Locus 6344

Sequence ID X_DroMel_CAF1
Location 15,998,662 – 15,998,822
Length 160
Max. P 0.980959
window10351 window10352 window10353

overview

Window 1

Location 15,998,662 – 15,998,782
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.67
Mean single sequence MFE -38.26
Consensus MFE -37.50
Energy contribution -37.74
Covariance contribution 0.24
Combinations/Pair 1.02
Mean z-score -1.68
Structure conservation index 0.98
SVM decision value 1.80
SVM RNA-class probability 0.977847
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15998662 120 - 22224390
GGCCAUAACCUGCGUCUGCUGGUGGCAAUACCACCAGAUGGCCGGAGGUCUUUGCCGAUGCAGUUAAUGAAGAUACGUUUCAAUUAGCUCAAUUCGAACGUGAAAGUGUGAAUAUGUGUA
(((.(..((((.((.((((((((((.....))))))).))).)).))))..).))).(((((((((((((((.....)))).))))))...(((((.((......)).))))).))))). ( -38.40)
>DroSec_CAF1 66671 120 - 1
GGCCAUAACCUGCGCCUGCUGGUGGCAAUACCACCAGAUGGCCGGAGGUCUUUGCCGAUGCAGUUAAUGAAGAUACGUUUCAAUUAGCUCAAUUCGAACGUGAAAGUGUGAAUAUGUGUA
(((.(..((((.((((..(((((((.....)))))))..)).)).))))..).))).(((((((((((((((.....)))).))))))...(((((.((......)).))))).))))). ( -39.80)
>DroSim_CAF1 60838 120 - 1
GGCCAUAACCUGCGCCUGCUGGUGGCAAUACCACCAGAUGGCCGGAGGUCUUUGCCGAUGCAGUUAAUGAAGAUACGUUUCAAUUAGCUCAAUUCGAACGUGAAAGUGUGAAUAUGUGUA
(((.(..((((.((((..(((((((.....)))))))..)).)).))))..).))).(((((((((((((((.....)))).))))))...(((((.((......)).))))).))))). ( -39.80)
>DroEre_CAF1 65684 120 - 1
GGCCAUAACCUGCGCCUGCUGGUGGCAAUACCACCAGAUGGCCGGAGGUCUCUGCCGAUGCAGUUAAUGAAGAUACGUUUCAAUUAGCUCAAUUCGAACGUGAAAGUGUGAAUAUGUGUA
(((....((((.((((..(((((((.....)))))))..)).)).))))....))).(((((((((((((((.....)))).))))))...(((((.((......)).))))).))))). ( -39.10)
>DroYak_CAF1 49875 120 - 1
GGCCAUAACCUGCGCCUGCUGGUGGCACUACAACCAGAUGGCCGGAGGUCUUUGCCGAUGCAGUUAAUGAAGAUACGUUUCAAUUAGCUCAAUUCGAACGUGAAAGUGUGAAUAUGUGUA
(((.(..((((.((((..((((((......).)))))..)).)).))))..).))).(((((((((((((((.....)))).))))))...(((((.((......)).))))).))))). ( -34.20)
>consensus
GGCCAUAACCUGCGCCUGCUGGUGGCAAUACCACCAGAUGGCCGGAGGUCUUUGCCGAUGCAGUUAAUGAAGAUACGUUUCAAUUAGCUCAAUUCGAACGUGAAAGUGUGAAUAUGUGUA
(((.(..((((.((((..(((((((.....)))))))..)).)).))))..).))).(((((((((((((((.....)))).))))))...(((((.((......)).))))).))))). (-37.50 = -37.74 +   0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,998,702 – 15,998,822
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.83
Mean single sequence MFE -29.87
Consensus MFE -27.13
Energy contribution -27.47
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.49
Structure conservation index 0.91
SVM decision value 1.88
SVM RNA-class probability 0.980959
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15998702 120 + 22224390
