Locus 1838

Sequence ID 3L_DroMel_CAF1
Location 5,160,715 – 5,160,808
Length 93
Max. P 0.896356
window2868 window2869

overview

Window 8

Location 5,160,715 – 5,160,808
Length 93
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 78.38
Mean single sequence MFE -18.92
Consensus MFE -12.32
Energy contribution -12.48
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.44
Structure conservation index 0.65
SVM decision value 0.35
SVM RNA-class probability 0.698425
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5160715 93 + 23771897
AGAG--AGAGAAACAAUAUUAUAGAGCGAGAGGGCG--AUAGCCGUGGGG-AA-UUUUCAAUUGAAAACGAACGCGUAUAAAUGCGCCCAUAUGGAAAA
....--....................(....)(((.--...)))(((((.-..-(((((....)))))....(((((....))))))))))........ ( -18.60)
>DroVir_CAF1 31370 84 + 1
-GACUGACAGCAG--AC--GAG----GGAGAGGGCGCGGCA----AGCGG-AA-UUUUCAAUUGAAAACGAAUGCGUAUAAAUGCGCCCAUAUGGAAAA
-..(((....)))--..--...----.....(((((((...----.(((.-..-(((((....)))))....))).......))))))).......... ( -21.10)
>DroEre_CAF1 24492 94 + 1
AGAGUGAGAGAAACAAUAUUAUAGAGCGAGAGGGCG--AUAGCCGG-GGG-AA-UUUUCAAUUGAAAACGAACGCGUAUAAAUGCGCCCAUAUGGAAAA
..................(((((.........(((.--...)))((-(..-..-(((((....)))))....(((((....)))))))).))))).... ( -17.00)
>DroWil_CAF1 33438 92 + 1
----UGAGUGUGUGGGUGUGCGACAGCGAGCGAGCG--AGAGAAAGGCGG-AAUUUUUCAAUUGAAAAUGAAUGCGUAUAAAUGCGCCCAUAUGGAAAA
----.....((((((((((......((......)).--........(((.-...(((((....)))))....)))........))))))))))...... ( -23.10)
>DroYak_CAF1 24476 94 + 1
AGAGUGAGAGAAACAAUAUUAAAGAGCGAGAGGGCG--AUAGGCGG-GGG-AA-UUUUCAAUUGAAAACGAACGCGUAUAAAUGCGCCCAUAUGGAAAA
...............................(((((--....(((.-(..-..-(((((....)))))....).))).......))))).......... ( -17.70)
>DroAna_CAF1 23198 96 + 1
AGAGAGAGAGAGAGAAUAUAGAAGAGGGAGAGGGCU--AUAGCCGGGGGAAAA-UUUUCAAUUGAAAACGAACGCGUAUAAAUGCGCCCAUAUGGAAAA
................................(((.--...)))(((......-(((((....)))))....(((((....)))))))).......... ( -16.00)
>consensus
AGAGUGAGAGAAACAAUAUUAAAGAGCGAGAGGGCG__AUAGCCGGGGGG_AA_UUUUCAAUUGAAAACGAACGCGUAUAAAUGCGCCCAUAUGGAAAA
...............................((((...................(((((....))))).....((((....)))))))).......... (-12.32 = -12.48 +   0.17)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,160,715 – 5,160,808
Length 93
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 78.38
Mean single sequence MFE -14.12
Consensus MFE -10.76
Energy contribution -10.62
Covariance contribution -0.14
Combinations/Pair 1.09
Mean z-score -1.58
Structure conservation index 0.76
SVM decision value 0.99
SVM RNA-class probability 0.896356
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5160715 93 - 23771897
UUUUCCAUAUGGGCGCAUUUAUACGCGUUCGUUUUCAAUUGAAAA-UU-CCCCACGGCUAU--CGCCCUCUCGCUCUAUAAUAUUGUUUCUCU--CUCU
..........((((((........))))))((((((....)))))-).-......(((...--.)))..........................--.... ( -14.10)
>DroVir_CAF1 31370 84 - 1
UUUUCCAUAUGGGCGCAUUUAUACGCAUUCGUUUUCAAUUGAAAA-UU-CCGCU----UGCCGCGCCCUCUCC----CUC--GU--CUGCUGUCAGUC-
..........((((((........(((..(((((((....)))))-..-.))..----))).)))))).....----...--(.--(((....))).)- ( -16.40)
>DroEre_CAF1 24492 94 - 1
UUUUCCAUAUGGGCGCAUUUAUACGCGUUCGUUUUCAAUUGAAAA-UU-CCC-CCGGCUAU--CGCCCUCUCGCUCUAUAAUAUUGUUUCUCUCACUCU
..........((((((........))))))((((((....)))))-).-...-..(((...--.)))................................ ( -14.10)
>DroWil_CAF1 33438 92 - 1
UUUUCCAUAUGGGCGCAUUUAUACGCAUUCAUUUUCAAUUGAAAAAUU-CCGCCUUUCUCU--CGCUCGCUCGCUGUCGCACACCCACACACUCA----
..........((((((........)).....(((((....)))))...-..))))......--.((..((.....)).))...............---- ( -10.80)
>DroYak_CAF1 24476 94 - 1
UUUUCCAUAUGGGCGCAUUUAUACGCGUUCGUUUUCAAUUGAAAA-UU-CCC-CCGCCUAU--CGCCCUCUCGCUCUUUAAUAUUGUUUCUCUCACUCU
..........(((((.....(((.(((...((((((....)))))-).-...-.))).)))--)))))............................... ( -14.90)
>DroAna_CAF1 23198 96 - 1
UUUUCCAUAUGGGCGCAUUUAUACGCGUUCGUUUUCAAUUGAAAA-UUUUCCCCCGGCUAU--AGCCCUCUCCCUCUUCUAUAUUCUCUCUCUCUCUCU
..........((((((........))))))((((((....)))))-)........(((...--.)))................................ ( -14.40)
>consensus
UUUUCCAUAUGGGCGCAUUUAUACGCGUUCGUUUUCAAUUGAAAA_UU_CCCCCCGGCUAU__CGCCCUCUCGCUCUAUAAUAUUGUUUCUCUCACUCU
..........((((((........)).....(((((....)))))...................))))............................... (-10.76 = -10.62 +  -0.14)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:01 2006