Locus 7200

Sequence ID X_DroMel_CAF1
Location 18,027,510 – 18,027,687
Length 177
Max. P 0.869080
window11762 window11763 window11764

overview

Window 2

Location 18,027,510 – 18,027,619
Length 109
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 95.15
Mean single sequence MFE -43.78
Consensus MFE -32.56
Energy contribution -33.76
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.86
Structure conservation index 0.74
SVM decision value 0.70
SVM RNA-class probability 0.825547
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18027510 109 + 22224390
GUGUGUGCCAAGUCGUCCUGGCGCGAGUCCUGCAAUGGAGGUUUCUUCAUUGGAGGAGGCUCCUCCAUUGGCCCAUUGCGCUUCGAUUGCAGUUUAAGCGCUUGGCUGU
......((((((.(((...(((....)))(((((((.(((((.....((.((((((.....)))))).))((.....))))))).))))))).....)))))))))... ( -45.50)
>DroSec_CAF1 16031 104 + 1
GUGUGAGCCAAGUCGUCCUGGCGCGAGUCCUGCAAUGG--GUUUCUUCAUUGG---AGGCUCCUCCAUUGGCCCAUUGCGCUUCGAUUGCAGUUUAAGCGCUUGGCUAU
.....((((((((......(((....)))..(((((((--((.....((.(((---((....))))).)))))))))))((((.(((....))).)))))))))))).. ( -44.20)
>DroSim_CAF1 16347 106 + 1
GUGUGAGCCAAGUCGUCCUGGCGCGAGUCCUGCAAUGGAGGUUUCUUCAUUGG---AGGCUCCUCCAUUGGCCCAUUGCGCUUCGAUUGCAGUUUAAGCGCUUGGCUAU
.....(((((((.(((...(((....)))(((((((.(((((.....((.(((---((....))))).))((.....))))))).))))))).....)))))))))).. ( -44.50)
>DroEre_CAF1 17974 106 + 1
GUGUGUGGCAAGUCGUCCUGGCGCGAGUCCUGCAAUGGAGGUUUCUUCAUUGG---AGGCUCCUCCAUUGGCCCAUUGCGCUUCGAUUGCAGUUUAAGCGCCUGGCUGU
..............(((..(((((..(..(((((((.(((((.....((.(((---((....))))).))((.....))))))).)))))))..)..))))).)))... ( -41.30)
>DroYak_CAF1 15283 106 + 1
GUGUGUACCAUGUCGUCCUGGCGCGAGUCCUGCAAUGGAGGUUUCUUCAUUGG---AGGCUCCUCCAUUGCCCCAUUGCGCUUCGAUUGCAGUUUAAGCGCUUGGCUGU
((((......(((.(((..(((((((.....((((((((((..((((.....)---)))..))))))))))....)))))))..))).)))......))))........ ( -43.40)
>consensus
GUGUGUGCCAAGUCGUCCUGGCGCGAGUCCUGCAAUGGAGGUUUCUUCAUUGG___AGGCUCCUCCAUUGGCCCAUUGCGCUUCGAUUGCAGUUUAAGCGCUUGGCUGU
......(((((((.(((..(((((((......(((((((((..(((..........)))..))))))))).....)))))))..))).((.......)))))))))... (-32.56 = -33.76 +   1.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,027,510 – 18,027,619
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 95.15
Mean single sequence MFE -34.42
Consensus MFE -27.45
Energy contribution -28.29
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -2.00
Structure conservation index 0.80
SVM decision value 0.86
SVM RNA-class probability 0.869080
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18027510 109 - 22224390
ACAGCCAAGCGCUUAAACUGCAAUCGAAGCGCAAUGGGCCAAUGGAGGAGCCUCCUCCAAUGAAGAAACCUCCAUUGCAGGACUCGCGCCAGGACGACUUGGCACACAC
...(((((((((((.....((.......))(((((((..((.((((((.....)))))).)).((....))))))))).((.......))))).)).))))))...... ( -35.90)
>DroSec_CAF1 16031 104 - 1
AUAGCCAAGCGCUUAAACUGCAAUCGAAGCGCAAUGGGCCAAUGGAGGAGCCU---CCAAUGAAGAAAC--CCAUUGCAGGACUCGCGCCAGGACGACUUGGCUCACAC
..((((((((((((.....((.......))((((((((.((.(((((....))---))).))......)--))))))).((.......))))).)).)))))))..... ( -35.90)
>DroSim_CAF1 16347 106 - 1
AUAGCCAAGCGCUUAAACUGCAAUCGAAGCGCAAUGGGCCAAUGGAGGAGCCU---CCAAUGAAGAAACCUCCAUUGCAGGACUCGCGCCAGGACGACUUGGCUCACAC
........((((((............))))))..(((((((((((.(((((((---.(((((.((....)).))))).))).))).).))).......))))))))... ( -34.61)
