Locus 4845

Sequence ID 3L_DroMel_CAF1
Location 13,585,010 – 13,585,207
Length 197
Max. P 0.998486
window7642 window7643 window7644

overview

Window 2

Location 13,585,010 – 13,585,129
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.26
Mean single sequence MFE -38.37
Consensus MFE -22.08
Energy contribution -25.87
Covariance contribution 3.79
Combinations/Pair 1.17
Mean z-score -2.20
Structure conservation index 0.58
SVM decision value 1.95
SVM RNA-class probability 0.983580
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13585010 119 + 23771897
AGCAGCAAACUUGUCUAAGCUUUCGACCAAGACAGAUAGAUAGGGUUGCGAAGA-GCCUUGGGGGCUCGGCGAAGAGCCGAGCUCUUGCAAUUACAAUUACGCAUAGACGGGGGAAAACA
.(((((...((((((((..((.((......)).)).))))))))))))).....-.(((((((((((((((.....))))))))))(((............)))....)))))....... ( -41.30)
>DroSim_CAF1 789 119 + 1
AGCAGCAAACUUGUCUAAGCUUUCGACCAAGACAGAUAGAUAGGGUUGCGAAGA-GCCUUGGGGGCUCGGCGAAGAGCCGAGCUCUUGCAAUUACAAUUACGCAUAGACGGGGGAAAACA
.(((((...((((((((..((.((......)).)).))))))))))))).....-.(((((((((((((((.....))))))))))(((............)))....)))))....... ( -41.30)
>DroAna_CAF1 27519 103 + 1
UGCAGCGAGCUUGCCUAAGCCUCCGUCCAAGACGGACAGG-------ACGAAAAGGCCUUAGGGAACGGGCGAA-------GCCUUCGCAAUUACAACUUCGUUGGGAAGGAAGGAA---
........((((((((((((((.(((((..........))-------)))...))).))))))...)))))...-------.(((((.((((.........)))).)))))......--- ( -32.50)
>consensus
AGCAGCAAACUUGUCUAAGCUUUCGACCAAGACAGAUAGAUAGGGUUGCGAAGA_GCCUUGGGGGCUCGGCGAAGAGCCGAGCUCUUGCAAUUACAAUUACGCAUAGACGGGGGAAAACA
.((.((((.(((((((...((.((......)).))..))))))).))))......((...(((((((((((.....)))))))))))))............))................. (-22.08 = -25.87 +   3.79)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,585,089 – 13,585,207
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 67.32
Mean single sequence MFE -30.53
Consensus MFE -17.55
Energy contribution -16.57
Covariance contribution -0.99
Combinations/Pair 1.29
Mean z-score -2.10
Structure conservation index 0.57
SVM decision value 3.12
SVM RNA-class probability 0.998486
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13585089 118 + 23771897
AGCUCUUGCAAUUACAAUUACGCAUAGACGGGGGAAAACAAAACAGCAUUGGAUGAUGAAGAGCUUGGCCAAGAGAAACGGCCAA-CGGUAAUUGUA-AUGGCCGACAAAGUUGGCAAAA
.((....)).(((((((((((((......(........).......((((....))))....))((((((.........))))))-..)))))))))-)).((((((...)))))).... ( -31.00)
>DroSim_CAF1 868 118 + 1
AGCUCUUGCAAUUACAAUUACGCAUAGACGGGGGAAAACAAAACAGCAGUGGAUGAUGAAGAGCUUGGCCAAGAGAAACGGCCAA-CGGUAAUUGUA-AUGGCCGACAAAGUUGGCAAAA
.((....)).(((((((((((.(((..((...(..........)....))..))).......(.((((((.........))))))-).)))))))))-)).((((((...)))))).... ( -30.30)
>DroAna_CAF1 27586 95 + 1
-GCCUUCGCAAUUACAACUUCGUUGGGAAGGAAGGAA----------------------GGUGGGUGGCCA-GAC-AAGGGCCACUUGCUAAUCGUAAAUGGUCAACAAUGUAGGUGAGG
-..((((((...((((.((((.....))))...((..----------------------((..(((((((.-...-...)))))))..))..))...............)))).)))))) ( -30.30)
>consensus
AGCUCUUGCAAUUACAAUUACGCAUAGACGGGGGAAAACAAAACAGCA_UGGAUGAUGAAGAGCUUGGCCAAGAGAAACGGCCAA_CGGUAAUUGUA_AUGGCCGACAAAGUUGGCAAAA
.......((((((((..(((....)))...................................(.((((((.........)))))).).)))))))).....((((((...)))))).... (-17.55 = -16.57 +  -0.99)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,585,089 – 13,585,207
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 67.32
Mean single sequence MFE -25.19
Consensus MFE -15.12
Energy contribution -15.13
Covariance contribution 0.01
Combinations/Pair 1.24
Mean z-score -1.73
Structure conservation index 0.60
SVM decision value 2.15
SVM RNA-class probability 0.989121
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13585089 118 - 23771897
UUUUGCCAACUUUGUCGGCCAU-UACAAUUACCG-UUGGCCGUUUCUCUUGGCCAAGCUCUUCAUCAUCCAAUGCUGUUUUGUUUUCCCCCGUCUAUGCGUAAUUGUAAUUGCAAGAGCU
....(((((......((((((.-...........-.))))))......)))))..(((((((((.((....((((.....((........)).....))))...))....)).))))))) ( -27.42)
>DroSim_CAF1 868 118 - 1
UUUUGCCAACUUUGUCGGCCAU-UACAAUUACCG-UUGGCCGUUUCUCUUGGCCAAGCUCUUCAUCAUCCACUGCUGUUUUGUUUUCCCCCGUCUAUGCGUAAUUGUAAUUGCAAGAGCU
.........((((....((.((-(((((((((((-(((((((.......))))))(((...............)))...................))).))))))))))).)).)))).. ( -27.16)
>DroAna_CAF1 27586 95 - 1
CCUCACCUACAUUGUUGACCAUUUACGAUUAGCAAGUGGCCCUU-GUC-UGGCCACCCACC----------------------UUCCUUCCUUCCCAACGAAGUUGUAAUUGCGAAGGC-
...........(((((((.(......).)))))))((((((...-...-.))))))...((----------------------(((....((((.....))))..((....))))))).- ( -21.00)
>consensus
UUUUGCCAACUUUGUCGGCCAU_UACAAUUACCG_UUGGCCGUUUCUCUUGGCCAAGCUCUUCAUCAUCCA_UGCUGUUUUGUUUUCCCCCGUCUAUGCGUAAUUGUAAUUGCAAGAGCU
((((((...(......)......(((((((((...(((((((.......)))))))...................................((....)))))))))))...))))))... (-15.12 = -15.13 +   0.01)

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 11:35:01 2006