Locus 3612

Sequence ID	X_DroMel_CAF1
Location	9,669,164 – 9,669,353
Length	189
Max. P	0.892228

overview

Window 2

Location	9,669,164 – 9,669,283
Length	119
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	84.45
Mean single sequence MFE	-35.60
Consensus MFE	-28.64
Energy contribution	-29.83
Covariance contribution	1.19
Combinations/Pair	1.13
Mean z-score	-1.73
Structure conservation index	0.80
SVM decision value	0.52
SVM RNA-class probability	0.766115
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9669164 119 - 22224390
GUGGCUGCUGCCAAUUGCUGUUCACUUUUCGGCUGUUGCCAUUUAAAAUGGGCAGUGAGCGUGUUGCAGCUUCAAAUUUUCACAGGGUAACUGAAAUCGCUAGUUUUCACGAUUUUGUC
(.((((((.(((..(..(((((((.(((..(((....)))....))).)))))))..)..).)).)))))).)........(((((((...(((((.(....).)))))..))))))). ( -34.90)
>DroSim_CAF1 18325 119 - 1
GUGGCUGCUGCCAAUUGCUGUUCACUUUUCGGCUGUUGCCAUUUAAAAUGGGCAGUGAGCGUGUUGCAGCUUCAAAUUUUCACAGGGUAACUGAAAUCGGUAGAUCCUAUGAUUUUGUC
..((((((.(((..(..(((((((.(((..(((....)))....))).)))))))..)..).)).)))))).((((...(((.(((((.((((....))))..))))).))).)))).. ( -39.70)
>DroEre_CAF1 11661 119 - 1
GUGGCUGCUGCCAAUUGCUGUUCACUUUUCGGCUGUUGCCAUUUAAAAUGGGCAGUGAGCGUGUUGCGGCUUCAAAUUCGUGCAGGGUAACUGAAAUCGGUACUUUCUACGGUUUCUUC
(.((((((.(((..(..(((((((.(((..(((....)))....))).)))))))..)..).)).)))))).)....(((((.((((((.(((....))))))))).)))))....... ( -38.50)
>DroYak_CAF1 15861 100 - 1
GUGGCUGCUGCCAAUUGCUGUUCACUUUUCGGCUGUUGCCAUUUAAAAUGGGCAGUGAGCGUGUUGCAGCUUCACAUUUUUACAGGGUACGCAAAUUCG-U------------------
((((((((.(((..(..(((((((.(((..(((....)))....))).)))))))..)..).)).)))))..))).........((((......)))).-.------------------ ( -29.30)
>consensus
GUGGCUGCUGCCAAUUGCUGUUCACUUUUCGGCUGUUGCCAUUUAAAAUGGGCAGUGAGCGUGUUGCAGCUUCAAAUUUUCACAGGGUAACUGAAAUCGGUAGUUUCUACGAUUUUGUC
(.((((((.(((..(..(((((((.(((..(((....)))....))).)))))))..)..).)).)))))).)...................(((((((..........)))))))... (-28.64 = -29.83 +   1.19)

