Locus 3500

Sequence ID X_DroMel_CAF1
Location 9,394,635 – 9,394,770
Length 135
Max. P 0.993988
window5729 window5730 window5731 window5732

overview

Window 9

Location 9,394,635 – 9,394,755
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.14
Mean single sequence MFE -29.12
Consensus MFE -28.31
Energy contribution -28.12
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -2.09
Structure conservation index 0.97
SVM decision value 1.58
SVM RNA-class probability 0.965583
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9394635 120 + 22224390
ACAUGAUUUAUAAGUCGAAUUAGAAGGAGCCACACGACGGGCAUGGAACAAGAGUGAAUUAAUUACGAAUUCAAGCCCGAAGAGGUAAUUAAUUCACUUCAUUUUCUUCCCCUGCAAAGU
...(((((....))))).....(((((((((........))).........(((((((((((((((...(((......)))...)))))))))))))))....))))))........... ( -29.00)
>DroSec_CAF1 8553 120 + 1
ACAUGAUUUAUAAGUCGAAUUAGAAGGAGCCACACGACGGGCAUGGAACAAGAGUGAAUUAAUUACGAAUUCAAGCCCGAAGAGGUAAUUAAUUCACUUCAUUUUCUUCCCCAGCAAAGU
.............((((.................))))(((...((((...(((((((((((((((...(((......)))...)))))))))))))))....))))..)))........ ( -29.03)
>DroSim_CAF1 12743 120 + 1
ACAUGAUUUAUAAGUCGAAUUAGAAGGAGCCACACGACGGGCAUGGAACAAGAGUGAAUUAAUUACGAAUUCAAGCCCGAAGAGGUAAUUAAUUCACUUCAUUUUCUUCCCCAGCAAAGU
.............((((.................))))(((...((((...(((((((((((((((...(((......)))...)))))))))))))))....))))..)))........ ( -29.03)
>DroYak_CAF1 12782 110 + 1
ACAUGAUUUAUAAGUCGAAUUAGAAGGAGCCACACGACGGGCAUGGAACAAGAGUGAAUUAAUUACGAAUUCAAGCCCGAAGAGGUAAUUAAUUCACUUCAUUUUCCUCC----------
...(((((....)))))........((((((........)))..((((...(((((((((((((((...(((......)))...)))))))))))))))....)))))))---------- ( -29.40)
>consensus
ACAUGAUUUAUAAGUCGAAUUAGAAGGAGCCACACGACGGGCAUGGAACAAGAGUGAAUUAAUUACGAAUUCAAGCCCGAAGAGGUAAUUAAUUCACUUCAUUUUCUUCCCCAGCAAAGU
...(((((....)))))........((((((........)))..((((...(((((((((((((((...(((......)))...)))))))))))))))....))))))).......... (-28.31 = -28.12 +  -0.19)

