Locus 3256

Sequence ID	X_DroMel_CAF1
Location	8,642,724 – 8,642,836
Length	112
Max. P	0.977336

overview

Window 1

Location	8,642,724 – 8,642,836
Length	112
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	77.33
Mean single sequence MFE	-26.41
Consensus MFE	-12.89
Energy contribution	-12.05
Covariance contribution	-0.84
Combinations/Pair	1.32
Mean z-score	-2.23
Structure conservation index	0.49
SVM decision value	0.80
SVM RNA-class probability	0.853266
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8642724 112 + 22224390
GCACAAAUUGUCCUUUAAUUGGUUUUGCGCAUUAAUUUUGCAAAAUUUAUUGCGCUUUGUGCUCGCCGCUUUGCC-GUGCAAGUCCGGCUGCAUUUUCAUUCGCAUUUGCAUU
(((((((....((.......))....(((((..(((((....)))))...))))))))))))..((((.(((((.-..)))))..))))((((..............)))).. ( -28.44)
>DroPse_CAF1 108446 103 + 1
G-CGAAAUUGUCCUUUAAUUGGUUUUGCGCAUUAAUUUUGCACAAUUUAUUGCGCUUUGUGUGUUGUGCUGUGCAUCUGCAAGU-----UGCAACUU---GCACAUUUGUG-U
(-((((((((.........)))))))))((((.......(((((((.(((........))).)))))))((((((..(((....-----.)))...)---)))))...)))-) ( -26.90)
>DroSim_CAF1 43665 112 + 1
GCACAAAUUGUCCUUUAAUUGGUUUUGCGCAUUAAUUUUGCAGAAUUUAUUGCGCUUUGUGCUCGGCGCUUUGCC-GUGCGAGUCCUGCUGCAUUUUCAUUCGCAUUCGCAUU
(((((((....((.......))....(((((..(((((....)))))...)))))))))))).((((.....)))-)((((((...(((.............))))))))).. ( -30.32)
>DroEre_CAF1 92020 88 + 1
CCACAAAUUGUCCUUUAAUUGGUUUUGCGCAUUAAUUUUGCAGAAUUUAUUGCGCUUUGUGCUCUGCGUUUUGCA-CU------------------------GCAUUUGCAUU
.((((((....((.......))....(((((..(((((....)))))...)))))))))))...((((...(((.-..------------------------)))..)))).. ( -18.60)
>DroYak_CAF1 82457 105 + 1
CCACAAAUUGUCCUUUAAUUGGUUUUGCGCAUUAAUUUUGCAGAAUUUAUUGCGCUUUGUGCUUUGCGUUUUGCA-UUGCGAGUUCGGUUGUGGU-------GCAUUUUCAUU
((((((.(((..(((...........(((((..(((((....)))))...))))).....((..(((.....)))-..)))))..))))))))).-------........... ( -25.50)
>DroPer_CAF1 95910 103 + 1
G-CGAAAUUGUCCUUUAAUUGGUUUUGCGCAUUAAUUUUGCACAAUUUAUUGCGCUUUGUGUGUUGUGCUGUGCAACUGCAAGU-----UGCAACUU---GCACAUUUGUG-U
(-((((((((.........)))))))))...........((((((......((((.....))))(((((..((((((.....))-----))))....---))))).)))))-) ( -28.70)
>consensus
GCACAAAUUGUCCUUUAAUUGGUUUUGCGCAUUAAUUUUGCAGAAUUUAUUGCGCUUUGUGCUCUGCGCUUUGCA_CUGCAAGU_____UGCAAUUU____CGCAUUUGCAUU
...............((((..((((((((.........))))))))..)))).((...((((..(((.....)))..((((........)))).........))))..))... (-12.89 = -12.05 +  -0.84)

alignment

secondary structure

dotplot

Window 2

Location	8,642,724 – 8,642,836
Length	112
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	77.33
Mean single sequence MFE	-24.17
Consensus MFE	-10.02
Energy contribution	-11.02
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-3.04
Structure conservation index	0.41
SVM decision value	1.79
SVM RNA-class probability	0.977336
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8642724 112 - 22224390
AAUGCAAAUGCGAAUGAAAAUGCAGCCGGACUUGCAC-GGCAAAGCGGCGAGCACAAAGCGCAAUAAAUUUUGCAAAAUUAAUGCGCAAAACCAAUUAAAGGACAAUUUGUGC
..(((...((((........))))((((........)-)))...)))....((((((((((((...(((((....)))))..)))))....((.......))....))))))) ( -28.50)
>DroPse_CAF1 108446 103 - 1
A-CACAAAUGUGC---AAGUUGCA-----ACUUGCAGAUGCACAGCACAACACACAAAGCGCAAUAAAUUGUGCAAAAUUAAUGCGCAAAACCAAUUAAAGGACAAUUUCG-C
.-......(((((---(..((((.-----....)))).))))))..............(((.(((...(((((((.......)))))))..((.......))...))).))-) ( -22.40)
>DroSim_CAF1 43665 112 - 1
AAUGCGAAUGCGAAUGAAAAUGCAGCAGGACUCGCAC-GGCAAAGCGCCGAGCACAAAGCGCAAUAAAUUCUGCAAAAUUAAUGCGCAAAACCAAUUAAAGGACAAUUUGUGC
..(((((.(((..((....))...)))....)))))(-(((.....)))).((((((((((((.(((.((.....)).))).)))))....((.......))....))))))) ( -32.50)
>DroEre_CAF1 92020 88 - 1
AAUGCAAAUGC------------------------AG-UGCAAAACGCAGAGCACAAAGCGCAAUAAAUUCUGCAAAAUUAAUGCGCAAAACCAAUUAAAGGACAAUUUGUGG
..(((....))------------------------).-(((.....)))...(((((((((((.(((.((.....)).))).)))))....((.......))....)))))). ( -17.90)
>DroYak_CAF1 82457 105 - 1
AAUGAAAAUGC-------ACCACAACCGAACUCGCAA-UGCAAAACGCAAAGCACAAAGCGCAAUAAAUUCUGCAAAAUUAAUGCGCAAAACCAAUUAAAGGACAAUUUGUGG
...........-------.((((((((......((..-(((.....)))..)).....(((((.(((.((.....)).))).))))).............)).....)))))) ( -19.50)
>DroPer_CAF1 95910 103 - 1
A-CACAAAUGUGC---AAGUUGCA-----ACUUGCAGUUGCACAGCACAACACACAAAGCGCAAUAAAUUGUGCAAAAUUAAUGCGCAAAACCAAUUAAAGGACAAUUUCG-C
.-......(((((---....((((-----((.....))))))..))))).........(((.(((...(((((((.......)))))))..((.......))...))).))-) ( -24.20)
>consensus
AAUGCAAAUGCG____AAAAUGCA_____ACUUGCAG_UGCAAAGCGCAAAGCACAAAGCGCAAUAAAUUCUGCAAAAUUAAUGCGCAAAACCAAUUAAAGGACAAUUUGUGC
....................................................(((((((((((.(((.((.....)).))).)))))....((.......))....)))))). (-10.02 = -11.02 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:00 2006