Locus 9490

Sequence ID	3R_DroMel_CAF1
Location	25,099,160 – 25,099,262
Length	102
Max. P	0.860661

overview

Window 4

Location	25,099,160 – 25,099,262
Length	102
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	82.03
Mean single sequence MFE	-28.15
Consensus MFE	-17.04
Energy contribution	-17.40
Covariance contribution	0.36
Combinations/Pair	1.20
Mean z-score	-2.51
Structure conservation index	0.61
SVM decision value	0.52
SVM RNA-class probability	0.768184
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25099160 102 + 27905053
UGGCAAGUACAAAUUGCCGUUACCGGCGAAUGCAGCCAAGCAAAAGGCUGCAAUCCUACAGGGGAAAACAUGGAA-AAAGCUGGCAAAGCAAAGAGUUGGGCG
.(((((.......))))).....((((...(((((((........))))))).((((....))))..........-...))))((..(((.....)))..)). ( -32.80)
>DroPse_CAF1 32595 89 + 1
CAAGAGCUACAAAUUGCCGUUACCCGCGAAUGCAGCCAAGC----GGCUGCAAUCCCA-AGAA--AAACAUGGAAAAAAGCUAAG-----AAAGAGUUA--CC
....((((.....((((........)))).(((((((....----)))))))...(((-.(..--...).))).....))))...-----.........--.. ( -19.80)
>DroSec_CAF1 28118 102 + 1
UGGCAAGUACAAAUUGCCGUUACCCGCGAAUGCAGCCAAGCAAAAGGCUGCAAUACUACAGGGGAAGCCAUGGAA-AAAGCUGGCAAGGCAAAGAGUUGGGCG
......(..(((.(((((....(((.....(((((((........)))))))........)))...((((.....-.....))))..)))))....)))..). ( -31.52)
>DroEre_CAF1 28542 95 + 1
UGGCAAGUACAAAUUGCCGUUACCCGCGGAUGCAGCCAAGCAAAAGGCUGCAAUCCCACUGGG--AAGCAUGGAA-AAAGCUGGC-----AAAGAGUUGGGCG
.(((((.......)))))(((.((((.((((((((((........)))))).))))...))))--.)))......-....(..((-----.....))..)... ( -33.90)
>DroYak_CAF1 29095 95 + 1
UGGCAAGUACAAAUUGCCGUUACCCGCGAAUGCAGCCAAGCAAAAGGCUGCAAUCCCACAGGG--AAACAUGGAA-AAAGCUGCC-----AAAGAGUUGGGCG
.(((((.......)))))(((.(((..((.(((((((........))))))).)).....)))--.)))......-...((..((-----((....)))))). ( -31.10)
>DroPer_CAF1 32419 88 + 1
CAAGAGCUACAAAUUGCCGUUACCCGCGAAUGCAGCCAAGC----GGCUGCAAUCCCA-AGAA--AAACAUGGAA-AAAGCUAAG-----AAAGAGUUA--CC
....((((.....((((........)))).(((((((....----)))))))...(((-.(..--...).)))..-..))))...-----.........--.. ( -19.80)
>consensus
UGGCAAGUACAAAUUGCCGUUACCCGCGAAUGCAGCCAAGCAAAAGGCUGCAAUCCCACAGGG__AAACAUGGAA_AAAGCUGGC_____AAAGAGUUGGGCG
((((((.......))))))......((((.(((((((........))))))).))(((............)))......))...................... (-17.04 = -17.40 +   0.36)

alignment

secondary structure

dotplot

Window 5

Location	25,099,160 – 25,099,262
Length	102
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	82.03
Mean single sequence MFE	-30.03
Consensus MFE	-19.70
Energy contribution	-20.57
Covariance contribution	0.86
Combinations/Pair	1.21
Mean z-score	-2.70
Structure conservation index	0.66
SVM decision value	0.83
SVM RNA-class probability	0.860661
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25099160 102 - 27905053
CGCCCAACUCUUUGCUUUGCCAGCUUU-UUCCAUGUUUUCCCCUGUAGGAUUGCAGCCUUUUGCUUGGCUGCAUUCGCCGGUAACGGCAAUUUGUACUUGCCA
.((...((...((((((((((.((...-..........(((......))).(((((((........)))))))...)).))))).)))))...))....)).. ( -29.60)
>DroPse_CAF1 32595 89 - 1
GG--UAACUCUUU-----CUUAGCUUUUUUCCAUGUUU--UUCU-UGGGAUUGCAGCC----GCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUAGCUCUUG
..--.........-----...((((........((((.--..((-((.((.(((((((----....))))))).)).)))).)))).........)))).... ( -25.53)
>DroSec_CAF1 28118 102 - 1
CGCCCAACUCUUUGCCUUGCCAGCUUU-UUCCAUGGCUUCCCCUGUAGUAUUGCAGCCUUUUGCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUACUUGCCA
.((...((...(((((..((((.....-.....))))....((((..(...(((((((........))))))).)..))))....)))))...))....)).. ( -32.50)
>DroEre_CAF1 28542 95 - 1
CGCCCAACUCUUU-----GCCAGCUUU-UUCCAUGCUU--CCCAGUGGGAUUGCAGCCUUUUGCUUGGCUGCAUCCGCGGGUAACGGCAAUUUGUACUUGCCA
.((...((...((-----((((((...-......))).--(((.(((((..(((((((........)))))))))))))))....)))))...))....)).. ( -33.70)
>DroYak_CAF1 29095 95 - 1
CGCCCAACUCUUU-----GGCAGCUUU-UUCCAUGUUU--CCCUGUGGGAUUGCAGCCUUUUGCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUACUUGCCA
.(((.........-----)))......-......(((.--.((((((((..(((((((........))))))))))))))).)))(((((.......))))). ( -33.20)
>DroPer_CAF1 32419 88 - 1
GG--UAACUCUUU-----CUUAGCUUU-UUCCAUGUUU--UUCU-UGGGAUUGCAGCC----GCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUAGCUCUUG
..--.........-----...((((..-.....(((..--((((-((.((.(((((((----....))))))).)).)))).))..)))......)))).... ( -25.62)
>consensus
CGCCCAACUCUUU_____GCCAGCUUU_UUCCAUGUUU__CCCUGUGGGAUUGCAGCCUUUUGCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUACUUGCCA
.........................................(((((((...(((((((........))))))).)))))))....(((((.......))))). (-19.70 = -20.57 +   0.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:35:48 2006