Locus 5441

Sequence ID 2R_DroMel_CAF1
Location 17,490,832 – 17,490,990
Length 158
Max. P 0.862128
window8683 window8684 window8685

overview

Window 3

Location 17,490,832 – 17,490,950
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.53
Mean single sequence MFE -28.01
Consensus MFE -23.44
Energy contribution -23.00
Covariance contribution -0.44
Combinations/Pair 1.08
Mean z-score -1.74
Structure conservation index 0.84
SVM decision value 0.35
SVM RNA-class probability 0.698783
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17490832 118 + 20766785
AAACUGCUAAAUUUUUUCAUCCAUUUUUUUGGACC--CACACCAAUCGUUAGCAGCUGGUUGCAAUUGCACCGAUUUAGGUGAUAGCACCACCUUCGAGUGCACUUCAACUUUAGGGAUA
...(((((((.........((((......))))..--...........)))))))..(((((.((.((((((((...(((((.......)))))))).))))).)))))))......... ( -30.75)
>DroSec_CAF1 18624 117 + 1
AAAUUGCUAAAUUUUUUCAUUCAUUU-UUUGUACC--CACUUCAACCGUUAGCAGCUGGUUGCAAUUGCACCGAUUUAGGUGAUAGCACCACCUUCGAGUGCACUUCAACUUUAGGGAUA
..(((.(((((...............-.(((((.(--((((.(........).)).))).))))).((((((((...(((((.......)))))))).))))).......))))).))). ( -26.50)
>DroSim_CAF1 31524 117 + 1
AAACUGCUAAAUUUUUUCAUUCAUUU-UUUGUACC--CACACCAACCGUUAGCAGCUGGUUGCAAUUGCACCGAUUUAGGUGAUAGCACCACCUUCGAGUGCACUUCAACUUUAGGGAUA
..........................-......((--(....((((((........))))))....((((((((...(((((.......)))))))).)))))...........)))... ( -26.20)
>DroYak_CAF1 27666 119 + 1
AAAGUACUCAACUUUUUCAUCCAUUU-UUUGGCCCCUCACACCAACCGUUAGCAGCUGGUUGCAAUUGCACCGAUUUAGGUGAUAGCACCACCUUCGAGUGCACUUCAAGUUUAGGGAUA
(((((.....))))).....(((...-..))).((((.((..((((((........))))))....((((((((...(((((.......)))))))).)))))......))..))))... ( -28.60)
>consensus
AAACUGCUAAAUUUUUUCAUCCAUUU_UUUGGACC__CACACCAACCGUUAGCAGCUGGUUGCAAUUGCACCGAUUUAGGUGAUAGCACCACCUUCGAGUGCACUUCAACUUUAGGGAUA
..................((((......(((...........((((((........))))))....((((((((...(((((.......)))))))).)))))...)))......)))). (-23.44 = -23.00 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,490,832 – 17,490,950
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.53
Mean single sequence MFE -34.80
Consensus MFE -27.67
Energy contribution -28.18
Covariance contribution 0.50
Combinations/Pair 1.12
Mean z-score -2.57
Structure conservation index 0.80
SVM decision value 0.83
SVM RNA-class probability 0.862128
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17490832 118 - 20766785
UAUCCCUAAAGUUGAAGUGCACUCGAAGGUGGUGCUAUCACCUAAAUCGGUGCAAUUGCAACCAGCUGCUAACGAUUGGUGUG--GGUCCAAAAAAAUGGAUGAAAAAAUUUAGCAGUUU
..........((((...(((((.((((((((((...)))))))...))))))))....)))).((((((((((.((....)).--)(((((......)))))........))))))))). ( -35.90)
>DroSec_CAF1 18624 117 - 1
UAUCCCUAAAGUUGAAGUGCACUCGAAGGUGGUGCUAUCACCUAAAUCGGUGCAAUUGCAACCAGCUGCUAACGGUUGAAGUG--GGUACAAA-AAAUGAAUGAAAAAAUUUAGCAAUUU
