Locus 5111

Sequence ID 2R_DroMel_CAF1
Location 16,631,526 – 16,631,652
Length 126
Max. P 0.994017
window8171 window8172 window8173

overview

Window 1

Location 16,631,526 – 16,631,627
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 95.39
Mean single sequence MFE -20.56
Consensus MFE -19.10
Energy contribution -19.06
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -1.27
Structure conservation index 0.93
SVM decision value 0.69
SVM RNA-class probability 0.823360
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16631526 101 - 20766785
GUUCCCACAUUCUGUGAGACAUACGGAGUCUGAUAAAAAUAACACAAAGUGAAGAUAUGUGGUCCAUUCCACACAAUUCCGUUGUACUUAUUAGUUAUUAA
...........((((((((((.(((((((.((..........(((...)))......(((((......))))))))))))))))).)))).)))....... ( -20.60)
>DroSec_CAF1 30858 99 - 1
GUUCCCACAUUCUGUGAGACAUACGGAGUCUGAUAAAAAUAACACAAAGUGAAGA--UGUGGUCCAUUCCACACAAUUCCGUUGUACUUAUUAGUUAUUAA
...........((((((((((.(((((((.((..........(((...)))....--(((((......))))))))))))))))).)))).)))....... ( -20.60)
>DroSim_CAF1 30746 99 - 1
GUUCCCACAUUCUGUGAGACAUACGGAGUCUGAUAAAAAUAACACAAAGUGAAGA--UGUGGUCCAUUCCACACAAUUCCGUUGUACUUAUUAGUUAUUAA
...........((((((((((.(((((((.((..........(((...)))....--(((((......))))))))))))))))).)))).)))....... ( -20.60)
>DroEre_CAF1 33900 99 - 1
GUUCCCACAUUCUGUGAGACAUACGGAGUCUGAUAAAAAUAACACAAAGUGAAGA--UGUGGAGUAUUCCACGCAAUUCCGUUGUACUUAUUAGUUAUUAA
...........((((((((((.(((((((.((..........(((...)))....--.((((......)))).)))))))))))).)))).)))....... ( -20.20)
>DroYak_CAF1 32196 99 - 1
GUUCUCACAUUCUGUGAGACAAACAGAGUCUGAUAAAAAUAACACAAAGUGAAGA--UGUGGAGCAUUCCACGCAAUUCCGUUGUACUUAUUAGUUAAUAA
..((((((.....))))))..........(((((((..(((((.....(.(((..--(((((......)))))...)))))))))..)))))))....... ( -20.80)
>consensus
GUUCCCACAUUCUGUGAGACAUACGGAGUCUGAUAAAAAUAACACAAAGUGAAGA__UGUGGUCCAUUCCACACAAUUCCGUUGUACUUAUUAGUUAUUAA
...........((((((((((.(((((((.((..........(((...)))......(((((......))))))))))))))))).)))).)))....... (-19.10 = -19.06 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,631,553 – 16,631,652
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 93.05
Mean single sequence MFE -21.72
Consensus MFE -18.94
Energy contribution -18.98
Covariance contribution 0.04
Combinations/Pair 1.06
Mean z-score -1.76
Structure conservation index 0.87
SVM decision value 1.73
SVM RNA-class probability 0.974186
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16631553 99 + 20766785
GUGUGGAAUGGACCACAUAUCUUCACUUUGUGUUAUUUUUAUCAGACUCCGUAUGUCUCACAGAAUGUGGGAACCUUGCGUUCCACUAACUCAACUCUU
..(((((((((.((((((........((((((...........((((.......))))))))))))))))...))....)))))))............. ( -21.80)
>DroSec_CAF1 30885 97 + 1
GUGUGGAAUGGACCACA--UCUUCACUUUGUGUUAUUUUUAUCAGACUCCGUAUGUCUCACAGAAUGUGGGAACCUUGCGUUCCACCAACUCAAAUCUU
(.(((((((((.(((((--(......((((((...........((((.......))))))))))))))))...))....))))))))............ ( -22.10)
