Locus 1568

Sequence ID 2R_DroMel_CAF1
Location 5,913,049 – 5,913,233
Length 184
Max. P 0.615038
window2628 window2629

overview

Window 8

Location 5,913,049 – 5,913,158
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.37
Mean single sequence MFE -27.10
Consensus MFE -15.42
Energy contribution -15.61
Covariance contribution 0.19
Combinations/Pair 1.20
Mean z-score -1.93
Structure conservation index 0.57
SVM decision value 0.17
SVM RNA-class probability 0.615038
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5913049 109 - 20766785
CCACUUUUGAGCAAUUAAAAUUAAAUGAAG-GUUUUCGGUUUCGAAAGUAAGGCGAAA-----AGUAAAGAGAGGGCAAAUGCAUUUAGCCCAAUUGCUUGGUAAUGAGUGGG----G-C
(((((((..(((((((.............(-.((((((.((((....).))).)))))-----).).......((((.((.....)).)))))))))))..)....)))))).----.-. ( -33.30)
>DroSec_CAF1 55057 101 - 1
CCACU--UGAGCAAUUAAAAUUAAAUGAAG-GUCUUCGGUUUCGAAAGUAAGGCGAAA-----AGUAAAGAG------AAUGCAUUUAGCCCAAUUGCUUGGUAAUGAGUGGG----G-C
(((((--(((((((((....(((((((...-.((((((.((((....).))).)))..-----.......))------)...)))))))...))))))))......)))))).----.-. ( -24.50)
>DroSim_CAF1 48269 101 - 1
CCACU--UGAGCAAUUAAAAUUAAAUGAAG-GCUUUCGGUUUUGAAAGUAAGGCGAAA-----AGUAAAGAG------AAUGCAUUUGGCCCAAUUGCUUGGUAAUGAGUGGG----G-G
(((((--(((((((((..............-(((((((....)))))))..(((.(((-----.(((.....------..))).))).))).))))))))......)))))).----.-. ( -27.10)
>DroAna_CAF1 55102 118 - 1
CCACU--UGAGCAAUUAAAAUUAAAUGAAACGUUUAGGGUUUCCCUCGAAAAGCCAAAGAAACUGGAUCGAGAACGCAAUUGCAUUAAACUCGAUGGCUUGGUAAUGACUCGGUGAGGGC
...((--(((((...................)))))))....((((((..((((((...........(((((((.((....)).))...)))))))))))(((....)))...)))))). ( -23.51)
>consensus
CCACU__UGAGCAAUUAAAAUUAAAUGAAG_GUUUUCGGUUUCGAAAGUAAGGCGAAA_____AGUAAAGAG______AAUGCAUUUAGCCCAAUUGCUUGGUAAUGAGUGGG____G_C
(((((..(((((((((....(((((((......(((((.((((....).))).)))))........................)))))))...)))))))))......)))))........ (-15.42 = -15.61 +   0.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,913,119 – 5,913,233
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.36
Mean single sequence MFE -28.05
Consensus MFE -18.96
Energy contribution -19.65
Covariance contribution 0.69
Combinations/Pair 1.12
Mean z-score -1.85
Structure conservation index 0.68
SVM decision value 0.13
SVM RNA-class probability 0.596410
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5913119 114 + 20766785
ACCGAAAAC-CUUCAUUUAAUUUUAAUUGCUCAAAAGUGGAAGGAACUCGAUGACAAUUGAAACUCUUUGAGGUUUCA---ACCACCCAGCGAUGCCUUC-AAUU-GCCGCAAAUGAGCU
...(((...-.)))..............(((((...((((..((((((((((....)))))..(((...)))))))).---.))))...(((((......-.)))-))......))))). ( -24.70)
>DroSec_CAF1 55121 112 + 1
ACCGAAGAC-CUUCAUUUAAUUUUAAUUGCUCA--AGUGGUAGGAACUCGAAGACAAUUGAAACUCUUUGAGGUUUCA---ACCACCCAGCGAUGCCUUC-AAUU-GCUGCAAAUGAGCU
...(((...-.)))..............(((((--.(((((.((((((((((((..........))))))).))))).---))))).(((((((......-.)))-))))....))))). ( -33.80)
>DroSim_CAF1 48333 112 + 1
ACCGAAAGC-CUUCAUUUAAUUUUAAUUGCUCA--AGUGGAGGGAACUCGAAGACAAUUGAAACUCUUUGAGGUUUCA---ACCACCCAGCGAUGCCUUC-AAUU-GCCGCAAAUGAGCU
..(....).-..................(((((--.((((..((((((((((((..........))))))).))))).---.))))...(((((......-.)))-))......))))). ( -28.20)
>DroAna_CAF1 55182 118 + 1
ACCCUAAACGUUUCAUUUAAUUUUAAUUGCUCA--AGUGGAAGAAACUCGAAGACAAUUGAAAAUCAUCGAGGUUAGAGGCGCCACCAAAUGAUGCCUUCCAAUUGGCCGCAAAUGAGCU
............................(((((--.((((..((..(((((.((..........)).)))))....((((((.((.....)).))))))....))..))))...))))). ( -25.50)
>consensus
ACCGAAAAC_CUUCAUUUAAUUUUAAUUGCUCA__AGUGGAAGGAACUCGAAGACAAUUGAAACUCUUUGAGGUUUCA___ACCACCCAGCGAUGCCUUC_AAUU_GCCGCAAAUGAGCU
............................(((((...((((..((((((((((((..........))))))).))))).....))))...(((..((..........)))))...))))). (-18.96 = -19.65 +   0.69)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:42 2006