>DroEre_CAF1 17974 106 - 1
ACAGCCAGGCGCUUAAACUGCAAUCGAAGCGCAAUGGGCCAAUGGAGGAGCCU---CCAAUGAAGAAACCUCCAUUGCAGGACUCGCGCCAGGACGACUUGCCACACAC
...(((.(((((.....(((((((.((.((.(...).))((.(((((....))---))).))........)).))))))).....))))).)).).............. ( -33.00)
>DroYak_CAF1 15283 106 - 1
ACAGCCAAGCGCUUAAACUGCAAUCGAAGCGCAAUGGGGCAAUGGAGGAGCCU---CCAAUGAAGAAACCUCCAUUGCAGGACUCGCGCCAGGACGACAUGGUACACAC
..((((..((((((............))))))......((((((((((..(.(---(....)).)...)))))))))).)).)).(..(((........)))..).... ( -32.70)
>consensus
ACAGCCAAGCGCUUAAACUGCAAUCGAAGCGCAAUGGGCCAAUGGAGGAGCCU___CCAAUGAAGAAACCUCCAUUGCAGGACUCGCGCCAGGACGACUUGGCACACAC
...(((..((((((............))))))....)))(((((((((....................)))))))))........(.((((((....)))))).).... (-27.45 = -28.29 +   0.84)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,027,585 – 18,027,687
Length 102
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 81.37
Mean single sequence MFE -28.25
Consensus MFE -14.14
Energy contribution -15.67
Covariance contribution 1.53
Combinations/Pair 1.21
Mean z-score -2.46
Structure conservation index 0.50
SVM decision value 0.11
SVM RNA-class probability 0.589635
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18027585 102 + 22224390
UUGCGCUUCGAUUGCAGUUUAAGCGCU-UGGCUGU------AUGAGCUUUAAGAGUU--------UUCUUUUAUUGUUUAU-UGCCUCAAGUGCCCCCAUAAGUAGGCAAUACUUUUU
..((((((.(((....))).)))))).-.(((...------((((((..((((((..--------..))))))..))))))-.))).....((((..(....)..))))......... ( -29.00)
>DroVir_CAF1 39638 112 + 1
UCGCAUUUCGAUUGCAUACUG--CGAC-UCGCAGUCUGGUCGUGAGCUUUAAGAGCUAAGGAGUAUUC-UUUAUUGUUCAU-UGCACAGAGUGGCCAUAUUA-UUGGCAAUCCUUGUU
........(((((((.....)--))).-)))((.((((((.((((((...(((((((....)))..))-))....))))))-.)).)))).))((((.....-.)))).......... ( -30.20)
>DroSim_CAF1 16419 102 + 1
UUGCGCUUCGAUUGCAGUUUAAGCGCU-UGGCUAU------AUGAGCUUUAAGAGUU--------UUCUUUUAUUGUUUAU-UGCCUCAAGUGCCCCCAUAAGUAGGCAAUACUUUUU
..((((((.(((....))).)))))).-.(((...------((((((..((((((..--------..))))))..))))))-.))).....((((..(....)..))))......... ( -29.00)
>DroEre_CAF1 18046 99 + 1
UUGCGCUUCGAUUGCAGUUUAAGCGCC-UGGCUGU------AUGAGCUUUAAGAGUU--------UUCUUUUAUUGUUUAU-UGCCUCAAGUGCCCUCAUAAGUAGGCAAUACUU---
..((((((.(((....))).)))))).-.(((...------((((((..((((((..--------..))))))..))))))-.))).....((((..(....)..))))......--- ( -28.80)
>DroYak_CAF1 15355 102 + 1
UUGCGCUUCGAUUGCAGUUUAAGCGCU-UGGCUGU------AUGAGCUUUAAGAGUU--------UUCUUUUAUUGUUUAU-UGCCUCAAGUGCCCCCAUAAGUAGGCAAUACUUUUU
..((((((.(((....))).)))))).-.(((...------((((((..((((((..--------..))))))..))))))-.))).....((((..(....)..))))......... ( -29.00)
>DroAna_CAF1 46270 103 + 1
UUG-ACUUCGAUUGCAGUUUAAGCGCCUCGGCUAU------UGGAGCUUUUAAAGUG--------UUCUUUUAUUGUUUAUUUGCCUCGAGUGCGCCCAUAAGUAGGCAAUACUUUUU
...-......(((((..((((.((((((((((...------..((((....((((..--------..))))....))))....)))..))).))))...))))...)))))....... ( -23.50)
>consensus
UUGCGCUUCGAUUGCAGUUUAAGCGCC_UGGCUGU______AUGAGCUUUAAGAGUU________UUCUUUUAUUGUUUAU_UGCCUCAAGUGCCCCCAUAAGUAGGCAAUACUUUUU
..((((((.(((....))).))))))...............((((((..((((((............))))))..)))))).(((((...(((....)))....)))))......... (-14.14 = -15.67 +   1.53)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:37 2006