Locus 1398

Sequence ID X_DroMel_CAF1
Location 4,213,516 – 4,213,676
Length 160
Max. P 0.999999
window2230 window2231 window2232 window2233

overview

Window 0

Location 4,213,516 – 4,213,636
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.15
Mean single sequence MFE -23.98
Consensus MFE -17.76
Energy contribution -19.20
Covariance contribution 1.44
Combinations/Pair 1.29
Mean z-score -2.18
Structure conservation index 0.74
SVM decision value 1.41
SVM RNA-class probability 0.951324
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4213516 120 + 22224390
UAAGUAAUUUCUCAUACGCCAGCGAGUUGAAUGUUUACAACAACUAGAUAAUGCGUAACUACCUAAUGAAUGAACUGAAAAUCAUUAGUUCGAAACGUAUUAUUUAAUUAUUGCAAUAUA
...(((........)))....((((((((........))))...((((((((((((..(........)..((((((((......))))))))..))))))))))))....))))...... ( -23.50)
>DroSec_CAF1 1664 118 + 1
CAAGUAAUUCCUCAUCCGCCAGCGAGUUGAAUGUUUACAAUAACUAGAUAAUACCUAACGAACUCAUGAAUG-ACUGAAAAUCAUAUGUUCGAAAGGUAUUACUAAAUUACUGCAACAU-
..(((((((..(((.(((....)).).)))..............(((.((((((((..(((((..((((.(.-......).))))..)))))..)))))))))))))))))).......- ( -25.30)
>DroSim_CAF1 1664 118 + 1
CAAGUAAUUCCUCAUCCGCCAGCGAGUUGAAUGUUUACAAUAACUAGAUAAUACCUGACGAACUCAUGAAUG-ACUGAAAAUCAUGUGUUCGAAAGGUAUUACUAAAUUACUGCAAGAU-
..(((((((..(((.(((....)).).)))..............(((.((((((((..(((((.(((((.(.-......).))))).)))))..)))))))))))))))))).......- ( -29.90)
>DroEre_CAF1 1696 119 + 1
UGAGCAAUUUCUCACACGCCAACGAGUUGAAUGUUAACAAUAACUUAAUAAUCCGUUUCGCAUUUAUGAAUG-AUUAAAGCACAUAACUUCGAAUCGAAUUAUUAAAUCACUGUAACAUA
((((......)))).....(((....))).((((((.((.....((((((((.((.((((...(((((....-.........)))))...)))).)).)))))))).....)))))))). ( -17.22)
>consensus
CAAGUAAUUCCUCAUACGCCAGCGAGUUGAAUGUUUACAAUAACUAGAUAAUACCUAACGAACUCAUGAAUG_ACUGAAAAUCAUAAGUUCGAAACGUAUUACUAAAUUACUGCAACAU_
.....................(((.((((........))))...((((((((((((..(((((((((((.(........).)))))))))))..)))))))))))).....)))...... (-17.76 = -19.20 +   1.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,213,516 – 4,213,636
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.15
Mean single sequence MFE -34.38
Consensus MFE -29.75
Energy contribution -30.25
Covariance contribution 0.50
Combinations/Pair 1.29
Mean z-score -3.98
Structure conservation index 0.87
SVM decision value 3.81
SVM RNA-class probability 0.999634
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4213516 120 - 22224390
UAUAUUGCAAUAAUUAAAUAAUACGUUUCGAACUAAUGAUUUUCAGUUCAUUCAUUAGGUAGUUACGCAUUAUCUAGUUGUUGUAAACAUUCAACUCGCUGGCGUAUGAGAAAUUACUUA
....((((((((((((.(((((.(((..(...(((((((............)))))))...)..))).))))).))))))))))))...((((...((....))..)))).......... ( -27.60)
>DroSec_CAF1 1664 118 - 1
-AUGUUGCAGUAAUUUAGUAAUACCUUUCGAACAUAUGAUUUUCAGU-CAUUCAUGAGUUCGUUAGGUAUUAUCUAGUUAUUGUAAACAUUCAACUCGCUGGCGGAUGAGGAAUUACUUG
-...(((((((((((..(((((((((..(((((.(((((........-...))))).)))))..)))))))))..))))))))))).(((((..(.....)..)))))............ ( -36.80)
>DroSim_CAF1 1664 118 - 1
-AUCUUGCAGUAAUUUAGUAAUACCUUUCGAACACAUGAUUUUCAGU-CAUUCAUGAGUUCGUCAGGUAUUAUCUAGUUAUUGUAAACAUUCAACUCGCUGGCGGAUGAGGAAUUACUUG
-...(((((((((((..(((((((((..(((((.(((((........-...))))).)))))..)))))))))..))))))))))).(((((..(.....)..)))))............ ( -37.70)
>DroEre_CAF1 1696 119 - 1
UAUGUUACAGUGAUUUAAUAAUUCGAUUCGAAGUUAUGUGCUUUAAU-CAUUCAUAAAUGCGAAACGGAUUAUUAAGUUAUUGUUAACAUUCAACUCGUUGGCGUGUGAGAAAUUGCUCA
.((((((((((((((((((((((((.((((...(((((.........-....)))))...)))).)))))))))))))))))).))))))((((....)))).(.(..(....)..).). ( -35.42)
