Locus 1548

Sequence ID 3R_DroMel_CAF1
Location 4,426,332 – 4,426,489
Length 157
Max. P 0.999868
window2558 window2559 window2560 window2561

overview

Window 8

Location 4,426,332 – 4,426,449
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 94.19
Mean single sequence MFE -33.90
Consensus MFE -30.40
Energy contribution -30.68
Covariance contribution 0.28
Combinations/Pair 1.12
Mean z-score -2.88
Structure conservation index 0.90
SVM decision value 4.31
SVM RNA-class probability 0.999868
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4426332 117 + 27905053
AAAUCACAUCUGUUUAUUUGGGCCUUGCUGAGAUUGUGCAAUGGCAUUGCUUGUUUUGUCCAACCAAAAUCUCCGGUGGCAAACAUGAGCAACAAUUUCAGGAUACCAGAAGCCACA
................(((((....(.((((((((((((....))..((((..(((((.(((.((.........))))))))).)..)))))))))))))).)..)))))....... ( -32.00)
>DroSec_CAF1 27188 117 + 1
AAAUCACUUCUGUUUAUUUUGGCCUUGUUGAGAUUGUGCAAUGGCACUGCUUGUUUUGUGCAACCAAAAUCUCCGGUUGCAAACAUGAGCAAAAAUUUCAGGAUACCAGAAGCCACA
......((((((..((((((((((((((.........)))).)))..((((..(....(((((((.........)))))))...)..)))).......))))))).))))))..... ( -34.40)
>DroSim_CAF1 29678 117 + 1
AAAUCACUUCUGUUUAUUUUGGCCUUGUUGAGAUUGUGCAAUGGCACUGCUUGUUUUGUGCAACCAAAAUCUCCGGUUGCAAACAUGAGCAACAAUUUCAGGAUAGUAGAAGCCACA
......((((((((.(((((((..(((((......((((....)))).(((..(....(((((((.........)))))))...)..))))))))..)))))))))))))))..... ( -33.60)
>DroEre_CAF1 27379 117 + 1
AAAUCACUUCUGUUUGUUUUGGCCUUGUUGAGAUUGUGCAAUGGCAUUGCUUGUUUUGUGCAACCAAAAUCUCCGGUUGCAAACAUAAGCAACAGUUUCAGGAUACCAGAAGCCACA
......((((((..((((((((((((((.........)))).))).((((((((....(((((((.........)))))))...))))))))......))))))).))))))..... ( -36.00)
>DroYak_CAF1 27632 117 + 1
AAAUCACUUCUGUUUAUUUUGGCCUUGUUGAGAACGUGCAAUGGCAUUGCUUGUUUUGUGCAACCAAAAUCUCCGGUUGCAAACAUAAGCAACAAUCUCAGGAUACCAAAAGCCACA
...........((...((((((...(.((((((..((((....))))(((((((....(((((((.........)))))))...)))))))....)))))).)..))))))...)). ( -33.50)
>consensus
AAAUCACUUCUGUUUAUUUUGGCCUUGUUGAGAUUGUGCAAUGGCAUUGCUUGUUUUGUGCAACCAAAAUCUCCGGUUGCAAACAUGAGCAACAAUUUCAGGAUACCAGAAGCCACA
......((((((..((((((((((((((.........)))).)))..(((((((....(((((((.........)))))))...))))))).......))))))).))))))..... (-30.40 = -30.68 +   0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,426,332 – 4,426,449
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 94.19
Mean single sequence MFE -31.66
Consensus MFE -27.54
Energy contribution -28.14
Covariance contribution 0.60
Combinations/Pair 1.06
Mean z-score -1.99
Structure conservation index 0.87
SVM decision value 2.24
SVM RNA-class probability 0.991013
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4426332 117 - 27905053
UGUGGCUUCUGGUAUCCUGAAAUUGUUGCUCAUGUUUGCCACCGGAGAUUUUGGUUGGACAAAACAAGCAAUGCCAUUGCACAAUCUCAGCAAGGCCCAAAUAAACAGAUGUGAUUU
