Locus 4295

Sequence ID X_DroMel_CAF1
Location 11,320,341 – 11,320,491
Length 150
Max. P 0.993640
window7060 window7061 window7062 window7063

overview

Window 0

Location 11,320,341 – 11,320,451
Length 110
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 77.80
Mean single sequence MFE -25.39
Consensus MFE -16.80
Energy contribution -17.48
Covariance contribution 0.68
Combinations/Pair 1.21
Mean z-score -1.98
Structure conservation index 0.66
SVM decision value 1.17
SVM RNA-class probability 0.925803
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11320341 110 + 22224390
AUAUACAAUAAUAACAUAGGCAUAAAAACACAAUCGUACACAGUGCGUAUGAGCGUUAAUAAUGCGACUGCAUUGAAAAGCAUUGCGCAUACGCACCGUUGGUUUUG---UGA
............................(((((......((.(((((((((.(((((..((((((....))))))...)))...)).))))))))).)).....)))---)). ( -27.40)
>DroSec_CAF1 24453 109 + 1
AUAUACAAUAAUAACAUAGGAAUAAAAACAGAAUCGUACACAGUGCGUAUGAGCGAUAAUUAUGCGGCUGCAUUGAAAAGCAUUACGCAUACGCACCGUUGACUUU----UAA
..................((.............((((((.......))))))(((.....((((((..(((........)))...))))))))).)).........----... ( -20.10)
>DroSim_CAF1 21244 109 + 1
AUAUACAAUAAUAACAUAGGAAUAAAAACAGAAGCGUACACAGUGCGUAUGAGCGAUAAUUAUGCGGCUGCAUUGAAAAGCAUUACGCAUACGCACCGUUGACUUU----UGA
............................((((((((...((.(((((((((.((.......((((....))))......))......))))))))).)))).))))----)). ( -23.72)
>DroEre_CAF1 20402 105 + 1
UAACACAAUAAACACAUAG---UGAAAAUAAAAGC--GCACAGUGCGUAUGAGCGAUAAGAAUGCGGCUGGAUUAAAAAGCAUUACUCAUGCGCACCGUUGGUUUUU---UGA
.....(((.((((.((..(---((..........)--))((.(((((((((((.......(((((..............))))).))))))))))).)))))))).)---)). ( -25.94)
>DroYak_CAF1 23740 91 + 1
----------------------UGAAAACAGAAGCGCGCACAGUGCGUAUGCGUGAUAUUAAUGCGGCUGCAUUCAAAAGCAUUACUCAUGCGCACCGUUGCUUUUUUUCUGA
----------------------......((((((.(((.((.(((((((((.(((((.(((((((....)))))...))..))))).))))))))).)))))....)))))). ( -29.80)
>consensus
AUAUACAAUAAUAACAUAGG_AUAAAAACAGAAGCGUACACAGUGCGUAUGAGCGAUAAUAAUGCGGCUGCAUUGAAAAGCAUUACGCAUACGCACCGUUGAUUUU____UGA
.............................(((((((...((.(((((((((.(((.......))).(((.........)))......))))))))).)))))))))....... (-16.80 = -17.48 +   0.68)

