Locus 4090

Sequence ID	2L_DroMel_CAF1
Location	11,777,020 – 11,777,134
Length	114
Max. P	0.955573

overview

Window 4

Location	11,777,020 – 11,777,134
Length	114
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	89.84
Mean single sequence MFE	-34.88
Consensus MFE	-27.78
Energy contribution	-28.06
Covariance contribution	0.28
Combinations/Pair	1.04
Mean z-score	-2.05
Structure conservation index	0.80
SVM decision value	1.28
SVM RNA-class probability	0.939463
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11777020 114 + 22407834
AAGCUCGCAUUUGUGUUCCUGUU-UGGAUUAGCCAGGAGCAGCUGCACUUGGCUCCUCGACUGUUUGUUGUUUGUCCUGGCUCGACUCUAAGUCGGCAAACUCAAAUUCAAAUUC
......(.(((((.(((((..((-(((((((((((((((((((.(((.((((....)))).)))..)))))...)))))))).)).))))))..))..))).))))).)...... ( -33.30)
>DroSec_CAF1 34953 113 + 1
AAGCUCGCAUUUGUGUUCCUGUUUUGGCUUAGCCAGGAGCAGCUGCACUUGGCUCCUCGGCUGUUUGUUGUUUGUCCUGGCUCGACUCUAAGUCGGCAAACUCAAACUCAAAU--
.((((.((....((((..((((((((((...)))).))))))..))))...)).....))))(((((..(((((.....((.((((.....)))))).....))))).)))))-- ( -35.40)
>DroSim_CAF1 34043 113 + 1
AAGCUCGCAUUUGUGUUCCUGUUUUGGCUUAGCCAGGAGCAGCUGCACUUGGCUCCUCGGCUGUUUGUUGUUUGUCCUGGCUCGACUCUAAGUCGGCAAACUCAAACUCAAAU--
.((((.((....((((..((((((((((...)))).))))))..))))...)).....))))(((((..(((((.....((.((((.....)))))).....))))).)))))-- ( -35.40)
>DroEre_CAF1 45448 107 + 1
AAGCCUGCAUUGCUGCUCCUGUUUUGGCUUUGCCAGGAGCAGCUGCACUUGGCUCCUCUGCUGUUUGUUGUUUGUCCUGGCUCGACUCUAAGUCGGCAAAUUC------AAAU--
.((((((((..(((((((((.....(((...))))))))))))))))...))))........(((((..(((((.((.((((........))))))))))).)------))))-- ( -37.20)
>DroYak_CAF1 36525 107 + 1
AAACUUGCAUUUGUGUUCCUAUUUCGGCUUGGCCAGGAGCAGCUGCACUUGGCUCCUUUGCUGUUUGUUGUUUGUCCUGGCUCGACUCUAAGUCGGCAAAUUC------AAAU--
....(((.((((((................((((((((..(((.(((..((((......))))..))).)))..))))))))((((.....)))))))))).)------))..-- ( -33.10)
>consensus
AAGCUCGCAUUUGUGUUCCUGUUUUGGCUUAGCCAGGAGCAGCUGCACUUGGCUCCUCGGCUGUUUGUUGUUUGUCCUGGCUCGACUCUAAGUCGGCAAACUCAAA_UCAAAU__
......((.........((......))...((((((((..(((.(((..((((......))))..))).)))..))))))))((((.....)))))).................. (-27.78 = -28.06 +   0.28)

alignment

secondary structure

dotplot

Window 5

Location	11,777,020 – 11,777,134
Length	114
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	89.84
Mean single sequence MFE	-32.10
Consensus MFE	-26.78
Energy contribution	-26.18
Covariance contribution	-0.60
Combinations/Pair	1.16
Mean z-score	-1.92
Structure conservation index	0.83
SVM decision value	1.46
SVM RNA-class probability	0.955573
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11777020 114 - 22407834
GAAUUUGAAUUUGAGUUUGCCGACUUAGAGUCGAGCCAGGACAAACAACAAACAGUCGAGGAGCCAAGUGCAGCUGCUCCUGGCUAAUCCA-AACAGGAACACAAAUGCGAGCUU
............((((((((((((.....))))(((((((((............)))(((.(((........))).)))))))))..(((.-....)))........)))))))) ( -34.00)
>DroSec_CAF1 34953 113 - 1
--AUUUGAGUUUGAGUUUGCCGACUUAGAGUCGAGCCAGGACAAACAACAAACAGCCGAGGAGCCAAGUGCAGCUGCUCCUGGCUAAGCCAAAACAGGAACACAAAUGCGAGCUU
--....(((((((.(((((.((((.....))))..((.(......).......((((.((((((..((.....))))))))))))...........))....))))).))))))) ( -31.00)
>DroSim_CAF1 34043 113 - 1
--AUUUGAGUUUGAGUUUGCCGACUUAGAGUCGAGCCAGGACAAACAACAAACAGCCGAGGAGCCAAGUGCAGCUGCUCCUGGCUAAGCCAAAACAGGAACACAAAUGCGAGCUU
--....(((((((.(((((.((((.....))))..((.(......).......((((.((((((..((.....))))))))))))...........))....))))).))))))) ( -31.00)
>DroEre_CAF1 45448 107 - 1
--AUUU------GAAUUUGCCGACUUAGAGUCGAGCCAGGACAAACAACAAACAGCAGAGGAGCCAAGUGCAGCUGCUCCUGGCAAAGCCAAAACAGGAGCAGCAAUGCAGGCUU
--.(((------(..((.((((((.....)))).)).))..))))...............(((((...((((((((((((((............))))))))))..))))))))) ( -38.10)
>DroYak_CAF1 36525 107 - 1
--AUUU------GAAUUUGCCGACUUAGAGUCGAGCCAGGACAAACAACAAACAGCAAAGGAGCCAAGUGCAGCUGCUCCUGGCCAAGCCGAAAUAGGAACACAAAUGCAAGUUU
--....------((((((((((((.....)))).(((((((.............((......)).....((....)))))))))....((......)).........)))))))) ( -26.40)
>consensus
__AUUUGA_UUUGAGUUUGCCGACUUAGAGUCGAGCCAGGACAAACAACAAACAGCCGAGGAGCCAAGUGCAGCUGCUCCUGGCUAAGCCAAAACAGGAACACAAAUGCGAGCUU
............((((((((((((.....)))).(((((((.............((......)).....((....)))))))))....((......)).........)))))))) (-26.78 = -26.18 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:05 2006