Locus 8433

Sequence ID 3R_DroMel_CAF1
Location 22,486,287 – 22,486,427
Length 140
Max. P 0.999749
window13577 window13578 window13579

overview

Window 7

Location 22,486,287 – 22,486,398
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 84.47
Mean single sequence MFE -42.46
Consensus MFE -39.02
Energy contribution -38.94
Covariance contribution -0.08
Combinations/Pair 1.25
Mean z-score -3.51
Structure conservation index 0.92
SVM decision value 4.00
SVM RNA-class probability 0.999749
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22486287 111 + 27905053
AGGGUUGGGCUGAGUGCUCAGGUGCUAGUUGCUAGGUGGUUGCUAGUACAAUAGCUGCCAGGCUGACGGGUCAUGGAUAUGGCUCCUGAGUGCUCUGCAUUCAACUUGUUU
.((((((.((.(((..(((((((((((((.(((....))).))))))))..(((((....)))))..(((((((....))))))))))))..))).))...)))))).... ( -48.50)
>DroSec_CAF1 119187 102 + 1
AGGGUUGAGCUGAGGACUCAGGUGCAAA---------GGUUGCUGGUACAAUAGCUGCCAGGCUGACGGGUCAUAAAUAUGGCUCCUGAGUGCUCUGCAUUCAACUUGUUU
.(((((((((.(((.(((((((.((...---------(((.((((......)))).))).((((....)))).........)).))))))).))).))..))))))).... ( -42.20)
>DroSim_CAF1 117012 102 + 1
AGGGUUGGGCUAAGGGCUCAGGUGCAAA---------GGUUGCUGGUACAAUAGCUGCCAGGCUGACGGGCCAUGAAUAUGGCUCCUGAGUGCUCUGUAUUCAACUUGUUC
.(((((((((..((.(((((((.((...---------(((.((((......)))).))).((((....)))).........)).))))))).))..))..))))))).... ( -40.20)
>DroEre_CAF1 120401 94 + 1
AGGCUUGGGCUGAGCGCUCAGGUGCAAA---------GGUUGCUGUUACAAUAGCUGCCAGGC--------CGUGAAUGUGGCUCUUGAGUGCUCUGCAUUCAACUUGCUC
.(((..(.((.(((((((((((......---------(((.(((((....))))).))).(((--------((......)))))))))))))))).))......)..))). ( -37.80)
>DroYak_CAF1 119583 102 + 1
AGGGUUGGGUUGAGCGCUCAGGUGCAAA---------GGUUGCUGAUACAAUAGCUGCCAGGCUGCCUUGCCAUGAAUAUGGCUCUUGAGUGCUCUGCAUUCAACUUGUUC
.(((((((((.(((((((((((.((...---------(((.((((......)))).))).(((......))).........)).)))))))))))...))))))))).... ( -43.60)
>consensus
AGGGUUGGGCUGAGCGCUCAGGUGCAAA_________GGUUGCUGGUACAAUAGCUGCCAGGCUGACGGGCCAUGAAUAUGGCUCCUGAGUGCUCUGCAUUCAACUUGUUC
.(((((((((.(((((((((((.((............(((.((((......)))).))).(((......))).........)).))))))))))).))..))))))).... (-39.02 = -38.94 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 22,486,287 – 22,486,398
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 84.47
Mean single sequence MFE -27.98
Consensus MFE -18.61
Energy contribution -20.02
Covariance contribution 1.41
Combinations/Pair 1.08
Mean z-score -1.80
Structure conservation index 0.67
SVM decision value 0.11
SVM RNA-class probability 0.586857
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22486287 111 - 27905053
AAACAAGUUGAAUGCAGAGCACUCAGGAGCCAUAUCCAUGACCCGUCAGCCUGGCAGCUAUUGUACUAGCAACCACCUAGCAACUAGCACCUGAGCACUCAGCCCAACCCU
......((((...((.(((..((((((.((((......(((....)))...)))).(((((((..((((.......))))))).)))).))))))..))).)).))))... ( -31.70)
>DroSec_CAF1 119187 102 - 1
AAACAAGUUGAAUGCAGAGCACUCAGGAGCCAUAUUUAUGACCCGUCAGCCUGGCAGCUAUUGUACCAGCAACC---------UUUGCACCUGAGUCCUCAGCUCAACCCU
......(((((..((.(((.(((((((.((((......(((....)))...)))).(((........)))....---------......))))))).))).)))))))... ( -31.20)
>DroSim_CAF1 117012 102 - 1
