Locus 3610

Sequence ID 3L_DroMel_CAF1
Location 10,633,653 – 10,633,745
Length 92
Max. P 0.849125
window5625 window5626

overview

Window 5

Location 10,633,653 – 10,633,745
Length 92
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 68.75
Mean single sequence MFE -23.50
Consensus MFE -12.99
Energy contribution -14.49
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.55
SVM decision value 0.78
SVM RNA-class probability 0.849125
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10633653 92 + 23771897
-AGCAGCUGUUGCACCUGUUGUC-------ACG-AAAAAAGGG-CCUAAUAAAUGG------GCUG---GUUACCCAAAAGGCAGCUGCAAAAGUUGCUAGGGAUAGUGGA
-(((((((.(((((...((((((-------...-.......((-((((.....)))------)))(---(....))....))))))))))).)))))))............ ( -30.20)
>DroSec_CAF1 515854 87 + 1
-----GCUGUUGCACCUGUUGUC-------ACG-AAUAAAGGG-UUUAAUAAAUGG------GCUGGUGGUUUCCCAAAAGGCAGCUGCAAAAGUUGCUAGGGAUAG----
-----(((((((.((((.((((.-------...-.)))).)))-).)))).....)------))........((((....(((((((.....))))))).))))...---- ( -21.00)
>DroSim_CAF1 517770 78 + 1
-AGCAGCUGUUGCACCUGUUGUC-------ACG-AAAAA-----------UAAUGG------GCUG---GUUCCCCAAAAGGCAGCUGCAAAAGUUGCUAGGGAUAG----
-(((((((.(((((.((((((((-------.((-.....-----------...)))------))((---(....)))...))))).))))).)))))))........---- ( -23.30)
>DroEre_CAF1 524148 89 + 1
-AGCAGCUGUUGCACCUGUUGUC-------ACG-AAACAAGGGACCUAAUUAAUGG------GCUG---GUUCCCCAAAGGGCAGCUGCUAAAGUUGCUAGGGACAG----
-(((((((...(((...((((((-------.(.-......((((((..........------...)---))))).....))))))))))...)))))))........---- ( -26.82)
>DroWil_CAF1 810004 97 + 1
AGACGGCUCUUGCACCUGUUAGCCAAACACACACAACAAAGGG-AUUAAUAAAUUUUCUUUAAAUG---G--CCUCGACCGGCAGCUGCAAAAG--GCAAAAGAU------
....(.((.(((((.(((((.................((((..-(.........)..))))....(---(--......))))))).))))).))--.).......------ ( -18.30)
>DroYak_CAF1 526484 72 + 1
-AGCAGCUGUUGCACCUGUUGUC-------ACG-AAAAA-------UAAUAAAGAA------AAUG-------------GGGCAGCUGCAAGAGUUGCUGGGGAUAG----
-(((((((.(((((...((((((-------...-.....-------..........------....-------------.))))))))))).)))))))........---- ( -21.40)
>consensus
_AGCAGCUGUUGCACCUGUUGUC_______ACG_AAAAAAGGG___UAAUAAAUGG______GCUG___GUUCCCCAAAAGGCAGCUGCAAAAGUUGCUAGGGAUAG____
.(((((((.(((((.(((((............................................................))))).))))).)))))))............ (-12.99 = -14.49 +   1.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,633,653 – 10,633,745
Length 92
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 68.75
Mean single sequence MFE -20.78
Consensus MFE -9.41
Energy contribution -10.67
Covariance contribution 1.25
Combinations/Pair 1.12
Mean z-score -1.57
Structure conservation index 0.45
SVM decision value 0.09
SVM RNA-class probability 0.578232
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10633653 92 - 23771897
UCCACUAUCCCUAGCAACUUUUGCAGCUGCCUUUUGGGUAAC---CAGC------CCAUUUAUUAGG-CCCUUUUUU-CGU-------GACAACAGGUGCAACAGCUGCU-
............((((.((.(((((.((((((..(((((...---..))------)))......)))-)........-.((-------....)))).))))).)).))))- ( -25.50)
>DroSec_CAF1 515854 87 - 1
----CUAUCCCUAGCAACUUUUGCAGCUGCCUUUUGGGAAACCACCAGC------CCAUUUAUUAAA-CCCUUUAUU-CGU-------GACAACAGGUGCAACAGC-----
----.............((.(((((.(((.((..(((....)))..)).------.(((..((....-......)).-.))-------)....))).))))).)).----- ( -15.20)
>DroSim_CAF1 517770 78 - 1
----CUAUCCCUAGCAACUUUUGCAGCUGCCUUUUGGGGAAC---CAGC------CCAUUA-----------UUUUU-CGU-------GACAACAGGUGCAACAGCUGCU-
----........((((.((.(((((.(((....((((....)---))).------.(((..-----------.....-.))-------)....))).))))).)).))))- ( -20.50)
>DroEre_CAF1 524148 89 - 1
----CUGUCCCUAGCAACUUUAGCAGCUGCCCUUUGGGGAAC---CAGC------CCAUUAAUUAGGUCCCUUGUUU-CGU-------GACAACAGGUGCAACAGCUGCU-
----.................((((((((....((((....)---))).------...........(..(((((((.-...-------))))..)))..)..))))))))- ( -23.80)
>DroWil_CAF1 810004 97 - 1
------AUCUUUUGC--CUUUUGCAGCUGCCGGUCGAGG--C---CAUUUAAAGAAAAUUUAUUAAU-CCCUUUGUUGUGUGUGUUUGGCUAACAGGUGCAAGAGCCGUCU
------.......(.--((((((((.(((..((((((((--(---(((.(((((.............-..)))))..))).)).)))))))..))).)))))))).).... ( -25.46)
>DroYak_CAF1 526484 72 - 1
----CUAUCCCCAGCAACUCUUGCAGCUGCCC-------------CAUU------UUCUUUAUUA-------UUUUU-CGU-------GACAACAGGUGCAACAGCUGCU-
----........((((.((.(((((.(((...-------------(((.------..........-------.....-.))-------)....))).))))).)).))))- ( -14.23)
>consensus
____CUAUCCCUAGCAACUUUUGCAGCUGCCUUUUGGGGAAC___CAGC______CCAUUUAUUA___CCCUUUUUU_CGU_______GACAACAGGUGCAACAGCUGCU_
.............(((.((.(((((.(((((.....)).........................................((........))..))).))))).)).))).. ( -9.41 = -10.67 +   1.25)

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 11:02:10 2006