>DroSim_CAF1 30773 97 + 1
GUGUGGAAUGGACCACA--UCUUCACUUUGUGUUAUUUUUAUCAGACUCCGUAUGUCUCACAGAAUGUGGGAACCUUGCGUUCCACCAACUCAACUCUU
(.(((((((((.(((((--(......((((((...........((((.......))))))))))))))))...))....))))))))............ ( -22.10)
>DroEre_CAF1 33927 97 + 1
GCGUGGAAUACUCCACA--UCUUCACUUUGUGUUAUUUUUAUCAGACUCCGUAUGUCUCACAGAAUGUGGGAACCUUUAGUUCCACUAACUCAACUUUU
..(((((....))))).--....(((((((((...........((((.......))))))))))..)))(((((.....)))))............... ( -20.80)
>DroYak_CAF1 32223 97 + 1
GCGUGGAAUGCUCCACA--UCUUCACUUUGUGUUAUUUUUAUCAGACUCUGUUUGUCUCACAGAAUGUGAGAACCUUUCGUUCCACUAACUCAACUUUU
..((((((((...((((--.........))))..........(((((...)))))((((((.....))))))......))))))))............. ( -21.80)
>consensus
GUGUGGAAUGGACCACA__UCUUCACUUUGUGUUAUUUUUAUCAGACUCCGUAUGUCUCACAGAAUGUGGGAACCUUGCGUUCCACUAACUCAACUCUU
..((((((((...((((...........)))).......................((((((.....))))))......))))))))............. (-18.94 = -18.98 +   0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,631,553 – 16,631,652
Length 99
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 93.05
Mean single sequence MFE -24.00
Consensus MFE -22.34
Energy contribution -21.86
Covariance contribution -0.48
Combinations/Pair 1.08
Mean z-score -1.76
Structure conservation index 0.93
SVM decision value 2.44
SVM RNA-class probability 0.994017
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16631553 99 - 20766785
AAGAGUUGAGUUAGUGGAACGCAAGGUUCCCACAUUCUGUGAGACAUACGGAGUCUGAUAAAAAUAACACAAAGUGAAGAUAUGUGGUCCAUUCCACAC
.............(((((((....)....(((((((((((.((((.......)))).))........(((...))).))).))))))....)))))).. ( -23.80)
>DroSec_CAF1 30885 97 - 1
AAGAUUUGAGUUGGUGGAACGCAAGGUUCCCACAUUCUGUGAGACAUACGGAGUCUGAUAAAAAUAACACAAAGUGAAGA--UGUGGUCCAUUCCACAC
.............(((((((....)....(((((((.(((.((((.......)))).))).......(((...)))..))--)))))....)))))).. ( -23.70)
>DroSim_CAF1 30773 97 - 1
AAGAGUUGAGUUGGUGGAACGCAAGGUUCCCACAUUCUGUGAGACAUACGGAGUCUGAUAAAAAUAACACAAAGUGAAGA--UGUGGUCCAUUCCACAC
.............(((((((....)....(((((((.(((.((((.......)))).))).......(((...)))..))--)))))....)))))).. ( -23.70)
>DroEre_CAF1 33927 97 - 1
AAAAGUUGAGUUAGUGGAACUAAAGGUUCCCACAUUCUGUGAGACAUACGGAGUCUGAUAAAAAUAACACAAAGUGAAGA--UGUGGAGUAUUCCACGC
.....(((.((((..(((((.....)))))((.((((((((.....)))))))).)).......)))).)))........--.((((......)))).. ( -22.40)
>DroYak_CAF1 32223 97 - 1
AAAAGUUGAGUUAGUGGAACGAAAGGUUCUCACAUUCUGUGAGACAAACAGAGUCUGAUAAAAAUAACACAAAGUGAAGA--UGUGGAGCAUUCCACGC
.............(((((((....)((((.((((((.(((.((((.......)))).))).......(((...)))..))--)))))))).)))))).. ( -26.40)
>consensus
AAGAGUUGAGUUAGUGGAACGCAAGGUUCCCACAUUCUGUGAGACAUACGGAGUCUGAUAAAAAUAACACAAAGUGAAGA__UGUGGUCCAUUCCACAC
.....(((.(((((((((((.....)))).)))....(((.((((.......)))).)))....)))).)))..........(((((......))))). (-22.34 = -21.86 +  -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 11:36:49 2006