Locus 3888

Sequence ID 3L_DroMel_CAF1
Location 11,257,433 – 11,257,545
Length 112
Max. P 0.845391
window6049 window6050

overview

Window 9

Location 11,257,433 – 11,257,545
Length 112
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 81.45
Mean single sequence MFE -25.44
Consensus MFE -14.67
Energy contribution -15.79
Covariance contribution 1.12
Combinations/Pair 1.14
Mean z-score -2.26
Structure conservation index 0.58
SVM decision value 0.77
SVM RNA-class probability 0.845391
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11257433 112 + 23771897
AUUUAUGCAUUUUGCUUUGCCAUAAAUCAUAAUGGCAGUGCAAGUCCCCCACUU---UACUA-CUUUUAUGGAACUGUGCACAGUAGCAAAAGUAGUCGUUUUAUGAC--ACAAAAAA
.....(((.(((((((.((((((........))))))((((((((.((......---.....-.......)).))).)))))...))))))))))(((((...)))))--........ ( -27.37)
>DroSec_CAF1 58444 109 + 1
AUUUGUGCAUUUUGCUUUGCCAUAAAUCAUAAUGGCAGUGCAAGUCCCCCACUU---UACUA-CUUUUAUGGAACUGUGCACA---GCAAGAGUAGUCGUUUUACAAC--ACGAAAAA
.((((((..(((((((.((((((........))))))((((((((.((......---.....-.......)).))).))))))---))))))((((.....))))..)--)))))... ( -28.97)
>DroSim_CAF1 59977 109 + 1
AUUUGUGCAUUUUGCUUUGCCAUAAAUCAUAAUGGCAGUGCAAGUCCCCCACUU---UACUA-CUUUUAUGGAACUGUGCACA---GCAAAAGUAGUCGUUUUACAAC--ACGAAAAA
.((((((..(((((((.((((((........))))))((((((((.((......---.....-.......)).))).))))))---))))))((((.....))))..)--)))))... ( -28.87)
>DroYak_CAF1 61710 111 + 1
AUUUGUGCAUUUUGCUUUGCCAUAAAUCAUAAUGGCAGUGCAUGUCCCCCAGUU---UACUA-CUUUUAUGGAACAGUGCACA---GAAAAAGUAGACGUUUUAUGACCAAAUAAAAA
(((((..((((((((((((((((........))))).((((((.(((...(((.---....)-)).....)))...)))))).---...))))))))......)))..)))))..... ( -27.20)
>DroAna_CAF1 58858 100 + 1
AUUUGUGCAUUUUGUUUUGCCAUAAAUCAUAAGGCCAGUGCAUGCC--CUACUUCUAUUCUAUCUUUUAAGGAAAUAAACACUG-AGAGAAAGUAGA----UUCCAA-----------
....(((((((..((((((..........)))))).)))))))...--((((((........(((((((..(.......)..))-))))))))))).----......----------- ( -14.80)
>consensus
AUUUGUGCAUUUUGCUUUGCCAUAAAUCAUAAUGGCAGUGCAAGUCCCCCACUU___UACUA_CUUUUAUGGAACUGUGCACA___GCAAAAGUAGUCGUUUUACAAC__ACGAAAAA
....(((((((((((.(((((((........))))))).)))))....(((..................)))....)))))).................................... (-14.67 = -15.79 +   1.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,257,433 – 11,257,545
Length 112
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 81.45
Mean single sequence MFE -26.90
Consensus MFE -15.63
Energy contribution -16.51
Covariance contribution 0.88
Combinations/Pair 1.20
Mean z-score -1.99
Structure conservation index 0.58
SVM decision value 0.28
SVM RNA-class probability 0.668173
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11257433 112 - 23771897
UUUUUUGU--GUCAUAAAACGACUACUUUUGCUACUGUGCACAGUUCCAUAAAAG-UAGUA---AAGUGGGGGACUUGCACUGCCAUUAUGAUUUAUGGCAAAGCAAAAUGCAUAAAU
...(((((--(.(((...((.((((((((((..((((....))))....))))))-)))).---..)).(....)((((..((((((........))))))..)))).))))))))). ( -32.10)
>DroSec_CAF1 58444 109 - 1
UUUUUCGU--GUUGUAAAACGACUACUCUUGC---UGUGCACAGUUCCAUAAAAG-UAGUA---AAGUGGGGGACUUGCACUGCCAUUAUGAUUUAUGGCAAAGCAAAAUGCACAAAU
......((--((.(((.......)))..((((---((((((.((((((.......-.....---......)))))))))))((((((........)))))).)))))...)))).... ( -28.47)
>DroSim_CAF1 59977 109 - 1
UUUUUCGU--GUUGUAAAACGACUACUUUUGC---UGUGCACAGUUCCAUAAAAG-UAGUA---AAGUGGGGGACUUGCACUGCCAUUAUGAUUUAUGGCAAAGCAAAAUGCACAAAU
......((--((.(((.......)))((((((---((((((.((((((.......-.....---......)))))))))))((((((........)))))).))))))).)))).... ( -30.07)
>DroYak_CAF1 61710 111 - 1
UUUUUAUUUGGUCAUAAAACGUCUACUUUUUC---UGUGCACUGUUCCAUAAAAG-UAGUA---AACUGGGGGACAUGCACUGCCAUUAUGAUUUAUGGCAAAGCAAAAUGCACAAAU
................................---((((((.((((((.....((-(....---.)))..))))))(((..((((((........))))))..)))...))))))... ( -27.00)
>DroAna_CAF1 58858 100 - 1
-----------UUGGAA----UCUACUUUCUCU-CAGUGUUUAUUUCCUUAAAAGAUAGAAUAGAAGUAG--GGCAUGCACUGGCCUUAUGAUUUAUGGCAAAACAAAAUGCACAAAU
-----------(((...----((((((((.(((-.....((((......))))....)))...)))))))--)((((......(((.((.....)).)))........)))).))).. ( -16.84)
>consensus
UUUUUCGU__GUUGUAAAACGACUACUUUUGC___UGUGCACAGUUCCAUAAAAG_UAGUA___AAGUGGGGGACUUGCACUGCCAUUAUGAUUUAUGGCAAAGCAAAAUGCACAAAU
....................................(((((.((((((......................))))))(((..((((((........))))))..)))...))))).... (-15.63 = -16.51 +   0.88)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:11 2006