alignment

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secondary structure

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Window 0

Location 9,394,635 – 9,394,755
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.14
Mean single sequence MFE -28.80
Consensus MFE -27.08
Energy contribution -27.32
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.94
SVM decision value 0.49
SVM RNA-class probability 0.755657
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9394635 120 - 22224390
ACUUUGCAGGGGAAGAAAAUGAAGUGAAUUAAUUACCUCUUCGGGCUUGAAUUCGUAAUUAAUUCACUCUUGUUCCAUGCCCGUCGUGUGGCUCCUUCUAAUUCGACUUAUAAAUCAUGU
.....(((..((((.((...((.(((((((((((((...((((....))))...))))))))))))))))).)))).)))..((((..(((......)))...))))............. ( -29.20)
>DroSec_CAF1 8553 120 - 1
ACUUUGCUGGGGAAGAAAAUGAAGUGAAUUAAUUACCUCUUCGGGCUUGAAUUCGUAAUUAAUUCACUCUUGUUCCAUGCCCGUCGUGUGGCUCCUUCUAAUUCGACUUAUAAAUCAUGU
.........(((..(((...((.(((((((((((((...((((....))))...)))))))))))))))...)))....)))((((..(((......)))...))))............. ( -28.70)
>DroSim_CAF1 12743 120 - 1
ACUUUGCUGGGGAAGAAAAUGAAGUGAAUUAAUUACCUCUUCGGGCUUGAAUUCGUAAUUAAUUCACUCUUGUUCCAUGCCCGUCGUGUGGCUCCUUCUAAUUCGACUUAUAAAUCAUGU
.........(((..(((...((.(((((((((((((...((((....))))...)))))))))))))))...)))....)))((((..(((......)))...))))............. ( -28.70)
>DroYak_CAF1 12782 110 - 1
----------GGAGGAAAAUGAAGUGAAUUAAUUACCUCUUCGGGCUUGAAUUCGUAAUUAAUUCACUCUUGUUCCAUGCCCGUCGUGUGGCUCCUUCUAAUUCGACUUAUAAAUCAUGU
----------((((((.((..(((((((((((((((...((((....))))...)))))))))))))).)..))((((((.....)))))).))))))...................... ( -28.60)
>consensus
ACUUUGCUGGGGAAGAAAAUGAAGUGAAUUAAUUACCUCUUCGGGCUUGAAUUCGUAAUUAAUUCACUCUUGUUCCAUGCCCGUCGUGUGGCUCCUUCUAAUUCGACUUAUAAAUCAUGU
.........(((..(((...((.(((((((((((((...((((....))))...)))))))))))))))...)))....)))((((..(((......)))...))))............. (-27.08 = -27.32 +   0.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,394,675 – 9,394,770
Length 95
Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 83.16
Mean single sequence MFE -24.10
Consensus MFE -20.69
Energy contribution -20.47
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -3.92
Structure conservation index 0.86
SVM decision value 2.44
SVM RNA-class probability 0.993988
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9394675 95 + 22224390
GCAUGGAACAAGAGUGAAUUAAUUACGAAUUCAAGCCCGAAGAGGUAAUUAAUUCACUUCAUUUUCUUCCCCUGCAAAGUUGGCUGAAAACCAAA
(((.((((.(((((((((((((((((...(((......)))...)))))))))))))))....)).))))..)))....((((.(....))))). ( -26.40)
>DroSim_CAF1 12783 95 + 1
GCAUGGAACAAGAGUGAAUUAAUUACGAAUUCAAGCCCGAAGAGGUAAUUAAUUCACUUCAUUUUCUUCCCCAGCAAAGUUGACUGAAAACCAAA
...(((.....(((((((((((((((...(((......)))...)))))))))))))))..(((((.....((((...))))...)))))))).. ( -23.70)
>DroYak_CAF1 12822 73 + 1
GCAUGGAACAAGAGUGAAUUAAUUACGAAUUCAAGCCCGAAGAGGUAAUUAAUUCACUUCAUUUUCCUCC----------------------AAA
....((((...(((((((((((((((...(((......)))...)))))))))))))))....))))...----------------------... ( -22.20)
>consensus
GCAUGGAACAAGAGUGAAUUAAUUACGAAUUCAAGCCCGAAGAGGUAAUUAAUUCACUUCAUUUUCUUCCCC_GCAAAGUUG_CUGAAAACCAAA
....((((...(((((((((((((((...(((......)))...)))))))))))))))....))))............................ (-20.69 = -20.47 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,394,675 – 9,394,770
Length 95
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 83.16
Mean single sequence MFE -24.33
Consensus MFE -20.42
Energy contribution -20.20
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.89
Structure conservation index 0.84
SVM decision value 2.03
SVM RNA-class probability 0.986129
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9394675 95 - 22224390
UUUGGUUUUCAGCCAACUUUGCAGGGGAAGAAAAUGAAGUGAAUUAAUUACCUCUUCGGGCUUGAAUUCGUAAUUAAUUCACUCUUGUUCCAUGC
.(((((.....)))))....(((..((((.((...((.(((((((((((((...((((....))))...))))))))))))))))).)))).))) ( -26.90)
>DroSim_CAF1 12783 95 - 1
UUUGGUUUUCAGUCAACUUUGCUGGGGAAGAAAAUGAAGUGAAUUAAUUACCUCUUCGGGCUUGAAUUCGUAAUUAAUUCACUCUUGUUCCAUGC
..(((((..((((.......))))..))....((..(((((((((((((((...((((....))))...)))))))))))))).)..)))))... ( -24.10)
>DroYak_CAF1 12822 73 - 1
UUU----------------------GGAGGAAAAUGAAGUGAAUUAAUUACCUCUUCGGGCUUGAAUUCGUAAUUAAUUCACUCUUGUUCCAUGC
...----------------------...((((...((.(((((((((((((...((((....))))...)))))))))))))))...)))).... ( -22.00)
>consensus
UUUGGUUUUCAG_CAACUUUGC_GGGGAAGAAAAUGAAGUGAAUUAAUUACCUCUUCGGGCUUGAAUUCGUAAUUAAUUCACUCUUGUUCCAUGC
.........................((((.((...((.(((((((((((((...((((....))))...))))))))))))))))).)))).... (-20.42 = -20.20 +  -0.22)

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 11:00:58 2006