Locus 1379

Sequence ID	X_DroMel_CAF1
Location	4,118,619 – 4,118,844
Length	225
Max. P	0.857849

overview

Window 0

Location	4,118,619 – 4,118,725
Length	106
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.99
Mean single sequence MFE	-36.27
Consensus MFE	-28.92
Energy contribution	-29.43
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.08
Structure conservation index	0.80
SVM decision value	0.82
SVM RNA-class probability	0.857849
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4118619 106 + 22224390
--------UGCACAUACUU-UGGUUUGUGUCGGGCCAUAAAUUGUGUGCAUUCGUCGGC-----CGCUGCCUGGUGUUUGUGUAAUUUAUUCGCAUAUUUCAGUGGAGCGUGGAGUGACA
--------((((((((...-(((((((...))))))).....))))))))...((((.(-----(((.(((((.((..((((..(.....)..))))...)).))).))))))..)))). ( -34.30)
>DroSec_CAF1 9710 111 + 1
--------UGCACAUACUU-UGGUUUGUGUCGGGACAUAAAUUGUGUGCAUUCGUCGGCUGGUCCGCUGCCUGGUGUUUGUGUAAUUUAUUCGCAUAUUUCAGUGGAGCGUGGAGUGACA
--------((((((((...-..((((((((....)))))))))))))))).(((((.((.(.(((((((....((((..(((.....)))..))))....))))))).))).)).))).. ( -35.90)
>DroSim_CAF1 5480 120 + 1
CGGUUAAUUGCACAUACUUNUGGUUUGUGUCGGGCCAUAAAUUGUGUGCAUUCGUCGGCUGGUCCGCUGCCUGGUGUUUGUGUAAUUUAUUCGCAUAUUUCAGUGGAGCGUGGAGUGACA
..((((..((((((((....(((((((...))))))).....))))))))....((.((.(.(((((((....((((..(((.....)))..))))....))))))).))).)).)))). ( -37.60)
>DroYak_CAF1 6253 106 + 1
--------UGCACAUACUU-UGGUUUGUGUUGGGCCAUAAAUUGUGUGCAUUCGUCGGU-----CGCUGCCUGGUGUUUGUGUAAUUUAUUCGCAUAUUUCACUGGAGCGCGGAGUGACA
--------((((((((...-((((((.....)))))).....))))))))...((((.(-----(((.(((..(((..((((..(.....)..))))...)))..).))))))..)))). ( -37.30)
>consensus
________UGCACAUACUU_UGGUUUGUGUCGGGCCAUAAAUUGUGUGCAUUCGUCGGC_____CGCUGCCUGGUGUUUGUGUAAUUUAUUCGCAUAUUUCAGUGGAGCGUGGAGUGACA
........((((((((....((((((.....)))))).....))))))))...((((.......((((.(((((.((.((((.........)))).)).)))).).)))).....)))). (-28.92 = -29.43 +   0.50)

alignment

secondary structure

dotplot

Window 1

Location	4,118,725 – 4,118,844
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.44
Mean single sequence MFE	-35.58
Consensus MFE	-30.61
Energy contribution	-31.99
Covariance contribution	1.38
Combinations/Pair	1.03
Mean z-score	-1.67
Structure conservation index	0.86
SVM decision value	0.25
SVM RNA-class probability	0.655133
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4118725 119 - 22224390
UGCCCCUGCUGGAUGUCUGCCCUCGUUUCUGUCUUGACUUG-GGCCACAUCUAUUACGCCCGCUCCCCAAAAACUUAACGGGGGUAGGCAUUCCUGGCAUUUUGUAGCAUAAUUUCAGGC
....((((..(((((((((((((((((...((.(((...((-(((............))))).....)))..))..)))))))))))))))))...((........)).......)))). ( -38.60)
>DroSec_CAF1 9821 120 - 1
UGCCCCUGCUGGAUGUCUGCCCUCGUUUCUGUCUUGACUUGGGGCCACAUCUAUUACGCCCGCUCCUCAAAAACUUAACAGGGGUAGGCAUUCCUGGCAUUUUGUAGCAUAAUUUCAGGC
....((((..((((((((((((..(((...((.((((...(((((............)))).)...))))..))..)))..))))))))))))...((........)).......)))). ( -36.20)
>DroSim_CAF1 5600 120 - 1
UGCCCCUGCUGGAUGUCUGCCCUCGUUUCUGUCUUGACUUGGGGCCACAUCUAUUACGCCCGCUCCCCAAAAACUUAACGGGGGUAGGCAUUCCUGGCAUUUUGUAGCAUAAUUUCAGGC
....((((..(((((((((((((((((...((.(((....(((((............)))).)....)))..))..)))))))))))))))))...((........)).......)))). ( -39.10)
>DroYak_CAF1 6359 112 - 1
UGCCCCUUUUGGAUGUCUGCCCUUGUUUCUGUCUUGACUUG--------UCUAUUACGCCCGCUCCCCAAAAACUUAACGGGGGUAGGCAUUCCUGGCAUUUUGUAGCAUAAUUUCAGGC
.(((......(((((((((((((((((...((.(((....(--------(...........))....)))..))..)))))))))))))))))...((........)).........))) ( -28.40)
>consensus
UGCCCCUGCUGGAUGUCUGCCCUCGUUUCUGUCUUGACUUG_GGCCACAUCUAUUACGCCCGCUCCCCAAAAACUUAACGGGGGUAGGCAUUCCUGGCAUUUUGUAGCAUAAUUUCAGGC
.(((......(((((((((((((((((...((.((.....(((((................)))))...)).))..)))))))))))))))))...((........)).........))) (-30.61 = -31.99 +   1.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:53 2006