alignment

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secondary structure

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Window 1

Location 11,320,341 – 11,320,451
Length 110
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 77.80
Mean single sequence MFE -27.04
Consensus MFE -20.06
Energy contribution -20.54
Covariance contribution 0.48
Combinations/Pair 1.11
Mean z-score -2.47
Structure conservation index 0.74
SVM decision value 2.41
SVM RNA-class probability 0.993640
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11320341 110 - 22224390
UCA---CAAAACCAACGGUGCGUAUGCGCAAUGCUUUUCAAUGCAGUCGCAUUAUUAACGCUCAUACGCACUGUGUACGAUUGUGUUUUUAUGCCUAUGUUAUUAUUGUAUAU
.((---(((.....((((((((((((.((...(.....)(((((....)))))......)).))))))))))))......)))))....(((((..(((....))).))))). ( -30.10)
>DroSec_CAF1 24453 109 - 1
UUA----AAAGUCAACGGUGCGUAUGCGUAAUGCUUUUCAAUGCAGCCGCAUAAUUAUCGCUCAUACGCACUGUGUACGAUUCUGUUUUUAUUCCUAUGUUAUUAUUGUAUAU
...----.......((((((((((((.(..(((.((....((((....)))))).)))..).))))))))))))(((((((...((...(((....)))..)).))))))).. ( -26.50)
>DroSim_CAF1 21244 109 - 1
UCA----AAAGUCAACGGUGCGUAUGCGUAAUGCUUUUCAAUGCAGCCGCAUAAUUAUCGCUCAUACGCACUGUGUACGCUUCUGUUUUUAUUCCUAUGUUAUUAUUGUAUAU
.((----.((((..((((((((((((.(..(((.((....((((....)))))).)))..).))))))))))))....)))).))............................ ( -26.50)
>DroEre_CAF1 20402 105 - 1
UCA---AAAAACCAACGGUGCGCAUGAGUAAUGCUUUUUAAUCCAGCCGCAUUCUUAUCGCUCAUACGCACUGUGC--GCUUUUAUUUUCA---CUAUGUGUUUAUUGUGUUA
...---...(((((((((((((.(((((((((((..............)))))......)))))).))))))))((--((...........---....))))....)).))). ( -24.40)
>DroYak_CAF1 23740 91 - 1
UCAGAAAAAAAGCAACGGUGCGCAUGAGUAAUGCUUUUGAAUGCAGCCGCAUUAAUAUCACGCAUACGCACUGUGCGCGCUUCUGUUUUCA----------------------
........((((((..(((((((((((.((((((..(((....)))..))))))...))..((....))...)))))))))..))))))..---------------------- ( -27.70)
>consensus
UCA____AAAACCAACGGUGCGUAUGCGUAAUGCUUUUCAAUGCAGCCGCAUUAUUAUCGCUCAUACGCACUGUGUACGCUUCUGUUUUUAU_CCUAUGUUAUUAUUGUAUAU
..............((((((((((((.(((((((..............)))))......)).))))))))))))....................................... (-20.06 = -20.54 +   0.48)

