Locus 2074

Sequence ID 3L_DroMel_CAF1
Location 5,695,513 – 5,695,665
Length 152
Max. P 0.999045
window3233 window3234 window3235

overview

Window 3

Location 5,695,513 – 5,695,629
Length 116
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 82.72
Mean single sequence MFE -19.29
Consensus MFE -12.01
Energy contribution -12.20
Covariance contribution 0.19
Combinations/Pair 1.21
Mean z-score -1.69
Structure conservation index 0.62
SVM decision value -0.06
SVM RNA-class probability 0.505224
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5695513 116 - 23771897
AGAGUCUUUCUCUUUUAAGUAAAAACUAGACAGGGCGCACAGAAAAUGCACACAGCUCCUGUCUACUUUCAAUUUAAACUUAGUCUUUUUUAAUCCUAUUUGCAAAGCCAGCUUAA
((((.....)))).((((((......(((((((((((((.......))).....)).))))))))(((((((.......((((......))))......))).))))...)))))) ( -20.52)
>DroSec_CAF1 68098 103 - 1
AGAGUUUUUCUCUUUUAAGUAAAAACUAGACAGGG-------------CACACAGCUCCUGUCUACUUUCAAUUUAAACUUAAUCUUUUUUAAUCCUAUUUGCAAAGCCAGCUUAA
((((.....)))).((((((......(((((((((-------------(.....)).))))))))(((((((.......((((......))))......))).))))...)))))) ( -21.02)
>DroSim_CAF1 68419 103 - 1
AGAGUUUUUCUCUUUUAAGUAAAAACUAGACAGGG-------------CACACAGCUUCUGUCUACUUUCAAUUUAAACUUAAUCUUUUUUAAUCCUAUUUGCAAAGCCAGCUUAA
((((.....)))).((((((......(((((((((-------------(.....)).))))))))(((((((.......((((......))))......))).))))...)))))) ( -18.02)
>DroEre_CAF1 71434 116 - 1
AGGGCUUUUCUUUUUUAAGUGAACUCUAAGCAGGGCAUACAUAAAAUGCACACCACUCUGGUCCACUUUCAAUUUAAAGUUAAUCUUUUUUAAUCCUAUUUGCACAGCCAGCCUUG
((((((......(((((.(((..((((....))))..))).)))))((((.(((.....)))..(((((......)))))....................)))).....)))))). ( -17.60)
>consensus
AGAGUUUUUCUCUUUUAAGUAAAAACUAGACAGGG_____________CACACAGCUCCUGUCUACUUUCAAUUUAAACUUAAUCUUUUUUAAUCCUAUUUGCAAAGCCAGCUUAA
.(((((.......(((((((..(((.(((((((((.....................))))))))).)))..))))))).((((......))))................))))).. (-12.01 = -12.20 +   0.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,695,549 – 5,695,665
Length 116
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 78.80
Mean single sequence MFE -26.80
Consensus MFE -12.49
Energy contribution -13.55
Covariance contribution 1.06
Combinations/Pair 1.17
Mean z-score -2.50
Structure conservation index 0.47
SVM decision value 0.11
SVM RNA-class probability 0.588134
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5695549 116 + 23771897
AGUUUAAAUUGAAAGUAGACAGGAGCUGUGUGCAUUUUCUGUGCGCCCUGUCUAGUUUUUACUUAAAAGAGAAAGACUCUUUCAAAGUACUCUCAACAAAUUUUCACACCGAA---UGU
.((..(((((((((.((((((((....(((..((.....))..))))))))))).))))(((((.((((((.....))))))..))))).........)))))..))......---... ( -29.70)
>DroSec_CAF1 68134 105 + 1
AGUUUAAAUUGAAAGUAGACAGGAGCUGUGUG-------------CCCUGUCUAGUUUUUACUUAAAAGAGAAAAACUCUUUCAAAGUACUCUCAACA-AUUUUCACACCGAAUAGUGU
