Locus 1341

Sequence ID	2R_DroMel_CAF1
Location	5,168,166 – 5,168,294
Length	128
Max. P	0.974650

overview

Window 0

Location	5,168,166 – 5,168,269
Length	103
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	83.32
Mean single sequence MFE	-35.65
Consensus MFE	-28.05
Energy contribution	-30.17
Covariance contribution	2.12
Combinations/Pair	1.19
Mean z-score	-4.65
Structure conservation index	0.79
SVM decision value	1.73
SVM RNA-class probability	0.974650
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5168166 103 + 20766785
GGGGCGAAUGGCCAAAAGGCAGGGGAGGGUUGACUUUUUGGCUUAAAAUCUUUUGGUUUUGUUUGUGGCGAGUUG-CCAUAAACAAAGCCAGAGGUUU---AAAAAG
.........(((((((((((((.......))).))))))))))..((((((((.(((((((((((((((.....)-))))))))))))))))))))))---...... ( -41.30)
>DroSec_CAF1 43798 103 + 1
GGGGCGAAUGGCCAAAAGGCAGGGGUGAGUUGACUUUUUGGCUUAAAAUCUUUUGGUUUUGUUUGUGGCGAGUUG-GCAUAAACAAAGCCAGAGGUUU---AAACAG
.........(((((((((((((.......))).))))))))))..((((((((.(((((((((((((.(.....)-.)))))))))))))))))))))---...... ( -36.70)
>DroSim_CAF1 30352 104 + 1
GGGGCGAAUGGCCAAAAGGCAGGGGAAGGUUGACUUUUUGGCUUAAAAUCUUUUGGUUUUGUUUGUGGCGAGUUGGGCAAAAACAAACCCAGAAGUUU---AAAAAA
.........(((((((((((((.......))).))))))))))......(((((((.(((((((.((.(......).)).))))))).)))))))...---...... ( -29.30)
>DroEre_CAF1 45751 106 + 1
GGGGCGAAUGGCCAAAAGGCAGGGGAGGGUUGACUUUUUGGCUUAAAAUCUUUUGGUUUUGUUUGUGGCGAAUUG-CCAUAAACAAAGCCGGAGGUUUUCUAAGGAA
.....(((.(((((((((((((.......))).))))))))))......((((((((((((((((((((.....)-)))))))))))))))))))..)))....... ( -40.90)
>DroYak_CAF1 44050 102 + 1
GGGGCGAAUGGCCAAAAGGCAGGGGAGGGUUGACUUUUUGGCUUAAAAUCUUUUGGUUUUGUUUGUGG-GAGUUG-CCAUAAACAAAGCCGAAGGUUU---AAAAAA
.........(((((((((((((.......))).))))))))))..((((((((.((((((((((((((-......-))))))))))))))))))))))---...... ( -38.00)
>DroAna_CAF1 65743 79 + 1
-----------------------GCAGGGUUGACUUUUUGGCUUAAAAUCUU-UGGUUUUGUUUGUGGCCAGUUG-CCGUAAACAAGGCCAGGGGAUU---UAAUAA
-----------------------....(((..(....)..)))((((.((((-((((((((((((((((.....)-))))))))))))))))))).))---)).... ( -27.70)
>consensus
GGGGCGAAUGGCCAAAAGGCAGGGGAGGGUUGACUUUUUGGCUUAAAAUCUUUUGGUUUUGUUUGUGGCGAGUUG_CCAUAAACAAAGCCAGAGGUUU___AAAAAA
.........(((((((((((((.......))).))))))))))......(((((((((((((((((((........)))))))))))))))))))............ (-28.05 = -30.17 +   2.12)

