Locus 10120

Sequence ID 3R_DroMel_CAF1
Location 27,140,302 – 27,140,501
Length 199
Max. P 0.946749
window16106 window16107 window16108

overview

Window 6

Location 27,140,302 – 27,140,403
Length 101
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 74.98
Mean single sequence MFE -17.28
Consensus MFE -3.39
Energy contribution -6.07
Covariance contribution 2.68
Combinations/Pair 1.18
Mean z-score -1.60
Structure conservation index 0.20
SVM decision value 0.17
SVM RNA-class probability 0.617379
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27140302 101 - 27905053
AUCAUAAGCUGACUUA-----CUUUCUUCUGGAAGAAAAGUAACAUUCUAGUUCUGCGAUCUAGUUCACUGAUGCUUUUCCUCGAGUGUACAGCAUCAACUUCUCA
.......((((...((-----(((((((....))).))))))((((((.((....((.(((.((....))))))).....)).)))))).))))............ ( -21.50)
>DroSec_CAF1 42112 101 - 1
AUCAUAAGCUGAGUUACAGAACUUUCUUCUGGA-----AGUAACAUUCUAGUUCUGCGAUCUAGUUCACUGAGGCUUUUCCUCGAGUGUACAGCAUCAACUUCUCA
.......((((.((..(((((((.......(((-----(......)))))))))))..))......((((((((.....)))).))))..))))............ ( -24.11)
>DroSim_CAF1 44462 97 - 1
AUCAUAAGCUGAGUUACAGAACUUUCUUU---------AGUAACAUUCUAGUUCUGCGAUCUAGUUCACUGAUGCUUUUCCCCGAGUGUACAGCAUCAACUUCUCA
......(((((..(..(((((((......---------...........)))))))..)..)))))...(((((((...............)))))))........ ( -19.09)
>DroEre_CAF1 42629 86 - 1
----------------CAGAACUUUCCUCUGAA---CAAGUAACAUUCUAGUUCUGCGCUCCAGUUUCC-CAUUCUUUUUCUCAAGUGUACAGCUUCAACUUCUCA
----------------((((.......))))..---.............((((.((((((..((.....-..........))..)))))).))))........... (  -9.46)
>DroYak_CAF1 44495 86 - 1
----------------CAGAACUUUCUUCUGUA---CAUGCAACAUUCUAGUUCUGCGCUCUAGUUUCC-CACUUUUUUCCCCAAGUGUACAGCAUCAACCUCUCA
----------------(((((((......(((.---...))).......))))))).(((...((....-(((((........))))).)))))............ ( -12.22)
>consensus
AUCAUAAGCUGA_UUACAGAACUUUCUUCUGGA____AAGUAACAUUCUAGUUCUGCGAUCUAGUUCACUGAUGCUUUUCCUCGAGUGUACAGCAUCAACUUCUCA
.......((((.....(((((((..........................)))))))...............((((((......)))))).))))............ ( -3.39 =  -6.07 +   2.68)

alignment

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secondary structure

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dotplot

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Window 7

Location 27,140,403 – 27,140,501
Length 98
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 78.64
Mean single sequence MFE -31.04
Consensus MFE -24.88
Energy contribution -25.00
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -1.83
Structure conservation index 0.80
SVM decision value 1.37
SVM RNA-class probability 0.946749
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27140403 98 + 27905053
GCAAUAGCUUAGUGGUUGCAACUUAAU----------------GUUGCCAAAAUCUGCACCUCCAGACUUUUAUGCCAGUGUAGUCUUAGCUACAUUCUGGCGCGGUAAGAAAA
(((((.((...)).))))).......(----------------.(((((((((((((......)))).))))..(((((((((((....))))))..)))))..))))).)... ( -27.20)
>DroSec_CAF1 42213 109 + 1
GCAAUA-----GUGGUUGCAACGUAACUGCAGCAAACACUUGAGUAGCCCAAAUCUGAUCCCCCAGACUUUUAUGCCAGUGUAGUCUUAGCUACAAGCUGGAGCGGCGAGAAAA
(((((.-----...)))))..(((..((.((((......(((.(((.......((((......))))......))))))((((((....)))))).)))).))..)))...... ( -28.52)
>DroSim_CAF1 44559 109 + 1
GCAACA-----GUGGUUGCAACGUAACUGAAGCAAACACUUGAGUUGCCCAAAUCUGCACCAGCAGACUUUUAUGCCAGUGUAGUCUUAGCUACAUGCUGGCGCGGCGAGAAAA
(((((.-----...)))))...((((((.(((......))).)))))).....(((((....)))))((((..((((((((((((....)))))..)))))))..).))).... ( -37.40)
>consensus
GCAAUA_____GUGGUUGCAACGUAACUG_AGCAAACACUUGAGUUGCCCAAAUCUGCACCACCAGACUUUUAUGCCAGUGUAGUCUUAGCUACAUGCUGGCGCGGCGAGAAAA
(((((.........))))).........................(((((....((((......))))......((((((((((((....))))))..)))))).)))))..... (-24.88 = -25.00 +   0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 27,140,403 – 27,140,501
Length 98
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 78.64
Mean single sequence MFE -32.00
Consensus MFE -21.09
Energy contribution -21.87
Covariance contribution 0.78
Combinations/Pair 1.04
Mean z-score -1.92
Structure conservation index 0.66
SVM decision value 0.85
SVM RNA-class probability 0.867172
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27140403 98 - 27905053
UUUUCUUACCGCGCCAGAAUGUAGCUAAGACUACACUGGCAUAAAAGUCUGGAGGUGCAGAUUUUGGCAAC----------------AUUAAGUUGCAACCACUAAGCUAUUGC
..........(((((((..(((((......)))))))))).....((..(((.(((((((....((....)----------------).....)))).))).)))..))...)) ( -29.10)
>DroSec_CAF1 42213 109 - 1
UUUUCUCGCCGCUCCAGCUUGUAGCUAAGACUACACUGGCAUAAAAGUCUGGGGGAUCAGAUUUGGGCUACUCAAGUGUUUGCUGCAGUUACGUUGCAACCAC-----UAUUGC
.......(((...((((..(((((......))))))))).....((((((((....)))))))).)))......((((.((((.((......)).)))).)))-----)..... ( -29.90)
>DroSim_CAF1 44559 109 - 1
UUUUCUCGCCGCGCCAGCAUGUAGCUAAGACUACACUGGCAUAAAAGUCUGCUGGUGCAGAUUUGGGCAACUCAAGUGUUUGCUUCAGUUACGUUGCAACCAC-----UGUUGC
.......(((..(((((..(((((......))))))))))....((((((((....)))))))).)))((((.((((....)))).)))).....(((((...-----.))))) ( -37.00)
>consensus
UUUUCUCGCCGCGCCAGCAUGUAGCUAAGACUACACUGGCAUAAAAGUCUGGAGGUGCAGAUUUGGGCAACUCAAGUGUUUGCU_CAGUUACGUUGCAACCAC_____UAUUGC
.......(((..(((((..(((((......))))))))))....((((((((....)))))))).)))...........................((((...........)))) (-21.09 = -21.87 +   0.78)

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 13:49:18 2006