.((..(((((((((.((((((((.((.....)-------------))))))))).))).(((((.((((((.....))))))..))))).......))-))))..))............ ( -29.10)
>DroSim_CAF1 68455 105 + 1
AGUUUAAAUUGAAAGUAGACAGAAGCUGUGUG-------------CCCUGUCUAGUUUUUACUUAAAAGAGAAAAACUCUUUCAAAGUACUCUCAACA-AUUUUCACACCGAAUAGUGU
.((..(((((((((.(((((((..((.....)-------------).))))))).))).(((((.((((((.....))))))..))))).......))-))))..))............ ( -24.00)
>DroEre_CAF1 71470 110 + 1
ACUUUAAAUUGAAAGUGGACCAGAGUGGUGUGCAUUUUAUGUAUGCCCUGCUUAGAGUUCACUUAAAAAAGAAAAGCCCUUUCAAAGUAC------CU-UUUUUCACACCGCAUAG--U
(((((.......(((((((((.(((((((((((((...)))))))))..)))).).))))))))......((((.....)))))))))..------..-.................--. ( -24.40)
>consensus
AGUUUAAAUUGAAAGUAGACAGGAGCUGUGUG_____________CCCUGUCUAGUUUUUACUUAAAAGAGAAAAACUCUUUCAAAGUACUCUCAACA_AUUUUCACACCGAAUAGUGU
........(((((((((((((((.......................))))))))((((((.(((....))))))))).))))))).................................. (-12.49 = -13.55 +   1.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,695,549 – 5,695,665
Length 116
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 78.80
Mean single sequence MFE -29.74
Consensus MFE -18.40
Energy contribution -19.52
Covariance contribution 1.13
Combinations/Pair 1.21
Mean z-score -3.28
Structure conservation index 0.62
SVM decision value 3.34
SVM RNA-class probability 0.999045
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5695549 116 - 23771897
ACA---UUCGGUGUGAAAAUUUGUUGAGAGUACUUUGAAAGAGUCUUUCUCUUUUAAGUAAAAACUAGACAGGGCGCACAGAAAAUGCACACAGCUCCUGUCUACUUUCAAUUUAAACU
.((---(.....))).......(((((((((((((.(((((((.....)))))))))))).....(((((((((((((.......))).....)).))))))))))))))))....... ( -31.40)
>DroSec_CAF1 68134 105 - 1
ACACUAUUCGGUGUGAAAAU-UGUUGAGAGUACUUUGAAAGAGUUUUUCUCUUUUAAGUAAAAACUAGACAGGG-------------CACACAGCUCCUGUCUACUUUCAAUUUAAACU
(((((....)))))......-.(((((((((((((.(((((((.....)))))))))))).....(((((((((-------------(.....)).))))))))))))))))....... ( -34.80)
>DroSim_CAF1 68455 105 - 1
ACACUAUUCGGUGUGAAAAU-UGUUGAGAGUACUUUGAAAGAGUUUUUCUCUUUUAAGUAAAAACUAGACAGGG-------------CACACAGCUUCUGUCUACUUUCAAUUUAAACU
(((((....)))))......-.(((((((((((((.(((((((.....)))))))))))).....(((((((((-------------(.....)).))))))))))))))))....... ( -31.80)
>DroEre_CAF1 71470 110 - 1
A--CUAUGCGGUGUGAAAAA-AG------GUACUUUGAAAGGGCUUUUCUUUUUUAAGUGAACUCUAAGCAGGGCAUACAUAAAAUGCACACCACUCUGGUCCACUUUCAAUUUAAAGU
(--(((.(.((((((.....-..------((((((((..((((.(((.(((....))).)))))))...)))))..)))........)))))).)..))))..(((((......))))) ( -20.96)
>consensus
ACACUAUUCGGUGUGAAAAU_UGUUGAGAGUACUUUGAAAGAGUUUUUCUCUUUUAAGUAAAAACUAGACAGGG_____________CACACAGCUCCUGUCUACUUUCAAUUUAAACU
......................(((((((((((((.(((((((.....)))))))))))).....(((((((((.....................)))))))))))))))))....... (-18.40 = -19.52 +   1.13)

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 10:23:49 2006