AAACGUAUCUUCAUUAACUGCAUCGGCAAAGACCUCCGGCCAUCUGGUGGUAUUGCCACCAGCAGACGCAGGUUAUGGCCUGUAUUAAAACCAAGAAAAAAAAAAAAAAAACACACAGAG
.......((((......((((...(((((..(((.((((....)))).))).)))))....))))..((((((....)))))).........))))........................ ( -29.90)
>DroSim_CAF1 60878 109 + 1
AAACGUAUCUUCAUUAACUGCAUCGGCAAAGACCUCCGGCCAUCUGGUGGUAUUGCCACCAGCAGGCGCAGGUUAUGGCCUGUAUUAAAACCAAAAAAAAAGGAA-----------AGAG
.......((((.......(((....)))......(((.(((..(((((((.....)))))))..)))((((((....))))))..................))))-----------))). ( -32.70)
>DroYak_CAF1 49915 108 + 1
AAACGUAUCUUCAUUAACUGCAUCGGCAAAGACCUCCGGCCAUCUGGUUGUAGUGCCACCAGCAGGCGCAGGUUAUGGCCUGUAUUAAAACAAAAAAAAG----A-AUAAAUA-------
.......((((......((((...((((...((..((((....))))..))..))))....))))..((((((....))))))..............)))----)-.......------- ( -27.00)
>consensus
AAACGUAUCUUCAUUAACUGCAUCGGCAAAGACCUCCGGCCAUCUGGUGGUAUUGCCACCAGCAGGCGCAGGUUAUGGCCUGUAUUAAAACCAAAAAAAAA__AA_A_AAA_A___AGAG
.............((((.((((..(((...(((((.((.(...(((((((.....)))))))..).)).)))))...)))))))))))................................ (-27.13 = -27.47 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,998,702 – 15,998,822
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 84.83
Mean single sequence MFE -31.23
Consensus MFE -28.40
Energy contribution -28.30
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -1.56
Structure conservation index 0.91
SVM decision value 0.76
SVM RNA-class probability 0.842327
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15998702 120 - 22224390
CUCUGUGUGUUUUUUUUUUUUUUUUCUUGGUUUUAAUACAGGCCAUAACCUGCGUCUGCUGGUGGCAAUACCACCAGAUGGCCGGAGGUCUUUGCCGAUGCAGUUAAUGAAGAUACGUUU
......((((((((.............((((((......))))))((((.((((((..(((((((.....)))))))..(((.((....))..)))))))))))))..)))))))).... ( -36.40)
>DroSim_CAF1 60878 109 - 1
CUCU-----------UUCCUUUUUUUUUGGUUUUAAUACAGGCCAUAACCUGCGCCUGCUGGUGGCAAUACCACCAGAUGGCCGGAGGUCUUUGCCGAUGCAGUUAAUGAAGAUACGUUU
....-----------...((((....(((((......)).(((.(..((((.((((..(((((((.....)))))))..)).)).))))..).)))....))).....))))........ ( -31.10)
>DroYak_CAF1 49915 108 - 1
-------UAUUUAU-U----CUUUUUUUUGUUUUAAUACAGGCCAUAACCUGCGCCUGCUGGUGGCACUACAACCAGAUGGCCGGAGGUCUUUGCCGAUGCAGUUAAUGAAGAUACGUUU
-------.......-(----((((...((((.........(((.(..((((.((((..((((((......).)))))..)).)).))))..).)))...)))).....)))))....... ( -26.20)
>consensus
CUCU___U_UUU_U_UU__UUUUUUUUUGGUUUUAAUACAGGCCAUAACCUGCGCCUGCUGGUGGCAAUACCACCAGAUGGCCGGAGGUCUUUGCCGAUGCAGUUAAUGAAGAUACGUUU
........................((((.(((........(((.(..((((.((((..(((((((.....)))))))..)).)).))))..).))).........))).))))....... (-28.40 = -28.30 +  -0.11)

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 12:11:17 2006