GAACAAGUUGAAUACAGAGCACUCAGGAGCCAUAUUCAUGGCCCGUCAGCCUGGCAGCUAUUGUACCAGCAACC---------UUUGCACCUGAGCCCUUAGCCCAACCCU
......((((....(.(((..((((((.(((((....)))))......((..((..(((........)))..))---------...)).))))))..))).)..))))... ( -25.20)
>DroEre_CAF1 120401 94 - 1
GAGCAAGUUGAAUGCAGAGCACUCAAGAGCCACAUUCACG--------GCCUGGCAGCUAUUGUAACAGCAACC---------UUUGCACCUGAGCGCUCAGCCCAAGCCU
......(((....((.((((.((((((.(((........)--------)))).((((...((((....))))..---------.))))...)))).)))).))...))).. ( -24.30)
>DroYak_CAF1 119583 102 - 1
GAACAAGUUGAAUGCAGAGCACUCAAGAGCCAUAUUCAUGGCAAGGCAGCCUGGCAGCUAUUGUAUCAGCAACC---------UUUGCACCUGAGCGCUCAACCCAACCCU
......((((......((((.((((.(.(((((....)))))...((((...((..(((........)))..))---------.)))).).)))).))))....))))... ( -27.50)
>consensus
GAACAAGUUGAAUGCAGAGCACUCAGGAGCCAUAUUCAUGACCCGUCAGCCUGGCAGCUAUUGUACCAGCAACC_________UUUGCACCUGAGCCCUCAGCCCAACCCU
......((((...((.(((..((((((.((((......(((....)))...)))).(((........)))...................))))))..))).)).))))... (-18.61 = -20.02 +   1.41)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,486,319 – 22,486,427
Length 108
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 88.57
Mean single sequence MFE -32.16
Consensus MFE -25.67
Energy contribution -25.51
Covariance contribution -0.16
Combinations/Pair 1.16
Mean z-score -1.71
Structure conservation index 0.80
SVM decision value 0.61
SVM RNA-class probability 0.797533
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22486319 108 + 27905053
UAGGUGGUUGCUAGUACAAUAGCUGCCAGGCUGACGGGUCAUGGAUAUGGCUCCUGAGUGCUCUGCAUUCAACUUGUUUGCAGGACCAUUUCUAUUUCAAGCGGCUUA
.....(((.((((......)))).)))((((((.(..(..(((((.((((.((((((((((...)))))))...((....))))))))).)))))..)..))))))). ( -36.60)
>DroSec_CAF1 119215 103 + 1
-----GGUUGCUGGUACAAUAGCUGCCAGGCUGACGGGUCAUAAAUAUGGCUCCUGAGUGCUCUGCAUUCAACUUGUUUGCAGGACCAUUUCUAUUUCAAGUGGCUUU
-----(((.((((......)))).)))..((.((((((((((....))))))).(((((((...)))))))....))).))(((.((((((.......))))))))). ( -31.20)
>DroSim_CAF1 117040 103 + 1
-----GGUUGCUGGUACAAUAGCUGCCAGGCUGACGGGCCAUGAAUAUGGCUCCUGAGUGCUCUGUAUUCAACUUGUUCGCAGGACCAUUUCUAUUUCAAGUGGCUUU
-----(((.((((......)))).)))..((.((((((((((....))))))).(((((((...)))))))....))).))(((.((((((.......))))))))). ( -31.60)
>DroEre_CAF1 120429 95 + 1
-----GGUUGCUGUUACAAUAGCUGCCAGGC--------CGUGAAUGUGGCUCUUGAGUGCUCUGCAUUCAACUUGCUCGCAGGACCAUUUCUAUUUCAAGUGGCUUU
-----(((.(((((....))))).)))((((--------(.((((((((((..((((((((...))))))))...)).))))(((.....)))..))))...))))). ( -31.10)
>DroYak_CAF1 119611 103 + 1
-----GGUUGCUGAUACAAUAGCUGCCAGGCUGCCUUGCCAUGAAUAUGGCUCUUGAGUGCUCUGCAUUCAACUUGUUCGCAGGACCAUUUCUAUUUCAAGUGGCUUU
-----(((.((((......)))).)))((((..(.(((....(((.((((...((((((((...))))))))((((....)))).))))))).....))))..)))). ( -30.30)
>consensus
_____GGUUGCUGGUACAAUAGCUGCCAGGCUGACGGGCCAUGAAUAUGGCUCCUGAGUGCUCUGCAUUCAACUUGUUCGCAGGACCAUUUCUAUUUCAAGUGGCUUU
.....(((.((((......)))).)))((((((.........(((.((((....(((((((...))))))).((((....)))).))))))).........)))))). (-25.67 = -25.51 +  -0.16)

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 13:11:22 2006