Locus 5543

Sequence ID 3R_DroMel_CAF1
Location 14,643,741 – 14,643,839
Length 98
Max. P 0.954210
window9038 window9039

overview

Window 8

Location 14,643,741 – 14,643,839
Length 98
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 67.42
Mean single sequence MFE -26.28
Consensus MFE -2.78
Energy contribution -3.42
Covariance contribution 0.64
Combinations/Pair 1.31
Mean z-score -2.68
Structure conservation index 0.11
SVM decision value 0.00
SVM RNA-class probability 0.534880
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14643741 98 + 27905053
UUACGGCACCCAAGCACCACACACACACACGCCACG---CAUG--UGAGUGUGUGCGUGAGUGCAAUUUCAUUAAUGGCUAAUUAAUUGCAACUUUAUUUCGC
.....(((.....(((((((.(((((((.(((....---...)--)).))))))).))).))))......((((((.....)))))))))............. ( -28.90)
>DroVir_CAF1 66538 95 + 1
UUACGCAAUGCAAGCUGGAAAUUAAGC-A--C-----UGUAUGUCGGAUUGUGCCUGUGUGUUCUGUUUUAAUAUGAAACACUUAAUUGCAGCUUUAUUUCGU
..(((.((((.((((((..((((((((-(--(-----.(((((......)))))..))).....((((((.....))))))))))))).)))))))))).))) ( -22.70)
>DroSec_CAF1 58927 101 + 1
UUACGCCACCCAAGCACCACACACACACACACCAUGAUGUGUG--UGCGUGUGUGCGUGAGUGCAAUUUCAUUAAUGGCUAAUUAAUUGCAACUUUAUUUCGC
....((........((((((((((.(((((((......)))))--)).))))))).)))..(((((((..((((.....)))).)))))))..........)) ( -32.90)
>DroSim_CAF1 65899 93 + 1
UUACGCCACCCAAGCACCACACACACACACACCAUGAUGUGUG--U--------GCGUGAGUGCAAUUUCAUUAAUGGCUAAUUAAUUGCAACUUUAUUUCGC
....(((......(((((((.(((((((((.....).))))))--)--------).))).)))).(((.....))))))........................ ( -26.40)
>DroEre_CAF1 57488 84 + 1
UUACGCCACCCAAGCACCG------------CCAUG-----UG--UGAGUGUGUGCGUGAGUGCAAUUUCAUUAAUGGCUAAUUAAUUGCAACUUUAUUUCGC
(((((((((.(..((((..------------....)-----))--)..).))).)))))).(((((((..((((.....)))).)))))))............ ( -21.10)
>DroMoj_CAF1 66860 84 + 1
UUACGGCGCACAAGCUGCAAAUGAACG-A--G-----C----------AUGUGUGCGUGUGUUCCGCUUUGAUAUGA-GCAAUUAAUUGCAGCUUUAUUUCGU
..((((.....(((((((((.(((..(-(--(-----(----------(..(....)..))))).((((......))-))..))).)))))))))....)))) ( -25.70)
>consensus
UUACGCCACCCAAGCACCACACACACA_A__CCAUG_U_U_UG__UGAGUGUGUGCGUGAGUGCAAUUUCAUUAAUGGCUAAUUAAUUGCAACUUUAUUUCGC
......................................................(((.((((((((((................)))))).)))).....))) ( -2.78 =  -3.42 +   0.64)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,643,741 – 14,643,839
Length 98
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 67.42
Mean single sequence MFE -29.75
Consensus MFE -4.61
Energy contribution -5.45
Covariance contribution 0.84
Combinations/Pair 1.30
Mean z-score -3.40
Structure conservation index 0.15
SVM decision value 1.44
SVM RNA-class probability 0.954210
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14643741 98 - 27905053
GCGAAAUAAAGUUGCAAUUAAUUAGCCAUUAAUGAAAUUGCACUCACGCACACACUCA--CAUG---CGUGGCGUGUGUGUGUGUGGUGCUUGGGUGCCGUAA
(((......((((...((((((.....))))))..))))(((((((.((((((((.((--((((---((...)))))))).)))).)))).)))))))))).. ( -36.20)
>DroVir_CAF1 66538 95 - 1
ACGAAAUAAAGCUGCAAUUAAGUGUUUCAUAUUAAAACAGAACACACAGGCACAAUCCGACAUACA-----G--U-GCUUAAUUUCCAGCUUGCAUUGCGUAA
(((.(((.((((((.((((((((((((............))))))....((((.............-----)--)-))))))))..))))))..))).))).. ( -20.12)
>DroSec_CAF1 58927 101 - 1
GCGAAAUAAAGUUGCAAUUAAUUAGCCAUUAAUGAAAUUGCACUCACGCACACACGCA--CACACAUCAUGGUGUGUGUGUGUGUGGUGCUUGGGUGGCGUAA
((...........((((((.(((((...)))))..))))))(((((.(((((((((((--(((((((....)))))))))))))).)))).))))).)).... ( -43.70)
>DroSim_CAF1 65899 93 - 1
GCGAAAUAAAGUUGCAAUUAAUUAGCCAUUAAUGAAAUUGCACUCACGC--------A--CACACAUCAUGGUGUGUGUGUGUGUGGUGCUUGGGUGGCGUAA
((((.......)))).........((((((.........((((((((((--------(--(((((((....))))))))))))).)))))...)))))).... ( -38.40)
>DroEre_CAF1 57488 84 - 1
GCGAAAUAAAGUUGCAAUUAAUUAGCCAUUAAUGAAAUUGCACUCACGCACACACUCA--CA-----CAUGG------------CGGUGCUUGGGUGGCGUAA
((...........((((((.(((((...)))))..))))))(((((.((((...(...--..-----...).------------..)))).))))).)).... ( -19.10)
>DroMoj_CAF1 66860 84 - 1
ACGAAAUAAAGCUGCAAUUAAUUGC-UCAUAUCAAAGCGGAACACACGCACACAU----------G-----C--U-CGUUCAUUUGCAGCUUGUGCGCCGUAA
(((.....(((((((((.....(((-(........))))((((....(((....)----------)-----)--.-.))))..)))))))))......))).. ( -21.00)
>consensus
GCGAAAUAAAGUUGCAAUUAAUUAGCCAUUAAUGAAAUUGCACUCACGCACACACUCA__CA_A_A_CAUGG__U_UGUGUGUGUGGUGCUUGGGUGGCGUAA
(((.......(((...((((((.....))))))..)))..((((((.((.......................................)).)))))).))).. ( -4.61 =  -5.45 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:42 2006