Locus 1

Sequence ID 2R_DroMel_CAF1
Location 687,371 – 687,501
Length 130
Max. P 0.988244
window1 window2 window3

overview

Window 1

Location 687,371 – 687,464
Length 93
pre Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 74.20
Mean single sequence MFE -15.87
Consensus MFE -12.25
Energy contribution -11.59
Covariance contribution -0.66
Combinations/Pair 1.17
Mean z-score -1.09
Structure conservation index 0.77
SVM decision value 0.27
SVM RNA-class probability 0.659709
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 687371 93 + 20766785
UAGAGGAUAACUCAAAUUUUUUCCCUUGCCAAACUCAAAGUAGCUUAACAAUUCUUGGAGCAGAGAAAGGAAAUAUAUAACACUUUCUUU--ACC
..(((.....))).............................((((...........))))((((((((.............))))))))--... ( -12.32)
>DroSec_CAF1 15700 93 + 1
UAGAGGAUAGCUCAAAUUUGUUCCCUUACCAAACUCGAAGUCGCUUAAUAAUUCCUGGAGCAGAGAAGGGAUAA--AUAACCCCUUCUUUACACC
..(((.....)))......(((((...........((....)).............)))))(((((((((....--.....)))))))))..... ( -18.75)
>DroSim_CAF1 2893 76 + 1
-----------------UUGUUCCCUUACCAAAAUCGAAGUCGCUUAAUAACUCUUGGAGCAGAGAAGGGAAAA--AUAGCACCUUCUCUACACC
-----------------..(((((...........((....)).............)))))((((((((.....--......))))))))..... ( -16.55)
>consensus
UAGAGGAUA_CUCAAAUUUGUUCCCUUACCAAACUCGAAGUCGCUUAAUAAUUCUUGGAGCAGAGAAGGGAAAA__AUAACACCUUCUUUACACC
..........................................((((...........))))((((((((.............))))))))..... (-12.25 = -11.59 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 2

Location 687,371 – 687,464
Length 93
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 74.20
Mean single sequence MFE -23.40
Consensus MFE -15.37
Energy contribution -15.49
Covariance contribution 0.11
Combinations/Pair 1.10
Mean z-score -1.98
Structure conservation index 0.66
SVM decision value 2.11
SVM RNA-class probability 0.988244
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 687371 93 - 20766785
GGU--AAAGAAAGUGUUAUAUAUUUCCUUUCUCUGCUCCAAGAAUUGUUAAGCUACUUUGAGUUUGGCAAGGGAAAAAAUUUGAGUUAUCCUCUA
.((--(.((((((.(..........))))))).)))(((.....((((((((((......)))))))))).)))........(((.....))).. ( -18.90)
>DroSec_CAF1 15700 93 - 1
GGUGUAAAGAAGGGGUUAU--UUAUCCCUUCUCUGCUCCAGGAAUUAUUAAGCGACUUCGAGUUUGGUAAGGGAACAAAUUUGAGCUAUCCUCUA
((.(((.(((((((((...--..))))))))).))).))((((.(((((((((........)))))))))(....)............))))... ( -29.50)
>DroSim_CAF1 2893 76 - 1
GGUGUAGAGAAGGUGCUAU--UUUUCCCUUCUCUGCUCCAAGAGUUAUUAAGCGACUUCGAUUUUGGUAAGGGAACAA-----------------
((.((((((((((......--.....)))))))))).)).....(((((((.((....))...)))))))(....)..----------------- ( -21.80)
>consensus
GGUGUAAAGAAGGUGUUAU__UUUUCCCUUCUCUGCUCCAAGAAUUAUUAAGCGACUUCGAGUUUGGUAAGGGAACAAAUUUGAG_UAUCCUCUA
((.(((.((((((.............)))))).))).)).....(((((((((........)))))))))......................... (-15.37 = -15.49 +   0.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 687,386 – 687,501
Length 115
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 82.23
Mean single sequence MFE -31.40
Consensus MFE -19.21
Energy contribution -18.55
Covariance contribution -0.66
Combinations/Pair 1.14
Mean z-score -2.29
Structure conservation index 0.61
SVM decision value 0.38
SVM RNA-class probability 0.713077
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 687386 115 - 20766785
UCGGACGUUGGUAACGAUUUACUUUGUAUAAUAACAAGGU--AAAGAAAGUGUUAUAUAUUUCCUUUCUCUGCUCCAAGAAUUGUUAAGCUACUUUGAGUUUGGCAAGGGAAAAAAU
..(((.....((((((.((((((((((......)))))))--))).....)))))).....))).........(((.....((((((((((......)))))))))).)))...... ( -28.60)
>DroSec_CAF1 15715 109 - 1
UCGGACGUUGG------CUUAUUUUGUGUAAUAACGAGGUGUAAAGAAGGGGUUAU--UUAUCCCUUCUCUGCUCCAGGAAUUAUUAAGCGACUUCGAGUUUGGUAAGGGAACAAAU
(((((.((((.------((((..((((......))))((.(((.(((((((((...--..))))))))).))).)).........)))))))))))))(((((.........))))) ( -32.70)
>DroSim_CAF1 2893 113 - 1
UCGGACGUUGGUAACGACUUAUUUUGUAUAAUAACGAGGUGUAGAGAAGGUGCUAU--UUUUCCCUUCUCUGCUCCAAGAGUUAUUAAGCGACUUCGAUUUUGGUAAGGGAACAA--
(((((.((((....)))).....((((.(((((((..((.((((((((((......--.....)))))))))).))....))))))).)))).))))).........(....)..-- ( -32.90)
>consensus
UCGGACGUUGGUAACGACUUAUUUUGUAUAAUAACGAGGUGUAAAGAAGGUGUUAU__UUUUCCCUUCUCUGCUCCAAGAAUUAUUAAGCGACUUCGAGUUUGGUAAGGGAACAAAU
..(((.((.(.........((((((((......))))))))...((((((.............))))))).))))).....(((((((((........))))))))).......... (-19.21 = -18.55 +  -0.66)

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 09:23:02 2006