Locus 5757

Sequence ID X_DroMel_CAF1
Location 14,935,671 – 14,935,827
Length 156
Max. P 0.997640
window9341 window9342 window9343

overview

Window 1

Location 14,935,671 – 14,935,787
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.16
Mean single sequence MFE -23.00
Consensus MFE -20.12
Energy contribution -20.72
Covariance contribution 0.60
Combinations/Pair 1.06
Mean z-score -1.77
Structure conservation index 0.87
SVM decision value 1.77
SVM RNA-class probability 0.976619
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14935671 116 + 22224390
UUGAAUUUUUUGGAGAAA----AAUCAAUAUUCUGAAGUUGGCACAAAAAACAGAAACCUCUUUAAACCGCAAGAGAAAUCUGAGUGCCAUUAAAAUCUUCAUUCGGGAAAUCAUUCUAA
.(((.(((((((((((..----..)).......(((((.((((((......((((...(((((........)))))...)))).)))))).......)))))))))))))))))...... ( -22.80)
>DroSec_CAF1 146 115 + 1
UUGAAUUUUUUGGAGAAA----AAUGAAUAUUCUGAAGUUGGCACAA-AAACAGAAACCUCUUUAAACCGAAAGAGAAAUCUGAGUGCCAUUAAAAUCUUCAUUCGGGAAAUCAUUCUAA
.(((.((((((((((((.----........)))(((((.((((((..-...((((...((((((......))))))...)))).)))))).......)))))))))))))))))...... ( -24.70)
>DroSim_CAF1 411 115 + 1
UUGAAUUUUUUGGAGAAA----AAUGAAUAUUCUGAAGUUGGCACAA-AAACAGAAACCUCUUUAAACCGAAAGAGAAAUCUGAGUGCCAUUAAAAUCUUCAUUCGGGAAAUCAUUCUAA
.(((.((((((((((((.----........)))(((((.((((((..-...((((...((((((......))))))...)))).)))))).......)))))))))))))))))...... ( -24.70)
>DroEre_CAF1 155 114 + 1
AGGA-AUUUUUGAAGAAA----AAUGAAUAUUCUGAAGUUGGCACAG-AAACAGAAACCUCGUUAAACCGAAAGAGAAAUCUGAGUGCCAUUGAAAUCUUCAUUCGGGAAAUCAUUCUAA
....-.............----(((((...(((((((..((((((..-...........(((......))).(((....)))..)))))).(((.....))))))))))..))))).... ( -21.80)
>DroYak_CAF1 438 118 + 1
UGGA-GUUUUUGAAGGAAAUGAAAUGAAUAUUCUGAAGUUGGCACAA-AAACAGAAACCUCCUUAAACCGAAAGAGAAAUCUGAGUGCCAUUAAAAUCUUCAUUCGGGAAAUCAUUAUAA
..((-.(((((((((((.((.......)).)))(((((.((((((..-...((((...(((.((......)).)))...)))).)))))).......))))))))))))).))....... ( -21.00)
>consensus
UUGAAUUUUUUGGAGAAA____AAUGAAUAUUCUGAAGUUGGCACAA_AAACAGAAACCUCUUUAAACCGAAAGAGAAAUCUGAGUGCCAUUAAAAUCUUCAUUCGGGAAAUCAUUCUAA
..((.((((((((((((.............)))(((((.((((((......((((...((((((......))))))...)))).)))))).......))))))))))))))))....... (-20.12 = -20.72 +   0.60)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,935,671 – 14,935,787
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.16
Mean single sequence MFE -26.74
Consensus MFE -22.14
Energy contribution -22.82
Covariance contribution 0.68
Combinations/Pair 1.04
Mean z-score -2.78
Structure conservation index 0.83
SVM decision value 2.90
SVM RNA-class probability 0.997640
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14935671 116 - 22224390
UUAGAAUGAUUUCCCGAAUGAAGAUUUUAAUGGCACUCAGAUUUCUCUUGCGGUUUAAAGAGGUUUCUGUUUUUUGUGCCAACUUCAGAAUAUUGAUU----UUUCUCCAAAAAAUUCAA
..((((.((((.......(((((.......((((((.((((..((((((........))))))..))))......)))))).))))).......))))----.))))............. ( -26.84)
>DroSec_CAF1 146 115 - 1
UUAGAAUGAUUUCCCGAAUGAAGAUUUUAAUGGCACUCAGAUUUCUCUUUCGGUUUAAAGAGGUUUCUGUUU-UUGUGCCAACUUCAGAAUAUUCAUU----UUUCUCCAAAAAAUUCAA
...((((........(((((((.(((((..((((((.((((..(((((((......)))))))..))))...-..)))))).....))))).))))))----)...........)))).. ( -28.11)
>DroSim_CAF1 411 115 - 1