.((.((.((((.............((((((..(((((.((((((((...))))).)))...)))))))))))(((.((((.........))))))).........)))).)).)).. ( -29.60)
>DroSec_CAF1 27188 117 - 1
UGUGGCUUCUGGUAUCCUGAAAUUUUUGCUCAUGUUUGCAACCGGAGAUUUUGGUUGCACAAAACAAGCAGUGCCAUUGCACAAUCUCAACAAGGCCAAAAUAAACAGAAGUGAUUU
.((.(((((((...............((((..((((((((((((((...))))))))))...))))))))((((....)))).......................))))))).)).. ( -32.00)
>DroSim_CAF1 29678 117 - 1
UGUGGCUUCUACUAUCCUGAAAUUGUUGCUCAUGUUUGCAACCGGAGAUUUUGGUUGCACAAAACAAGCAGUGCCAUUGCACAAUCUCAACAAGGCCAAAAUAAACAGAAGUGAUUU
.((.((((((..(((..((...((((((((..((((((((((((((...))))))))))...))))))).((((....))))......)))))...))..)))...)))))).)).. ( -30.80)
>DroEre_CAF1 27379 117 - 1
UGUGGCUUCUGGUAUCCUGAAACUGUUGCUUAUGUUUGCAACCGGAGAUUUUGGUUGCACAAAACAAGCAAUGCCAUUGCACAAUCUCAACAAGGCCAAAACAAACAGAAGUGAUUU
.((.(((((((.............((((((..((((((((((((((...))))))))))...))))))))))(((.(((...........)))))).........))))))).)).. ( -32.70)
>DroYak_CAF1 27632 117 - 1
UGUGGCUUUUGGUAUCCUGAGAUUGUUGCUUAUGUUUGCAACCGGAGAUUUUGGUUGCACAAAACAAGCAAUGCCAUUGCACGUUCUCAACAAGGCCAAAAUAAACAGAAGUGAUUU
(((...(((((((....(((((..((((((..((((((((((((((...))))))))))...))))))))))((....))....))))).....)))))))...))).......... ( -33.20)
>consensus
UGUGGCUUCUGGUAUCCUGAAAUUGUUGCUCAUGUUUGCAACCGGAGAUUUUGGUUGCACAAAACAAGCAAUGCCAUUGCACAAUCUCAACAAGGCCAAAAUAAACAGAAGUGAUUU
.((.(((((((.............((((((..((((((((((((((...))))))))))...))))))))))(((.(((...........)))))).........))))))).)).. (-27.54 = -28.14 +   0.60)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,426,372 – 4,426,489
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -27.22
Consensus MFE -23.34
Energy contribution -23.10
Covariance contribution -0.24
Combinations/Pair 1.16
Mean z-score -2.04
Structure conservation index 0.86
SVM decision value 2.20
SVM RNA-class probability 0.990081
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4426372 117 + 27905053
AUGGCAUUGCUUGUUUUGUCCAACCAAAAUCUCCGGUGGCAAACAUGAGCAACAAUUUCAGGAUACCAGAAGCCACAAUGAGAAAAGGCAUAUCAUGUAAAUUACAUCUCCACAUGU
.((((.(((((..(((((.(((.((.........))))))))).)..)))))....(((.((...)).)))))))....((((....((((...))))........))))....... ( -23.00)
>DroSec_CAF1 27228 117 + 1
AUGGCACUGCUUGUUUUGUGCAACCAAAAUCUCCGGUUGCAAACAUGAGCAAAAAUUUCAGGAUACCAGAAGCCACAAUGAGAAAAUGCAUAUCAUGUAAAUUACAUCUCCAUAUGC
.((((..((((..(....(((((((.........)))))))...)..)))).....(((.((...)).)))))))............((((((.(((((...)))))....)))))) ( -28.10)
>DroSim_CAF1 29718 117 + 1
AUGGCACUGCUUGUUUUGUGCAACCAAAAUCUCCGGUUGCAAACAUGAGCAACAAUUUCAGGAUAGUAGAAGCCACAAUGAGAAAAUGCAUAUCAUGUAAAUUUCAUCUCCAUAUGC
.((((..((((..(....(((((((.........)))))))...)..))))((.(((....))).))....))))..((((((...(((((...)))))..)))))).......... ( -26.20)
>DroEre_CAF1 27419 117 + 1
AUGGCAUUGCUUGUUUUGUGCAACCAAAAUCUCCGGUUGCAAACAUAAGCAACAGUUUCAGGAUACCAGAAGCCACAAUGGGAAAAUGCAUAUCGUGUAAAUUACAUUUCCAUAUGU
