Locus 5498

Sequence ID 3R_DroMel_CAF1
Location 14,467,968 – 14,468,109
Length 141
Max. P 0.989459
window8975 window8976 window8977

overview

Window 5

Location 14,467,968 – 14,468,072
Length 104
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.23
Mean single sequence MFE -27.83
Consensus MFE -25.44
Energy contribution -24.33
Covariance contribution -1.10
Combinations/Pair 1.16
Mean z-score -0.61
Structure conservation index 0.91
SVM decision value 0.12
SVM RNA-class probability 0.593221
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14467968 104 + 27905053
----------------AAUGUAUAAACACCUAAUUUUGGUAAGUGUUUUGGCCAAGAGCAUCUUGCCUGCAAGCCGUUCUGCAGUUGACCUUGCGUUGCAGGUCUUUGGCUGUCACAGAA
----------------...........(((.......)))..(((...(((((((((((..((((....))))..)))))......(((((.((...)))))))..)))))).))).... ( -28.50)
>DroSim_CAF1 25862 120 + 1
UUCGAUAUGUAAUGAAAAUGUAUAAACACCCAAUUUUGGUGAGUGUUUUGGCCAAGAGCAUCUUGCCUGCAAGCCGUUCUGCAGUUGACCUUGCGUUGCAGGUCUUUGGCUGUCACAGAA
.((.......................((((.......)))).(((...(((((((((((..((((....))))..)))))......(((((.((...)))))))..)))))).))).)). ( -30.70)
>DroYak_CAF1 28222 109 + 1
-----------AUGAAAAUGUAUCAACACCUUAUUUUUCUGAGUGUUUUAGCCAAGAGCAUCUUGCCUGCAAACCGUUCUGCAGCUGACUUUGUUUUGCAAGUCCUUGGCUGCCACAGAA
-----------.......(((...(((((.(((......)))))))).((((((((.((.....))(((((........)))))..(((((.(.....))))))))))))))..)))... ( -24.30)
>consensus
___________AUGAAAAUGUAUAAACACCUAAUUUUGGUGAGUGUUUUGGCCAAGAGCAUCUUGCCUGCAAGCCGUUCUGCAGUUGACCUUGCGUUGCAGGUCUUUGGCUGUCACAGAA
..........................................(((...((((((((.((.....))(((((........)))))..(((((.((...))))))))))))))).))).... (-25.44 = -24.33 +  -1.10)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,467,968 – 14,468,072
Length 104
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.23
Mean single sequence MFE -31.73
Consensus MFE -28.40
Energy contribution -28.73
Covariance contribution 0.34
Combinations/Pair 1.06
Mean z-score -2.47
Structure conservation index 0.89
SVM decision value 2.17
SVM RNA-class probability 0.989459
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14467968 104 - 27905053
UUCUGUGACAGCCAAAGACCUGCAACGCAAGGUCAACUGCAGAACGGCUUGCAGGCAAGAUGCUCUUGGCCAAAACACUUACCAAAAUUAGGUGUUUAUACAUU----------------
...((((...(((((.(((((((...)).)))))..((((((......))))))((.....))..)))))..(((((((((.......))))))))).))))..---------------- ( -30.60)
>DroSim_CAF1 25862 120 - 1
UUCUGUGACAGCCAAAGACCUGCAACGCAAGGUCAACUGCAGAACGGCUUGCAGGCAAGAUGCUCUUGGCCAAAACACUCACCAAAAUUGGGUGUUUAUACAUUUUCAUUACAUAUCGAA
...(((((..(((((.(((((((...)).)))))..((((((......))))))((.....))..)))))..(((((((((.......)))))))))...........)))))....... ( -33.30)
>DroYak_CAF1 28222 109 - 1
UUCUGUGGCAGCCAAGGACUUGCAAAACAAAGUCAGCUGCAGAACGGUUUGCAGGCAAGAUGCUCUUGGCUAAAACACUCAGAAAAAUAAGGUGUUGAUACAUUUUCAU-----------
(((((.((((((....(((((........))))).)))))......((((..((.((((.....)))).)).)))).).)))))....(((((((....)))))))...----------- ( -31.30)
>consensus
UUCUGUGACAGCCAAAGACCUGCAACGCAAGGUCAACUGCAGAACGGCUUGCAGGCAAGAUGCUCUUGGCCAAAACACUCACCAAAAUUAGGUGUUUAUACAUUUUCAU___________
...((((...(((((.(((((........)))))..((((((......))))))((.....))..)))))..(((((((((.......))))))))).)))).................. (-28.40 = -28.73 +   0.34)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,467,992 – 14,468,109
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.83
Mean single sequence MFE -38.00
Consensus MFE -34.33
Energy contribution -33.67
Covariance contribution -0.66
Combinations/Pair 1.06
Mean z-score -2.55
Structure conservation index 0.90
SVM decision value 1.42
SVM RNA-class probability 0.952342
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14467992 117 - 27905053
CUGGCUUGCCAGAAGAAGCC---UCUUCGACCAAGUCACAUUCUGUGACAGCCAAAGACCUGCAACGCAAGGUCAACUGCAGAACGGCUUGCAGGCAAGAUGCUCUUGGCCAAAACACUU
((((....))))((((.((.---((((.......(((((.....))))).(((...(((((((...)).)))))...(((((......)))))))))))).))))))............. ( -37.20)
>DroSim_CAF1 25902 117 - 1
---GUUUGCCAGAAGAAGCCUCCUCUUCGACCAAGUCACAUUCUGUGACAGCCAAAGACCUGCAACGCAAGGUCAACUGCAGAACGGCUUGCAGGCAAGAUGCUCUUGGCCAAAACACUC
---(((((((((((((.......)))))((.((.(((((.....))))).(((...(((((((...)).)))))...(((((......))))))))....)).)).))))..)))).... ( -36.80)
>DroYak_CAF1 28251 114 - 1
---GUGUGCCAGAAGAAGCC---UCUUCGACCAAGUCACAUUCUGUGGCAGCCAAGGACUUGCAAAACAAAGUCAGCUGCAGAACGGUUUGCAGGCAAGAUGCUCUUGGCUAAAACACUC
---(((((((((((((....---)))))(((...)))........))))((((((((((((........)))))..(((((((....)))))))((.....)).)))))))...)))).. ( -40.00)
>consensus
___GUUUGCCAGAAGAAGCC___UCUUCGACCAAGUCACAUUCUGUGACAGCCAAAGACCUGCAACGCAAGGUCAACUGCAGAACGGCUUGCAGGCAAGAUGCUCUUGGCCAAAACACUC
.......(((((((((.......)))))((.((.(((((.....))))).(((...(((((........)))))...(((((......))))))))....)).)).)))).......... (-34.33 = -33.67 +  -0.66)

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 11:56:42 2006