(((((((...((((...(((((.((((((((((...)))))))...))))))))....))))((((((....)))))).)).)--))))....-...(((((......)))))....... ( -32.80)
>DroSim_CAF1 31524 117 - 1
UAUCCCUAAAGUUGAAGUGCACUCGAAGGUGGUGCUAUCACCUAAAUCGGUGCAAUUGCAACCAGCUGCUAACGGUUGGUGUG--GGUACAAA-AAAUGAAUGAAAAAAUUUAGCAGUUU
..........((((((.(((((.((((((((((...)))))))...)))))))).(..((.(((((((....)))))))))..--).......-...............))))))..... ( -33.50)
>DroYak_CAF1 27666 119 - 1
UAUCCCUAAACUUGAAGUGCACUCGAAGGUGGUGCUAUCACCUAAAUCGGUGCAAUUGCAACCAGCUGCUAACGGUUGGUGUGAGGGGCCAAA-AAAUGGAUGAAAAAGUUGAGUACUUU
..((((...........(((((.((((((((((...)))))))...)))))))).(..((.(((((((....)))))))))..)))))(((..-...))).....(((((.....))))) ( -37.00)
>consensus
UAUCCCUAAAGUUGAAGUGCACUCGAAGGUGGUGCUAUCACCUAAAUCGGUGCAAUUGCAACCAGCUGCUAACGGUUGGUGUG__GGUACAAA_AAAUGAAUGAAAAAAUUUAGCAGUUU
.................(((((.((((((((((...)))))))...))))))))(((((.((((((((....)))))))).................(((((......)))))))))).. (-27.67 = -28.18 +   0.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,490,870 – 17,490,990
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.92
Mean single sequence MFE -36.91
Consensus MFE -34.62
Energy contribution -35.37
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.94
SVM decision value 0.37
SVM RNA-class probability 0.709537
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17490870 120 - 20766785
ACGGUUACUUGCAUUGGCGGAAUUGUAAACUAGCAUCAAGUAUCCCUAAAGUUGAAGUGCACUCGAAGGUGGUGCUAUCACCUAAAUCGGUGCAAUUGCAACCAGCUGCUAACGAUUGGU
......(((..(.(((((((..((((((....((.((((.(........).)))).))((((.((((((((((...)))))))...)))))))..))))))....))))))).)...))) ( -31.90)
>DroSec_CAF1 18661 120 - 1
ACGGUUACUUGCAUUGGCGGAAUUGUAAACUAGCCUCAAGUAUCCCUAAAGUUGAAGUGCACUCGAAGGUGGUGCUAUCACCUAAAUCGGUGCAAUUGCAACCAGCUGCUAACGGUUGAA
..((.((((((....(((..............))).)))))).)).....((((...(((((.((((((((((...)))))))...))))))))....))))((((((....)))))).. ( -38.34)
>DroSim_CAF1 31561 120 - 1
ACGGUUACUUGCAUUGGCGGAAUUGUAAACUAGCCUCAAGUAUCCCUAAAGUUGAAGUGCACUCGAAGGUGGUGCUAUCACCUAAAUCGGUGCAAUUGCAACCAGCUGCUAACGGUUGGU
..((.((((((....(((..............))).)))))).)).....((.....(((((.((((((((((...)))))))...))))))))...)).((((((((....)))))))) ( -38.74)
>DroYak_CAF1 27705 120 - 1
ACGGUUACUUGCAUUGGCGGAAUUGUAAACUAGCCUCAAGUAUCCCUAAACUUGAAGUGCACUCGAAGGUGGUGCUAUCACCUAAAUCGGUGCAAUUGCAACCAGCUGCUAACGGUUGGU
..((.((((((....(((..............))).)))))).)).......((...(((((.((((((((((...)))))))...))))))))....))((((((((....)))))))) ( -38.64)
>consensus
ACGGUUACUUGCAUUGGCGGAAUUGUAAACUAGCCUCAAGUAUCCCUAAAGUUGAAGUGCACUCGAAGGUGGUGCUAUCACCUAAAUCGGUGCAAUUGCAACCAGCUGCUAACGGUUGGU
..((.((((((....(((..............))).)))))).)).....((((...(((((.((((((((((...)))))))...))))))))....))))((((((....)))))).. (-34.62 = -35.37 +   0.75)

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 11:45:00 2006