Locus 5632

Sequence ID	X_DroMel_CAF1
Location	14,530,699 – 14,530,823
Length	124
Max. P	0.999939

overview

Window 6

Location	14,530,699 – 14,530,802
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.23
Mean single sequence MFE	-25.81
Consensus MFE	-22.94
Energy contribution	-23.14
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.89
SVM decision value	1.89
SVM RNA-class probability	0.981669
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14530699 103 - 22224390
AUUUAUGGGAACGUGCUUGGCUCAUUUCCAUUCGCUCACUUUCGGCAACAUUGUUCCCCGGAGAAUUCCACCAUUCUUCGGCAGAUACAAAAAAAAGAAACA----------------C-
......(((((((((..(((.......)))..)))........(....)...))))))((((((((......))))))))......................----------------.- ( -23.90)
>DroSec_CAF1 5445 107 - 1
AUUUAUGGGAACGUGCUUGGCUCAUUUCCAUUCGCUCACUUUCGGCAACAUUGUUCCCCGGAGAAUUCCUCCAUUCUUCGGCAGAUACAAAAACCAUAUACACGUA------------C-
...((((((((((((..(((.......)))..)))........(....)...)))).(((((((((......)))))))))............)))))........------------.- ( -25.00)
>DroSim_CAF1 5820 107 - 1
AUUUAUGGGAACGUGCUUGGCUCAUUUCCAUUCGCUCACUUUCGGCAACAUUGUUCCCCGGAGAAUUCCUCCAUUCUUCGGCAGAUACAAAAACCAUAUACACGUA------------C-
...((((((((((((..(((.......)))..)))........(....)...)))).(((((((((......)))))))))............)))))........------------.- ( -25.00)
>DroEre_CAF1 5336 119 - 1
AUUUAUGGGAACGUGCUUGCCUCAUUUCCAUUCGCUCACUUUCGGCAACAUUGUUCCCCGGAGAAUUCCUCCAUUCUUCGGCAGAUACAAAAACG-UAUACACAUGCAGACGCAGAUACA
......(((((((((.(((((......................))))))).)))))))((((((((......))))))))..............(-(((.....(((....))).)))). ( -28.95)
>DroYak_CAF1 5565 107 - 1
AUUUAUGGGAACGUGCUUGGCUCAUUUCCAUUCGCUGACUUUCGGCAACAUUGUUCCCCGGAGAAUUCCUCCAUUCUUCGGCAGAUACAAUAACC-UAUACAGAUA------------CA
...((((((...(((..(((.......)))..)((((.....)))).))(((((((.(((((((((......)))))))))..)).)))))..))-))))......------------.. ( -26.20)
>consensus
AUUUAUGGGAACGUGCUUGGCUCAUUUCCAUUCGCUCACUUUCGGCAACAUUGUUCCCCGGAGAAUUCCUCCAUUCUUCGGCAGAUACAAAAACCAUAUACACAUA____________C_
......(((((((((..(((.......)))..)))........(....)...))))))((((((((......))))))))........................................ (-22.94 = -23.14 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	14,530,722 – 14,530,823
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	97.62
Mean single sequence MFE	-22.96
Consensus MFE	-20.64
Energy contribution	-20.84
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.90
SVM decision value	0.83
SVM RNA-class probability	0.862521
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14530722 101 + 22224390
CGAAGAAUGGUGGAAUUCUCCGGGGAACAAUGUUGCCGAAAGUGAGCGAAUGGAAAUGAGCCAAGCACGUUCCCAUAAAUCAUAAAGGAAAGAAUUUACGA
((.(((((......))))).))((((((...(((..(....)..)))(..(((.......)))..)..))))))........................... ( -22.00)
>DroSec_CAF1 5472 101 + 1
CGAAGAAUGGAGGAAUUCUCCGGGGAACAAUGUUGCCGAAAGUGAGCGAAUGGAAAUGAGCCAAGCACGUUCCCAUAAAUCAUAAAGAAAAGAAUUUACGA