alignment

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secondary structure

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Window 2

Location 11,320,374 – 11,320,491
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.66
Mean single sequence MFE -31.73
Consensus MFE -18.72
Energy contribution -19.20
Covariance contribution 0.48
Combinations/Pair 1.17
Mean z-score -1.79
Structure conservation index 0.59
SVM decision value 0.25
SVM RNA-class probability 0.653900
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11320374 117 + 22224390
UCGUACACAGUGCGUAUGAGCGUUAAUAAUGCGACUGCAUUGAAAAGCAUUGCGCAUACGCACCGUUGGUUUUG---UGAGCAUAUUUCAUUUGUGUAAUUAUUGCAAUGAUGCGUGAAG
...(((((((((((((((.(((((..((((((....))))))...)))...)).)))))))))..........(---((((.....))))).)))))).((((.(((....))))))).. ( -30.80)
>DroSec_CAF1 24486 116 + 1
UCGUACACAGUGCGUAUGAGCGAUAAUUAUGCGGCUGCAUUGAAAAGCAUUACGCAUACGCACCGUUGACUUU----UAAGCAUAUUUCAUUUGUGCAAUUAUUGCAAUGAUGCGUGAAG
.....(((.(((((((...((.......((((....))))......))..)))))))..(((.(((((.....----...(((((.......)))))........))))).))))))... ( -31.01)
>DroSim_CAF1 21277 116 + 1
GCGUACACAGUGCGUAUGAGCGAUAAUUAUGCGGCUGCAUUGAAAAGCAUUACGCAUACGCACCGUUGACUUU----UGAGCAUAUUUCAUUUGUGCAAUUAUUGCAAUGAUGCGUGAAG
(((((...(((.(((((((.......))))))))))((........))..))))).((((((.(((((.....----...(((((.......)))))........))))).))))))... ( -32.49)
>DroEre_CAF1 20432 101 + 1
GC--GCACAGUGCGUAUGAGCGAUAAGAAUGCGGCUGGAUUAAAAAGCAUUACUCAUGCGCACCGUUGGUUUUU---UGAGCACAUUUCAUUUGAGU--------------UGUGUGUAG
((--((((((((((((((((.......(((((..............))))).))))))))))).(((.(.....---).)))...............--------------))))))).. ( -30.14)
>DroYak_CAF1 23751 102 + 1
GCGCGCACAGUGCGUAUGCGUGAUAUUAAUGCGGCUGCAUUCAAAAGCAUUACUCAUGCGCACCGUUGCUUUUUUUCUGAGCAUACUUCAUUUG-----------------UGUGUUUA-
..((((((((((((((((.(((((.(((((((....)))))...))..))))).))))))))).(((((((.......))))).))......))-----------------)))))...- ( -34.20)
>consensus
GCGUACACAGUGCGUAUGAGCGAUAAUAAUGCGGCUGCAUUGAAAAGCAUUACGCAUACGCACCGUUGAUUUU____UGAGCAUAUUUCAUUUGUGCAAUUAUUGCAAUGAUGCGUGAAG
.....(((.(((((((((.(((.......))).(((.........)))......))))))))).................(((((.......))))).................)))... (-18.72 = -19.20 +   0.48)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,320,374 – 11,320,491
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.66
Mean single sequence MFE -27.91
Consensus MFE -20.06
Energy contribution -20.54
Covariance contribution 0.48
Combinations/Pair 1.11
Mean z-score -2.42
Structure conservation index 0.72
SVM decision value 2.13
SVM RNA-class probability 0.988728
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11320374 117 - 22224390
CUUCACGCAUCAUUGCAAUAAUUACACAAAUGAAAUAUGCUCA---CAAAACCAACGGUGCGUAUGCGCAAUGCUUUUCAAUGCAGUCGCAUUAUUAACGCUCAUACGCACUGUGUACGA
......(((....)))......(((((...(((.......)))---..........((((((((((.((...(.....)(((((....)))))......)).)))))))))))))))... ( -28.20)
>DroSec_CAF1 24486 116 - 1
CUUCACGCAUCAUUGCAAUAAUUGCACAAAUGAAAUAUGCUUA----AAAGUCAACGGUGCGUAUGCGUAAUGCUUUUCAAUGCAGCCGCAUAAUUAUCGCUCAUACGCACUGUGUACGA
......(((((((((((.....))))...))))....)))...----...((..((((((((((((.(..(((.((....((((....)))))).)))..).))))))))))))..)).. ( -31.00)
>DroSim_CAF1 21277 116 - 1
CUUCACGCAUCAUUGCAAUAAUUGCACAAAUGAAAUAUGCUCA----AAAGUCAACGGUGCGUAUGCGUAAUGCUUUUCAAUGCAGCCGCAUAAUUAUCGCUCAUACGCACUGUGUACGC
......(((((((((((.....))))...))))....)))...----...((..((((((((((((.(..(((.((....((((....)))))).)))..).))))))))))))..)).. ( -31.00)
>DroEre_CAF1 20432 101 - 1
CUACACACA--------------ACUCAAAUGAAAUGUGCUCA---AAAAACCAACGGUGCGCAUGAGUAAUGCUUUUUAAUCCAGCCGCAUUCUUAUCGCUCAUACGCACUGUGC--GC
.....((((--------------..((....))..))))....---........((((((((.(((((((((((..............)))))......)))))).))))))))..--.. ( -25.34)
>DroYak_CAF1 23751 102 - 1
-UAAACACA-----------------CAAAUGAAGUAUGCUCAGAAAAAAAGCAACGGUGCGCAUGAGUAAUGCUUUUGAAUGCAGCCGCAUUAAUAUCACGCAUACGCACUGUGCGCGC
-........-----------------.........................((.(((((((((.(((.((((((..(((....)))..))))))...))).))....)))))))..)).. ( -24.00)
>consensus
CUUCACGCAUCAUUGCAAUAAUUACACAAAUGAAAUAUGCUCA____AAAACCAACGGUGCGUAUGCGUAAUGCUUUUCAAUGCAGCCGCAUUAUUAUCGCUCAUACGCACUGUGUACGC
......................................................((((((((((((.(((((((..............)))))......)).))))))))))))...... (-20.06 = -20.54 +   0.48)

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 11:21:30 2006