alignment

secondary structure

dotplot

Window 3

Location	9,669,244 – 9,669,353
Length	109
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	89.87
Mean single sequence MFE	-32.12
Consensus MFE	-22.91
Energy contribution	-23.23
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-1.68
Structure conservation index	0.71
SVM decision value	0.02
SVM RNA-class probability	0.545238
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9669244 109 + 22224390
GCAACAGCCGAAAAGUGAACAGCAAUUGGCAGCAGCCACCAAUUCAGGAGAGGCUUCACAAAAUGGAAACAGAAGUGCUGUGAGAGG---------GGGGGUAGAGAUGCUGGUGGAG
.......((.....(....)....((..(((.(.(((.((..(((.(.((..(((((......((....))))))).)).)..))).---------.))))).)...)))..)))).. ( -25.80)
>DroSim_CAF1 18405 116 + 1
GCAACAGCCGAAAAGUGAACAGCAAUUGGCAGCAGCCACCAAUUCAGGAGAGGCUUCACAAAAUGGAAACAGAAGUGCUGUGAAGGGGAGGGG--GAGGGGUGGAGAAGCUGGCGGAG
((....(((((...((.....))..)))))(((..(((((..(((........(((((((.(.((....))....)..))))))).......)--))..)))))....))).)).... ( -32.96)
>DroEre_CAF1 11741 113 + 1
GCAACAGCCGAAAAGUGAACAGCAAUUGGCAGCAGCCACCAAUUCAGGAGAGGCUUCACAAAAUGGAAACAGAAGUGCUGUGAAGGG-----GUUGGGGGUUGGAGAGGCUGGUGGAG
.((.(((((............((.....))..(((((.(((((((........(((((((.(.((....))....)..)))))))))-----))))).)))))....))))).))... ( -35.50)
>DroYak_CAF1 15922 118 + 1
GCAACAGCCGAAAAGUGAACAGCAAUUGGCAGCAGCCACCAAUUCAGGAGAGCCUUCACAAAAUGGACACAGAAGUGCUGUGAAGGGUGGGGGUGUGGGUGUGGAGAAGCUGGUGGAG
......(((((...((.....))..))))).....((((((.((((.(...((((((((...((((.(((....))))))).....)))))))).....).)))).....)))))).. ( -34.20)
>consensus
GCAACAGCCGAAAAGUGAACAGCAAUUGGCAGCAGCCACCAAUUCAGGAGAGGCUUCACAAAAUGGAAACAGAAGUGCUGUGAAGGG_____G__GGGGGGUGGAGAAGCUGGUGGAG
......(((((...((.....))..))))).....((((((.(((....))).(((((((.(.((....))....)..))))))).........................)))))).. (-22.91 = -23.23 +   0.31)

alignment

secondary structure

dotplot

Window 4

Location	9,669,244 – 9,669,353
Length	109
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	89.87
Mean single sequence MFE	-25.37
Consensus MFE	-20.82
Energy contribution	-20.82
Covariance contribution	-0.00
Combinations/Pair	1.12
Mean z-score	-2.02
Structure conservation index	0.82
SVM decision value	0.97
SVM RNA-class probability	0.892228
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9669244 109 - 22224390
CUCCACCAGCAUCUCUACCCCC---------CCUCUCACAGCACUUCUGUUUCCAUUUUGUGAAGCCUCUCCUGAAUUGGUGGCUGCUGCCAAUUGCUGUUCACUUUUCGGCUGUUGC
......((((............---------....((((((................))))))((((...((......)).)))))))).((((.((((.........)))).)))). ( -22.29)
>DroSim_CAF1 18405 116 - 1
CUCCGCCAGCUUCUCCACCCCUC--CCCCUCCCCUUCACAGCACUUCUGUUUCCAUUUUGUGAAGCCUCUCCUGAAUUGGUGGCUGCUGCCAAUUGCUGUUCACUUUUCGGCUGUUGC
......((((....(((((..((--........((((((((................))))))))........))...)))))..)))).((((.((((.........)))).)))). ( -24.88)
>DroEre_CAF1 11741 113 - 1
CUCCACCAGCCUCUCCAACCCCCAAC-----CCCUUCACAGCACUUCUGUUUCCAUUUUGUGAAGCCUCUCCUGAAUUGGUGGCUGCUGCCAAUUGCUGUUCACUUUUCGGCUGUUGC
...((.(((((...((((........-----..((((((((................))))))))..((....)).)))).))))).)).((((.((((.........)))).)))). ( -24.79)
>DroYak_CAF1 15922 118 - 1
CUCCACCAGCUUCUCCACACCCACACCCCCACCCUUCACAGCACUUCUGUGUCCAUUUUGUGAAGGCUCUCCUGAAUUGGUGGCUGCUGCCAAUUGCUGUUCACUUUUCGGCUGUUGC
......((((....((((..............((((((((((((....))))......)))))))).............))))..)))).((((.((((.........)))).)))). ( -29.53)
>consensus
CUCCACCAGCUUCUCCACCCCCC__C_____CCCUUCACAGCACUUCUGUUUCCAUUUUGUGAAGCCUCUCCUGAAUUGGUGGCUGCUGCCAAUUGCUGUUCACUUUUCGGCUGUUGC
...((.(((((......................((((((((................)))))))).......(((((...((((....))))......)))))......))))).)). (-20.82 = -20.82 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:46 2006