((.....(((((.....)))))((((((...(((..(....)..)))(..(((.......)))..)..))))))........................)). ( -22.80)
>DroSim_CAF1 5847 101 + 1
CGAAGAAUGGAGGAAUUCUCCGGGGAACAAUGUUGCCGAAAGUGAGCGAAUGGAAAUGAGCCAAGCACGUUCCCAUAAAUCAUAAAGAAAAGAAUUUACGA
((.....(((((.....)))))((((((...(((..(....)..)))(..(((.......)))..)..))))))........................)). ( -22.80)
>DroEre_CAF1 5375 100 + 1
CGAAGAAUGGAGGAAUUCUCCGGGGAACAAUGUUGCCGAAAGUGAGCGAAUGGAAAUGAGGCAAGCACGUUCCCAUAAAUCAUAAAGAA-GGAAUUUACGA
((.....(((((.....)))))((((((..(((((((....((...(.....)..))..))).)))).))))))...............-........)). ( -21.90)
>DroYak_CAF1 5592 101 + 1
CGAAGAAUGGAGGAAUUCUCCGGGGAACAAUGUUGCCGAAAGUCAGCGAAUGGAAAUGAGCCAAGCACGUUCCCAUAAAUCAUAAAGAAAAGAAUUUACGA
((.....(((((.....)))))((((((...((((.(....).))))(..(((.......)))..)..))))))........................)). ( -25.30)
>consensus
CGAAGAAUGGAGGAAUUCUCCGGGGAACAAUGUUGCCGAAAGUGAGCGAAUGGAAAUGAGCCAAGCACGUUCCCAUAAAUCAUAAAGAAAAGAAUUUACGA
((.(((((......))))).))((((((...(((..(....)..)))(..(((.......)))..)..))))))........................... (-20.64 = -20.84 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	14,530,722 – 14,530,823
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	97.62
Mean single sequence MFE	-25.77
Consensus MFE	-24.74
Energy contribution	-24.94
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-3.29
Structure conservation index	0.96
SVM decision value	4.69
SVM RNA-class probability	0.999939
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14530722 101 - 22224390
UCGUAAAUUCUUUCCUUUAUGAUUUAUGGGAACGUGCUUGGCUCAUUUCCAUUCGCUCACUUUCGGCAACAUUGUUCCCCGGAGAAUUCCACCAUUCUUCG
(((((((........))))))).....(((((((((..(((.......)))..)))........(....)...))))))((((((((......)))))))) ( -25.70)
>DroSec_CAF1 5472 101 - 1
UCGUAAAUUCUUUUCUUUAUGAUUUAUGGGAACGUGCUUGGCUCAUUUCCAUUCGCUCACUUUCGGCAACAUUGUUCCCCGGAGAAUUCCUCCAUUCUUCG
(((((((........))))))).....(((((((((..(((.......)))..)))........(....)...))))))((((((((......)))))))) ( -25.70)
>DroSim_CAF1 5847 101 - 1
UCGUAAAUUCUUUUCUUUAUGAUUUAUGGGAACGUGCUUGGCUCAUUUCCAUUCGCUCACUUUCGGCAACAUUGUUCCCCGGAGAAUUCCUCCAUUCUUCG
(((((((........))))))).....(((((((((..(((.......)))..)))........(....)...))))))((((((((......)))))))) ( -25.70)
>DroEre_CAF1 5375 100 - 1
UCGUAAAUUCC-UUCUUUAUGAUUUAUGGGAACGUGCUUGCCUCAUUUCCAUUCGCUCACUUUCGGCAACAUUGUUCCCCGGAGAAUUCCUCCAUUCUUCG
(((((((....-...))))))).....(((((((((.(((((......................))))))).)))))))((((((((......)))))))) ( -25.65)
>DroYak_CAF1 5592 101 - 1
UCGUAAAUUCUUUUCUUUAUGAUUUAUGGGAACGUGCUUGGCUCAUUUCCAUUCGCUGACUUUCGGCAACAUUGUUCCCCGGAGAAUUCCUCCAUUCUUCG
(((((((........))))))).....(((((((.(..(((.......)))..)((((.....)))).....)))))))((((((((......)))))))) ( -26.10)
>consensus
UCGUAAAUUCUUUUCUUUAUGAUUUAUGGGAACGUGCUUGGCUCAUUUCCAUUCGCUCACUUUCGGCAACAUUGUUCCCCGGAGAAUUCCUCCAUUCUUCG
(((((((........))))))).....(((((((((..(((.......)))..)))........(....)...))))))((((((((......)))))))) (-24.74 = -24.94 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:45 2006