUG
((((((((((-------------(((..........(((((.((((....))))...)))))......))))))........(....).........))))))).. ( -24.99)
>DroYak_CAF1 30918 94 - 1
-GUGAGUGGAAGUGGGUGGUUUUGCGGCCAUAAAAG-----------AUGGCCGGAUGUUGUAAAAUAUCCGCCAUGUACGAGGAUACGGAAGAGCGACAUUUGUA
-(..((((...(((.(((((.....((((((.....-----------))))))(((((((....)))))))))))).))).......(....).....))))..). ( -33.40)
>consensus
AGUGAGUGGUAGUGGGUGGU_UUGCGGCCAUAAAAG___________AUGGCCGGAAGUUGUAAAAUAUCCGCCAUGUGCGAGGAUACGGAAAAGCGACAUUUGUA
.(..((((...(((.(((((.....((((((................))))))(((.(((....))).)))))))).))).......((......)).))))..). (-18.46 = -19.99 +   1.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:49 2006