Locus 784

Sequence ID X_DroMel_CAF1
Location 2,183,043 – 2,183,217
Length 174
Max. P 0.644516
window1272 window1273

overview

Window 2

Location 2,183,043 – 2,183,140
Length 97
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 79.42
Mean single sequence MFE -30.17
Consensus MFE -15.52
Energy contribution -17.59
Covariance contribution 2.06
Combinations/Pair 1.04
Mean z-score -2.30
Structure conservation index 0.51
SVM decision value 0.23
SVM RNA-class probability 0.644516
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2183043 97 - 22224390
UGCAACUG------CAGCAAAAAGAUGAAGUUUUUCACUAAAAAAAAUUAACUGUAGUUGCACCGAGUGGUGGUAAGUAGAGAAACUGCUGUACUCCACUCA--------------G-
((((((((------(((((......)).(((((((.......)))))))..)))))))))))..((((((.(((((((((.....))))).)))))))))).--------------.- ( -33.20)
>DroSec_CAF1 54719 112 - 1
UGCAACUGCACAUGCAGCAAACAGAUGAAGUUUUUCACUAAA--AAAUUAACUGUAGUUGCCCCGAGUG---GCAAGUAGAGAAACUGCUGUCCUCCACUCCACUCGCCAGUGUGUG-
.......(((((((((((..((((.(((..((((.....)))--)..))).)))).)))))..((((((---(..(((.(((..((....)).))).))))))))))...)))))).- ( -31.90)
>DroSim_CAF1 55026 112 - 1
UGCAACUGCACAUGCAGCAAACAGAUGAAGUUUUUCACUAAA--AAAUUAACUGUAGUUGCCCCGAGUG---GCAAGUAGAGAAACUGCUGUCCUCCACUCCGCUCGCCAGUGUGUG-
.......(((((((((((..((((.(((..((((.....)))--)..))).)))).)))))..((((((---(..(((.(((..((....)).))).))))))))))...)))))).- ( -31.50)
>DroEre_CAF1 58779 108 - 1
UGCAUAUGU--GUACAGCAAACAGAUGAAGUUUUUCACAAAAAAAAAUUAACUCUAGUUGCCCCGAGUG---GUAAGCAGAGAAACUGCUGUUCUACAG-----UUACCAGUGUGUGU
.((((((..--((((.((((..(((...(((((((.......)))))))...)))..)))).....(((---(..(((((.....)))))...)))).)-----.)))..)))))).. ( -24.10)
>consensus
UGCAACUGC__AUGCAGCAAACAGAUGAAGUUUUUCACUAAA__AAAUUAACUGUAGUUGCCCCGAGUG___GCAAGUAGAGAAACUGCUGUCCUCCACUCC__UCGCCAGUGUGUG_
.(((((((((...............((((....))))...............)))))))))...(((((......(((((.....)))))......)))))................. (-15.52 = -17.59 +   2.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,183,106 – 2,183,217
Length 111
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 79.42
Mean single sequence MFE -23.53
Consensus MFE -9.43
Energy contribution -10.44
Covariance contribution 1.01
Combinations/Pair 1.13
Mean z-score -2.05
Structure conservation index 0.40
SVM decision value 0.14
SVM RNA-class probability 0.602302
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2183106 111 - 22224390
CUAGAGAAUUCAUUCAUGUUUACCAACUUGUUUUUGGGCA-AACAAACACCUAGCCAGGAAAUGCGAAAUUCUGCACCUGCAACUG------CAGCAAAAAGAUGAAGUUUUUCACUA
...(((((....(((((.(((........(((((..(((.-............)))..)))))(((......)))..((((....)------)))...))).)))))..))))).... ( -21.12)
>DroSec_CAF1 54791 111 - 1
CUAGAUAGUUAAUUCAUGUUUACCAACUU-UUUUUGGGCA-----AACACCUAGC-AGGAAAUGCGAAAUGCUGCACCUGCAACUGCACAUGCAGCAAACAGAUGAAGUUUUUCACUA
.......(((..(((.(((((.((((...-...))))..)-----))))....((-(.....)))))).(((((((..(((....)))..))))))))))((.((((....)))))). ( -27.10)
>DroSim_CAF1 55098 111 - 1
CUAGAUAGUUCAUUCAUGUUUGCCAACUU-UUUUUGGGCA-----AACACCUAGC-AGGAAAUGCGAAAUGCUGCACCUGCAACUGCACAUGCAGCAAACAGAUGAAGUUUUUCACUA
...((.(.((((((..((((((((.....-......))))-----))))....((-(.....)))....(((((((..(((....)))..)))))))....)))))).)...)).... ( -32.90)
>DroEre_CAF1 58849 107 - 1
CUAAAGCAUUCAUUUAUAUUUACCAACUU---UUUGCGC-----AAACACCUAGC-AGAAAAUGCAAAAUUCUGCACCUGCAUAUGU--GUACAGCAAACAGAUGAAGUUUUUCACAA
..(((((.(((((.............((.---(((((..-----..((((.((((-((....((((......)))).)))).)).))--))...))))).))))))))))))...... ( -20.51)
>DroYak_CAF1 58975 100 - 1
-------UUGCAUUCAUAUUUACCAACUU---UUUGGGCAUAACAAACACCUAGC-AGGAAAUGCAA-ACUCGCCACCUGCAUA------CACAGCAAACCUAUGAAGUUUUUCACUA
-------((((...........((((...---.))))................((-(((....((..-....))..)))))...------....)))).................... ( -16.00)
>consensus
CUAGAGAAUUCAUUCAUGUUUACCAACUU_UUUUUGGGCA____AAACACCUAGC_AGGAAAUGCGAAAUUCUGCACCUGCAACUG____UACAGCAAACAGAUGAAGUUUUUCACUA
............(((((.....((((.......))))((..............((.(((...((((......)))))))))...(((....)))))......)))))........... ( -9.43 = -10.44 +   1.01)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:45 2006