Locus 1302

Sequence ID	X_DroMel_CAF1
Location	3,887,075 – 3,887,184
Length	109
Max. P	0.743014

overview

Window 2

Location	3,887,075 – 3,887,184
Length	109
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	89.36
Mean single sequence MFE	-43.80
Consensus MFE	-33.23
Energy contribution	-34.73
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-2.91
Structure conservation index	0.76
SVM decision value	0.16
SVM RNA-class probability	0.611825
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3887075 109 + 22224390
---------UGGAU-GGGUCGCCACUUGAGCUGCCUAAAAUGGCACUUUAGUGCCUUUUGGGGCGUGUGAAAACAAAGGCGCCAAGUGUCGUGUAGCGUCAUUGAGUUUGC-CGACACUU
---------.....-.((.((((......((..(((((((.(((((....)))))))))))))).(((....)))..))))))((((((((.(((((........).))))-)))))))) ( -43.10)
>DroVir_CAF1 70829 110 + 1
U-UUG---GUUGUUG--GGCUCCACUUGAGCCGCCUAAAAUGGCACUUUAGUGCCUUUUGGGGCGUGCGAAAACAAAGGCGCCAAGUGUCGUGUAGCG-CAUUGAGU--GG-CAACACUU
.-(..---(((((((--.((..((((((.(((((((.(((.(((((....))))).))).))))((......))...)))..))))))..)).)))))-.))..)((--(.-...))).. ( -45.40)
>DroGri_CAF1 59357 116 + 1
CCUUGCUUGUUGUUGGGGGCUCCACUUGAGCCGCCUAAAAUGGCACUUUAGUGCCUUUUGGGGCGUACGAAAACAAAGGCGCCAAGUGUCGUGUUGCG-CAUUGAGU--GG-CAACACUU
(((.((.....)).))).....((((((.(((((((.(((.(((((....))))).))).))))((......))...)))..))))))..(((((((.-(((...))--))-)))))).. ( -45.00)
>DroSim_CAF1 1714 109 + 1
---------UGGAU-GGGUCGCCACUUGAGCUGCCUAAAAUGGCACUUUAGUGCCUUUUGGGGCGUGUGAAAACAAAGGCGCCAAGUGUCGUGUAGCGUCAUUGAGUUUGC-CGACACUU
---------.....-.((.((((......((..(((((((.(((((....)))))))))))))).(((....)))..))))))((((((((.(((((........).))))-)))))))) ( -43.10)
>DroEre_CAF1 5300 110 + 1
---------UGGAU-GGGUCGCCACUUGAGCUGCCUAAAAUGGCACUUUAGUGCCUUUUGGGGCGUGUGAAAACAAAGGCGCCAAGUGUCGUGUAGCGUCAUUGAGUUUGCCCGACACUU
---------.....-.((.((((......((..(((((((.(((((....)))))))))))))).(((....)))..))))))((((((((.(((((........).)))).)))))))) ( -43.10)
>DroYak_CAF1 7109 109 + 1
---------UGGAU-GGGUCGCCACUUGAGCUGCCUAAAAUGGCACUUUAGUGCCUUUUGGGGCGUGUGAAAACAAAGGCGCCAAGUGUCGUGUAGCGUCAUUGAGUUUGC-CGACACUU
---------.....-.((.((((......((..(((((((.(((((....)))))))))))))).(((....)))..))))))((((((((.(((((........).))))-)))))))) ( -43.10)
>consensus
_________UGGAU_GGGUCGCCACUUGAGCUGCCUAAAAUGGCACUUUAGUGCCUUUUGGGGCGUGUGAAAACAAAGGCGCCAAGUGUCGUGUAGCGUCAUUGAGUUUGC_CGACACUU
................((.((((......((..(((((((.(((((....))))))))))))))((......))...))))))((((((((.(((((........)).))).)))))))) (-33.23 = -34.73 +   1.50)

alignment

secondary structure

dotplot

Window 3

Location	3,887,075 – 3,887,184
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	89.36
Mean single sequence MFE	-35.17
Consensus MFE	-28.00
Energy contribution	-28.62
Covariance contribution	0.61
Combinations/Pair	1.03
Mean z-score	-2.57
Structure conservation index	0.80
SVM decision value	0.45
SVM RNA-class probability	0.743014
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3887075 109 - 22224390
AAGUGUCG-GCAAACUCAAUGACGCUACACGACACUUGGCGCCUUUGUUUUCACACGCCCCAAAAGGCACUAAAGUGCCAUUUUAGGCAGCUCAAGUGGCGACCC-AUCCA---------
.(((((((-..........)))))))...((.((((((((.....(((....))).(((..(((.(((((....))))).)))..))).)).)))))).))....-.....--------- ( -33.70)
>DroVir_CAF1 70829 110 - 1
AAGUGUUG-CC--ACUCAAUG-CGCUACACGACACUUGGCGCCUUUGUUUUCGCACGCCCCAAAAGGCACUAAAGUGCCAUUUUAGGCGGCUCAAGUGGAGCC--CAACAAC---CAA-A
...(((((-((--((((((.(-(((((.........))))))..))).....((.((((..(((.(((((....))))).)))..))))))...)))))....--)))))..---...-. ( -36.30)
>DroGri_CAF1 59357 116 - 1
AAGUGUUG-CC--ACUCAAUG-CGCAACACGACACUUGGCGCCUUUGUUUUCGUACGCCCCAAAAGGCACUAAAGUGCCAUUUUAGGCGGCUCAAGUGGAGCCCCCAACAACAAGCAAGG
..((((((-((--(.....))-.)))))))..(((((((.(((...((......))(((..(((.(((((....))))).)))..)))))))))))))...................... ( -39.40)
>DroSim_CAF1 1714 109 - 1
AAGUGUCG-GCAAACUCAAUGACGCUACACGACACUUGGCGCCUUUGUUUUCACACGCCCCAAAAGGCACUAAAGUGCCAUUUUAGGCAGCUCAAGUGGCGACCC-AUCCA---------
.(((((((-..........)))))))...((.((((((((.....(((....))).(((..(((.(((((....))))).)))..))).)).)))))).))....-.....--------- ( -33.70)
>DroEre_CAF1 5300 110 - 1
AAGUGUCGGGCAAACUCAAUGACGCUACACGACACUUGGCGCCUUUGUUUUCACACGCCCCAAAAGGCACUAAAGUGCCAUUUUAGGCAGCUCAAGUGGCGACCC-AUCCA---------
(((((((((((............)))...))))))))((((((.............(((..(((.(((((....))))).)))..))).((....)))))).)).-.....--------- ( -34.20)
>DroYak_CAF1 7109 109 - 1
AAGUGUCG-GCAAACUCAAUGACGCUACACGACACUUGGCGCCUUUGUUUUCACACGCCCCAAAAGGCACUAAAGUGCCAUUUUAGGCAGCUCAAGUGGCGACCC-AUCCA---------
.(((((((-..........)))))))...((.((((((((.....(((....))).(((..(((.(((((....))))).)))..))).)).)))))).))....-.....--------- ( -33.70)
>consensus
AAGUGUCG_GCAAACUCAAUGACGCUACACGACACUUGGCGCCUUUGUUUUCACACGCCCCAAAAGGCACUAAAGUGCCAUUUUAGGCAGCUCAAGUGGCGACCC_AUCCA_________
.(((((((...........)))))))...((.((((((((......((......))(((..(((.(((((....))))).)))..))).)).)))))).))................... (-28.00 = -28.62 +   0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:07 2006