>consensus
_AUGUUGCAGUAAUUUAAUAAUACCUUUCGAACAUAUGAUUUUCAGU_CAUUCAUGAGUUCGUUACGUAUUAUCUAGUUAUUGUAAACAUUCAACUCGCUGGCGGAUGAGAAAUUACUUA
....((((((((((((.(((((((((..(((((((((((............)))))))))))..))))))))).))))))))))))...((((...((....))..)))).......... (-29.75 = -30.25 +   0.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,213,556 – 4,213,676
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 71.60
Mean single sequence MFE -22.00
Consensus MFE -17.46
Energy contribution -17.69
Covariance contribution 0.23
Combinations/Pair 1.15
Mean z-score -3.55
Structure conservation index 0.79
SVM decision value 6.69
SVM RNA-class probability 0.999999
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4213556 120 + 22224390
CAACUAGAUAAUGCGUAACUACCUAAUGAAUGAACUGAAAAUCAUUAGUUCGAAACGUAUUAUUUAAUUAUUGCAAUAUAAUAGCAUAUGCAUAUAAUAUGAAUCUACACACACAGUUUA
....((((((((((((..(........)..((((((((......))))))))..))))))))))))(((((((((.(((......))))))).)))))...................... ( -21.00)
>DroSec_CAF1 1704 91 + 1
UAACUAGAUAAUACCUAACGAACUCAUGAAUG-ACUGAAAAUCAUAUGUUCGAAAGGUAUUACUAAAUUACUGCAACAU---AUCAUAUGCAAAG-------------------------
....(((.((((((((..(((((..((((.(.-......).))))..)))))..)))))))))))......((((....---......))))...------------------------- ( -20.20)
>DroSim_CAF1 1704 91 + 1
UAACUAGAUAAUACCUGACGAACUCAUGAAUG-ACUGAAAAUCAUGUGUUCGAAAGGUAUUACUAAAUUACUGCAAGAU---AUCAUAUGCAAAG-------------------------
....(((.((((((((..(((((.(((((.(.-......).))))).)))))..)))))))))))......((((....---......))))...------------------------- ( -24.80)
>consensus
UAACUAGAUAAUACCUAACGAACUCAUGAAUG_ACUGAAAAUCAUAUGUUCGAAAGGUAUUACUAAAUUACUGCAACAU___AUCAUAUGCAAAG_________________________
....(((.((((((((..(((((.(((((.(........).))))).)))))..)))))))))))......((((.............))))............................ (-17.46 = -17.69 +   0.23)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,213,556 – 4,213,676
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 71.60
Mean single sequence MFE -26.00
Consensus MFE -22.29
Energy contribution -21.85
Covariance contribution -0.44
Combinations/Pair 1.18
Mean z-score -3.69
Structure conservation index 0.86
SVM decision value 6.27
SVM RNA-class probability 0.999998
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4213556 120 - 22224390
UAAACUGUGUGUGUAGAUUCAUAUUAUAUGCAUAUGCUAUUAUAUUGCAAUAAUUAAAUAAUACGUUUCGAACUAAUGAUUUUCAGUUCAUUCAUUAGGUAGUUACGCAUUAUCUAGUUG
.....(((((((((((.......)))))))))))(((.........))).((((((.(((((.(((..(...(((((((............)))))))...)..))).))))).)))))) ( -23.60)
>DroSec_CAF1 1704 91 - 1
-------------------------CUUUGCAUAUGAU---AUGUUGCAGUAAUUUAGUAAUACCUUUCGAACAUAUGAUUUUCAGU-CAUUCAUGAGUUCGUUAGGUAUUAUCUAGUUA
-------------------------..(((((......---....)))))(((((..(((((((((..(((((.(((((........-...))))).)))))..)))))))))..))))) ( -26.70)
>DroSim_CAF1 1704 91 - 1
-------------------------CUUUGCAUAUGAU---AUCUUGCAGUAAUUUAGUAAUACCUUUCGAACACAUGAUUUUCAGU-CAUUCAUGAGUUCGUCAGGUAUUAUCUAGUUA
-------------------------..(((((......---....)))))(((((..(((((((((..(((((.(((((........-...))))).)))))..)))))))))..))))) ( -27.70)
>consensus
_________________________CUUUGCAUAUGAU___AUAUUGCAGUAAUUUAGUAAUACCUUUCGAACAAAUGAUUUUCAGU_CAUUCAUGAGUUCGUUAGGUAUUAUCUAGUUA
............................((((.............)))).(((((..(((((((((..(((((.(((((............))))).)))))..)))))))))..))))) (-22.29 = -21.85 +  -0.44)

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 10:08:28 2006