alignment

secondary structure

dotplot

Window 1

Location	5,168,166 – 5,168,269
Length	103
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	83.32
Mean single sequence MFE	-18.85
Consensus MFE	-12.54
Energy contribution	-13.33
Covariance contribution	0.79
Combinations/Pair	1.00
Mean z-score	-2.92
Structure conservation index	0.67
SVM decision value	0.60
SVM RNA-class probability	0.793886
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5168166 103 - 20766785
CUUUUU---AAACCUCUGGCUUUGUUUAUGG-CAACUCGCCACAAACAAAACCAAAAGAUUUUAAGCCAAAAAGUCAACCCUCCCCUGCCUUUUGGCCAUUCGCCCC
......---........((((((((((.(((-(.....)))).)))))))...............(((((((.((............)).))))))).....))).. ( -22.90)
>DroSec_CAF1 43798 103 - 1
CUGUUU---AAACCUCUGGCUUUGUUUAUGC-CAACUCGCCACAAACAAAACCAAAAGAUUUUAAGCCAAAAAGUCAACUCACCCCUGCCUUUUGGCCAUUCGCCCC
......---........((((((((((.((.-(.....).)).)))))))...............(((((((.((............)).))))))).....))).. ( -15.80)
>DroSim_CAF1 30352 104 - 1
UUUUUU---AAACUUCUGGGUUUGUUUUUGCCCAACUCGCCACAAACAAAACCAAAAGAUUUUAAGCCAAAAAGUCAACCUUCCCCUGCCUUUUGGCCAUUCGCCCC
......---...(((.(((.(((((((.((.(......).)).))))))).))).))).......(((((((.((............)).))))))).......... ( -17.80)
>DroEre_CAF1 45751 106 - 1
UUCCUUAGAAAACCUCCGGCUUUGUUUAUGG-CAAUUCGCCACAAACAAAACCAAAAGAUUUUAAGCCAAAAAGUCAACCCUCCCCUGCCUUUUGGCCAUUCGCCCC
.......(((.......((.(((((((.(((-(.....)))).))))))).))............(((((((.((............)).)))))))..)))..... ( -23.50)
>DroYak_CAF1 44050 102 - 1
UUUUUU---AAACCUUCGGCUUUGUUUAUGG-CAACUC-CCACAAACAAAACCAAAAGAUUUUAAGCCAAAAAGUCAACCCUCCCCUGCCUUUUGGCCAUUCGCCCC
......---........((((((((((.(((-......-))).)))))))...............(((((((.((............)).))))))).....))).. ( -19.20)
>DroAna_CAF1 65743 79 - 1
UUAUUA---AAUCCCCUGGCCUUGUUUACGG-CAACUGGCCACAAACAAAACCA-AAGAUUUUAAGCCAAAAAGUCAACCCUGC-----------------------
......---.......(((..((((((..((-(.....)))..))))))..)))-..((((((.......))))))........----------------------- ( -13.90)
>consensus
UUUUUU___AAACCUCUGGCUUUGUUUAUGG_CAACUCGCCACAAACAAAACCAAAAGAUUUUAAGCCAAAAAGUCAACCCUCCCCUGCCUUUUGGCCAUUCGCCCC
.................((.(((((((.(((........))).))))))).))....((((((.......))))))...........(((....))).......... (-12.54 = -13.33 +   0.79)

alignment

secondary structure

dotplot

Window 2

Location	5,168,204 – 5,168,294
Length	90
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	81.60
Mean single sequence MFE	-31.79
Consensus MFE	-25.08
Energy contribution	-25.08
Covariance contribution	0.01
Combinations/Pair	1.32
Mean z-score	-4.40
Structure conservation index	0.79
SVM decision value	1.62
SVM RNA-class probability	0.967882
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5168204 90 + 20766785
UGGCUUAAAAUCUUUUGGUUUUGUUUGUGGCGAGUUG-CCAUAAACAAAGCCAGAGGUUU---AAAAAGAGCGGGGGACUU--GAAAGCAAAGUUU------------
..((((.....((((((((((((((((((((.....)-)))))))))))))))))))...---.....))))...((((((--.......))))))------------ ( -34.32)
>DroSec_CAF1 43836 90 + 1
UGGCUUAAAAUCUUUUGGUUUUGUUUGUGGCGAGUUG-GCAUAAACAAAGCCAGAGGUUU---AAACAGAGCGGGGGACUU--GAAAGCAAAGUUU------------
..((((.....((((((((((((((((((.(.....)-.))))))))))))))))))...---.....))))...((((((--.......))))))------------ ( -29.72)
>DroSim_CAF1 30390 91 + 1
UGGCUUAAAAUCUUUUGGUUUUGUUUGUGGCGAGUUGGGCAAAAACAAACCCAGAAGUUU---AAAAAAAACGGGGGACUU--GAAAGCAAAGUUU------------
..((((.....(((((((.(((((((.((.(......).)).))))))).)))))))...---.........((....)).--..)))).......------------ ( -22.30)
>DroEre_CAF1 45789 91 + 1
UGGCUUAAAAUCUUUUGGUUUUGUUUGUGGCGAAUUG-CCAUAAACAAAGCCGGAGGUUUUCUAAGGAA--CGGGGGACUU--GAAAGCAAAGUUU------------
..((((........(((((((((((((((((.....)-))))))))))))))))(((((..((......--.))..)))))--..)))).......------------ ( -34.20)
>DroYak_CAF1 44088 89 + 1
UGGCUUAAAAUCUUUUGGUUUUGUUUGUGG-GAGUUG-CCAUAAACAAAGCCGAAGGUUU---AAAAAAUGUGGGGGACUG--GAAAGCAAAGUUU------------
..((((.((((((((.((((((((((((((-......-))))))))))))))))))))))---......(.(((....)))--.))))).......------------ ( -31.80)
>DroAna_CAF1 65758 103 + 1
UGGCUUAAAAUCUU-UGGUUUUGUUUGUGGCCAGUUG-CCGUAAACAAGGCCAGGGGAUU---UAAUAAGGACGUGGACUACUAAGGGAAAAGUUUCCCACUGCCAGG
(((((((((.((((-((((((((((((((((.....)-))))))))))))))))))).))---)))...................(((((....)))))...)))).. ( -38.40)
>consensus
UGGCUUAAAAUCUUUUGGUUUUGUUUGUGGCGAGUUG_CCAUAAACAAAGCCAGAGGUUU___AAAAAAAGCGGGGGACUU__GAAAGCAAAGUUU____________
..((((.....(((((((((((((((((((........)))))))))))))))))))...............((....)).....))))................... (-25.08 = -25.08 +   0.01)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:39 2006