Locus 2008

Sequence ID X_DroMel_CAF1
Location 5,512,125 – 5,512,266
Length 141
Max. P 0.999220
window3265 window3266 window3267

overview

Window 5

Location 5,512,125 – 5,512,232
Length 107
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.27
Mean single sequence MFE -25.15
Consensus MFE -16.33
Energy contribution -16.82
Covariance contribution 0.50
Combinations/Pair 1.24
Mean z-score -1.81
Structure conservation index 0.65
SVM decision value 0.49
SVM RNA-class probability 0.756006
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5512125 107 - 22224390
AAGUAUUUCAAUCUUUUUAUAAAUAAGCUAAGCUAUUCUAGGAAACGCAUCAAACAACGAGUGAGAUGCGUUAUGCUGCUGUUUA----UGCAAUGGCUCU---------UCAAUUACUU
(((((....................(((...))).....((((((((((((..((.....))..))))))))..(((..(((...----.)))..))))))---------)....))))) ( -20.20)
>DroSec_CAF1 2252 107 - 1
AAGAAUUUCAAUCUUUUUAUAAAUAAGCUAAGCUAUUCUAGGAAACGCAUCUAACACCGAGUGGGAUGCGUUCUGUUGCUGUUUA----UGCAAUUGCUCU---------UCAAUUACUU
((((..................((((((..(((.......((((.(((((((.((.....)).)))))))))))...))))))))----)((....)))))---------)......... ( -21.00)
>DroSim_CAF1 2150 102 - 1
AAGAAUUCC-AUCUUUUU-UAAAUAAGCUAAGCUAUUCUAGGA-ACGCAU-UAACACCGAGUG-GAUGCGUUCUGCUGCUGUUUA----UGCAAUGGCUCC---------UCAAUUACUU
..((...((-((......-((((((.((..(((.......(((-((((((-(.((.....)).-)))))))))))))))))))))----....))))....---------))........ ( -21.81)
>DroEre_CAF1 2277 114 - 1
AA------CAACCUUUUUAUAAAUAAACUAAGCUAUUCUGGGAAACGCAUCCUACACCUCGUGGGAUGCGUUCAGCCGCUGUCUACGUUUGCAGUAGCCUUUUAAAGUAACCAGUAGCUU
..------.....................((((((..(((((((.((((((((((.....))))))))))))).((..((((........))))..))............)))))))))) ( -37.60)
>consensus
AAGAAUUUCAAUCUUUUUAUAAAUAAGCUAAGCUAUUCUAGGAAACGCAUCUAACACCGAGUGGGAUGCGUUCUGCUGCUGUUUA____UGCAAUGGCUCU_________UCAAUUACUU
...............................((((((...((.(((((((((.((.....)).)))))))))...))((...........))))))))...................... (-16.33 = -16.82 +   0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,512,152 – 5,512,266
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 74.03
Mean single sequence MFE -30.47
Consensus MFE -17.64
Energy contribution -17.89
Covariance contribution 0.25
Combinations/Pair 1.12
Mean z-score -2.84
Structure conservation index 0.58
SVM decision value 3.44
SVM RNA-class probability 0.999220
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5512152 114 + 22224390
AGCAGCAUAACGCAUCUCACUCGUUGUUUGAUGCGUUUCCUAGAAUAGCUUAGCUUAUUUAUAAAAAGAUUGAAAUACUUCUAGGA------AUGCUCCCUACUGCGACAGCUCUUCAAA
.((((...((((((((..((.....))..))))))))((((((((((..(((((((.........))).))))..)).))))))))------..........)))).............. ( -28.40)
>DroSec_CAF1 2279 105 + 1
AGCAACAGAACGCAUCCCACUCGGUGUUAGAUGCGUUUCCUAGAAUAGCUUAGCUUAUUUAUAAAAAGAUUGAAAUUCUUCUAGGA------AUGCUCCCUACGCCGAAAG---------