UUAGAAUGAUUUCCCGAAUGAAGAUUUUAAUGGCACUCAGAUUUCUCUUUCGGUUUAAAGAGGUUUCUGUUU-UUGUGCCAACUUCAGAAUAUUCAUU----UUUCUCCAAAAAAUUCAA
...((((........(((((((.(((((..((((((.((((..(((((((......)))))))..))))...-..)))))).....))))).))))))----)...........)))).. ( -28.11)
>DroEre_CAF1 155 114 - 1
UUAGAAUGAUUUCCCGAAUGAAGAUUUCAAUGGCACUCAGAUUUCUCUUUCGGUUUAACGAGGUUUCUGUUU-CUGUGCCAACUUCAGAAUAUUCAUU----UUUCUUCAAAAAU-UCCU
..(((((((.(((..((((((.....))).((((((.((((..((((............))))..))))...-..))))))..))).)))...)))))----))...........-.... ( -23.60)
>DroYak_CAF1 438 118 - 1
UUAUAAUGAUUUCCCGAAUGAAGAUUUUAAUGGCACUCAGAUUUCUCUUUCGGUUUAAGGAGGUUUCUGUUU-UUGUGCCAACUUCAGAAUAUUCAUUUCAUUUCCUUCAAAAAC-UCCA
......(((......(((((((.(((((..((((((.((((..(((((((......)))))))..))))...-..)))))).....))))).)))))))........))).....-.... ( -27.04)
>consensus
UUAGAAUGAUUUCCCGAAUGAAGAUUUUAAUGGCACUCAGAUUUCUCUUUCGGUUUAAAGAGGUUUCUGUUU_UUGUGCCAACUUCAGAAUAUUCAUU____UUUCUCCAAAAAAUUCAA
................((((((.(((((..((((((.((((..(((((((......)))))))..))))......)))))).....))))).))))))...................... (-22.14 = -22.82 +   0.68)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,935,707 – 14,935,827
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.71
Mean single sequence MFE -29.16
Consensus MFE -27.72
Energy contribution -27.52
Covariance contribution -0.20
Combinations/Pair 1.15
Mean z-score -1.20
Structure conservation index 0.95
SVM decision value 0.60
SVM RNA-class probability 0.794610
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14935707 120 - 22224390
GUAGACAACUAAUUUACUUGGGCUGGUUGUUGAGGAGGUUUUAGAAUGAUUUCCCGAAUGAAGAUUUUAAUGGCACUCAGAUUUCUCUUGCGGUUUAAAGAGGUUUCUGUUUUUUGUGCC
...((((((((.(((....))).))))))))(.(((((((.......))))))))................(((((.((((..((((((........))))))..))))......))))) ( -30.60)
>DroSec_CAF1 182 119 - 1
GUAGACAACUAAUUUAUUUGGAAAGGUUGUUGCGGAGGUUUUAGAAUGAUUUCCCGAAUGAAGAUUUUAAUGGCACUCAGAUUUCUCUUUCGGUUUAAAGAGGUUUCUGUUU-UUGUGCC
((((.(((((..(((....)))..)))))))))(((((((.......))))))).................(((((.((((..(((((((......)))))))..))))...-..))))) ( -30.10)
>DroSim_CAF1 447 119 - 1
GUAGACAACUAAUUUACUUGAAAAGGUUGUUGCGGAGGUUUUAGAAUGAUUUCCCGAAUGAAGAUUUUAAUGGCACUCAGAUUUCUCUUUCGGUUUAAAGAGGUUUCUGUUU-UUGUGCC
((((.(((((..(((....)))..)))))))))(((((((.......))))))).................(((((.((((..(((((((......)))))))..))))...-..))))) ( -30.50)
>DroEre_CAF1 190 119 - 1
GUAGACAACUCAAUUACUUGGUAAGGUUGUUAAGGAGGUUUUAGAAUGAUUUCCCGAAUGAAGAUUUCAAUGGCACUCAGAUUUCUCUUUCGGUUUAACGAGGUUUCUGUUU-CUGUGCC
...(((((((..(((....)))..)))))))..(((((((.......))))))).(((.......)))...(((((.((((..((((............))))..))))...-..))))) ( -26.80)
>DroYak_CAF1 477 119 - 1
GUAGACAACUCAAUUACUUGGUAAGGUUGCAAAGGAGAUUUUAUAAUGAUUUCCCGAAUGAAGAUUUUAAUGGCACUCAGAUUUCUCUUUCGGUUUAAGGAGGUUUCUGUUU-UUGUGCC
...(.(((((..(((....)))..))))))...(((((((.......))))))).................(((((.((((..(((((((......)))))))..))))...-..))))) ( -27.80)
>consensus
GUAGACAACUAAUUUACUUGGAAAGGUUGUUGAGGAGGUUUUAGAAUGAUUUCCCGAAUGAAGAUUUUAAUGGCACUCAGAUUUCUCUUUCGGUUUAAAGAGGUUUCUGUUU_UUGUGCC
...(((((((..(((....)))..)))))))..(((((((.......))))))).................(((((.((((..(((((((......)))))))..))))......))))) (-27.72 = -27.52 +  -0.20)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:40 2006