.((((.((((((((....(((((((.........)))))))...))))))))....(((.((...)).)))))))..(((((((..(((((...))))).......))))))).... ( -30.10)
>DroYak_CAF1 27672 117 + 1
AUGGCAUUGCUUGUUUUGUGCAACCAAAAUCUCCGGUUGCAAACAUAAGCAACAAUCUCAGGAUACCAAAAGCCACAAUGGGAAAAUGCAUAUCGUGUAAAUUACAUCUCCAUAUGU
.((((.((((((((....(((((((.........)))))))...))))))))..(((....))).......))))............((((((.(((((...)))))....)))))) ( -28.70)
>consensus
AUGGCAUUGCUUGUUUUGUGCAACCAAAAUCUCCGGUUGCAAACAUGAGCAACAAUUUCAGGAUACCAGAAGCCACAAUGAGAAAAUGCAUAUCAUGUAAAUUACAUCUCCAUAUGU
.((((..(((((((....(((((((.........)))))))...)))))))...(((....))).......))))............((((((.(((((...)))))....)))))) (-23.34 = -23.10 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,426,372 – 4,426,489
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -30.78
Consensus MFE -26.70
Energy contribution -26.94
Covariance contribution 0.24
Combinations/Pair 1.12
Mean z-score -1.77
Structure conservation index 0.87
SVM decision value 1.69
SVM RNA-class probability 0.972466
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4426372 117 - 27905053
ACAUGUGGAGAUGUAAUUUACAUGAUAUGCCUUUUCUCAUUGUGGCUUCUGGUAUCCUGAAAUUGUUGCUCAUGUUUGCCACCGGAGAUUUUGGUUGGACAAAACAAGCAAUGCCAU
.((((((((.......)))))))).................((((((((.((...)).)))...((((((..(((((.((((((((...))))).)))...)))))))))))))))) ( -30.00)
>DroSec_CAF1 27228 117 - 1
GCAUAUGGAGAUGUAAUUUACAUGAUAUGCAUUUUCUCAUUGUGGCUUCUGGUAUCCUGAAAUUUUUGCUCAUGUUUGCAACCGGAGAUUUUGGUUGCACAAAACAAGCAGUGCCAU
(((...((((((((((((.....))).)))))))))....)))((((((.((...)).)))....(((((..((((((((((((((...))))))))))...))))))))).))).. ( -31.50)
>DroSim_CAF1 29718 117 - 1
GCAUAUGGAGAUGAAAUUUACAUGAUAUGCAUUUUCUCAUUGUGGCUUCUACUAUCCUGAAAUUGUUGCUCAUGUUUGCAACCGGAGAUUUUGGUUGCACAAAACAAGCAGUGCCAU
....((((...((......((((((...(((.((((.....((((...))))......)))).)))...)))))).((((((((((...)))))))))).........))...)))) ( -28.20)
>DroEre_CAF1 27419 117 - 1
ACAUAUGGAAAUGUAAUUUACACGAUAUGCAUUUUCCCAUUGUGGCUUCUGGUAUCCUGAAACUGUUGCUUAUGUUUGCAACCGGAGAUUUUGGUUGCACAAAACAAGCAAUGCCAU
......((((((((((((.....))).))))))))).....((((((((.((...)).)))...((((((..((((((((((((((...))))))))))...))))))))))))))) ( -32.00)
>DroYak_CAF1 27672 117 - 1
ACAUAUGGAGAUGUAAUUUACACGAUAUGCAUUUUCCCAUUGUGGCUUUUGGUAUCCUGAGAUUGUUGCUUAUGUUUGCAACCGGAGAUUUUGGUUGCACAAAACAAGCAAUGCCAU
......((((((((((((.....))).))))))))).....((((((((..(....)..)))..((((((..((((((((((((((...))))))))))...))))))))))))))) ( -32.20)
>consensus
ACAUAUGGAGAUGUAAUUUACAUGAUAUGCAUUUUCUCAUUGUGGCUUCUGGUAUCCUGAAAUUGUUGCUCAUGUUUGCAACCGGAGAUUUUGGUUGCACAAAACAAGCAAUGCCAU
(((...((((((((((((.....))).)))))))))....)))((((((.(.....).)))...((((((..((((((((((((((...))))))))))...))))))))))))).. (-26.70 = -26.94 +   0.24)

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 10:13:17 2006