.((........)).......(((((((..(..(((((.(((((((....(((((((.........))).)))).....))))))))------))))..)..)))))))...--------- ( -26.60)
>DroSim_CAF1 2177 100 + 1
AGCAGCAGAACGCAUC-CACUCGGUGUUA-AUGCGU-UCCUAGAAUAGCUUAGCUUAUUUA-AAAAAGAU-GGAAUUCUUCUAGGA------AUGCUCCCUACGCCGAAAG---------
....((.....))...-...(((((((..-..((((-((((((((...((...(((.....-...)))..-)).....))))))))------)))).....)))))))...--------- ( -31.10)
>DroEre_CAF1 2317 108 + 1
AGCGGCUGAACGCAUCCCACGAGGUGUAGGAUGCGUUUCCCAGAAUAGCUUAGUUUAUUUAUAAAAAGGUUG------UUAUGGGAGCCAUUAUGAUCUGUAA------AUUGCUUGAAU
(((((((((((((((((.((.....)).))))))))))((((.((((((((..((((....)))).))))))------)).)))))))).((((.....))))------...)))..... ( -35.80)
>consensus
AGCAGCAGAACGCAUCCCACUCGGUGUUAGAUGCGUUUCCUAGAAUAGCUUAGCUUAUUUAUAAAAAGAUUGAAAUUCUUCUAGGA______AUGCUCCCUACGCCGAAAG_________
((((....((((((((..((.....))..))))))))((((((((...........((((......))))........)))))))).......))))....................... (-17.64 = -17.89 +   0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,512,152 – 5,512,266
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 74.03
Mean single sequence MFE -29.17
Consensus MFE -19.17
Energy contribution -20.86
Covariance contribution 1.69
Combinations/Pair 1.12
Mean z-score -2.42
Structure conservation index 0.66
SVM decision value 2.98
SVM RNA-class probability 0.998014
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5512152 114 - 22224390
UUUGAAGAGCUGUCGCAGUAGGGAGCAU------UCCUAGAAGUAUUUCAAUCUUUUUAUAAAUAAGCUAAGCUAUUCUAGGAAACGCAUCAAACAACGAGUGAGAUGCGUUAUGCUGCU
..............((((((........------((((((((.(((((............)))))(((...))).))))))))((((((((..((.....))..)))))))).)))))). ( -30.00)
>DroSec_CAF1 2279 105 - 1
---------CUUUCGGCGUAGGGAGCAU------UCCUAGAAGAAUUUCAAUCUUUUUAUAAAUAAGCUAAGCUAUUCUAGGAAACGCAUCUAACACCGAGUGGGAUGCGUUCUGUUGCU
---------.....((((.(.(((((.(------(((((((((.....)................(((...))).)))))))))..((((((.((.....)).))))))))))).))))) ( -29.80)
>DroSim_CAF1 2177 100 - 1
---------CUUUCGGCGUAGGGAGCAU------UCCUAGAAGAAUUCC-AUCUUUUU-UAAAUAAGCUAAGCUAUUCUAGGA-ACGCAU-UAACACCGAGUG-GAUGCGUUCUGCUGCU
---------........(((((((((.(------((((((((.......-..(((...-.....)))........))))))))-).((((-(.((.....)).-)))))))))).)))). ( -26.83)
>DroEre_CAF1 2317 108 - 1
AUUCAAGCAAU------UUACAGAUCAUAAUGGCUCCCAUAA------CAACCUUUUUAUAAAUAAACUAAGCUAUUCUGGGAAACGCAUCCUACACCUCGUGGGAUGCGUUCAGCCGCU
.....(((...------...((((.....((((((.......------......................))))))))))((.((((((((((((.....))))))))))))...))))) ( -30.05)
>consensus
_________CUUUCGGCGUAGGGAGCAU______UCCUAGAAGAAUUUCAAUCUUUUUAUAAAUAAGCUAAGCUAUUCUAGGAAACGCAUCUAACACCGAGUGGGAUGCGUUCUGCUGCU
....................((.(((........((((((((.................................))))))))(((((((((.((.....)).)))))))))..))).)) (-19.17 = -20.86 +   1.69)

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 10:24:02 2006