Locus 3997

Sequence ID 2L_DroMel_CAF1
Location 11,630,192 – 11,630,372
Length 180
Max. P 0.961327
window6303 window6304 window6305

overview

Window 3

Location 11,630,192 – 11,630,303
Length 111
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 82.80
Mean single sequence MFE -29.08
Consensus MFE -16.86
Energy contribution -17.29
Covariance contribution 0.42
Combinations/Pair 1.23
Mean z-score -2.41
Structure conservation index 0.58
SVM decision value 0.08
SVM RNA-class probability 0.572989
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11630192 111 + 22407834
AAUUAGAAUAAUUUGGCCAGCUGUUGCUACAACUCAGCUCCUCCUCCACCUCAGAUGCUG-----CUCCUUGGUCAUUCUGC-UGGUGAUUACACCAGGAUAUUUGCCAAAAUAUUU
.....(((((.(((((((((..((.((((.....((((..((..........))..))))-----.....)))).)).)))(-(((((....)))))).......)))))).))))) ( -26.20)
>DroPse_CAF1 78075 97 + 1
AAUUAGAAUAAUUUUGUCAGCUGCUGCUAGAGCCGAGGCCCC-------------UGCUG-----CUCUGUGGCUG--GUGAUGGGUGAUGGGACUUAAAUAUUUGCCAAAAUAUUU
............((..(((.(.((..(.(((((.(((....)-------------).).)-----)))))..)).)--.)))..))...........((((((((....)))))))) ( -24.70)
>DroSec_CAF1 83523 111 + 1
AAUUAGAAUAAUUUGGCCAGCUGUUGCUACAACUCAGCUCCUCCUCCUCUUCAUAUGCUG-----CUCCUUGGCCAUUCUGC-UGGUGAUUACACCAGGAUAUUUGCCAAAAUAUUU
...(((((.....((((((((....)))......((((..................))))-----......))))))))))(-(((((....))))))(((((((....))))))). ( -27.37)
>DroSim_CAF1 87313 111 + 1
AAUUAGAAUAAUUUGGCCAGCUGUUGCUACAACUCAGCUCCUCCUCCUCUUCGGAUGCUG-----CUCGUUGGCCAUUCUGC-UGGUGAUUACACCAGGAUAUUUGCCAAAAUAUUU
...(((((.....((((((((.((((...)))).(((((((...........))).))))-----...)))))))))))))(-(((((....))))))(((((((....))))))). ( -34.60)
>DroEre_CAF1 113825 108 + 1
AAUUAGAAUAAUUUGGGCAGCUGUUGCUACAACACAGCUCCUCC---UCUUCAAAUGCUG-----CUCCUUGGCCAUUCUGC-UGGUGAUUACACCAGGAUAUUUGCCAAAAUAUUU
.....(((((....(((((((.((((........))))......---.........))))-----))).(((((.....(.(-(((((....)))))).).....)))))..))))) ( -27.09)
>DroYak_CAF1 86976 113 + 1
AAUUAGAAUAAUUUGGCCAGCUGUUGCUACAACUCAGCUCCUUC---UCUGCAGGUGCAGCUCAGCUCCUUGGCCAUUCUGC-UGGUGAUUACACCAGGAUAUUUGCCAAAAUAUUU
...(((((.....((((((((((..(((.((.(((((.......---.))).)).)).))).))))....)))))))))))(-(((((....))))))(((((((....))))))). ( -34.50)
>consensus
AAUUAGAAUAAUUUGGCCAGCUGUUGCUACAACUCAGCUCCUCC___UCUUCAGAUGCUG_____CUCCUUGGCCAUUCUGC_UGGUGAUUACACCAGGAUAUUUGCCAAAAUAUUU
...(((((.....((((((((....)))......((((..................))))...........))))))))))..(((((....)))))((((((((....)))))))) (-16.86 = -17.29 +   0.42)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,630,230 – 11,630,343
Length 113
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 91.02
Mean single sequence MFE -29.73
Consensus MFE -24.12
Energy contribution -25.16
Covariance contribution 1.04
Combinations/Pair 1.08
Mean z-score -1.43
Structure conservation index 0.81
SVM decision value 0.21
SVM RNA-class probability 0.633537
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11630230 113 - 22407834
CUAUUAACUUCUCGAGUUCACAGUCCAAAUUGUGACCAUUAAAUAUUUUGGCAAAUAUCCUGGUGUAAUCACCAGCAGAAUGACCAAGGAG-----CAGCAUCUGAGGUGGAGGAGGA
.......((((((..(.(((((((....))))))).)......(((((((.........((((((....)))))))))))))(((..(((.-----.....)))..))).)))))).. ( -29.90)
>DroSec_CAF1 83561 113 - 1
CUAUUUACUUCUCGAGUUCACAGUCCAAAGUGUGACCAUUAAAUAUUUUGGCAAAUAUCCUGGUGUAAUCACCAGCAGAAUGGCCAAGGAG-----CAGCAUAUGAAGAGGAGGAGGA
.......((((((..(.(((((.(....).))))).)........(((((((.......((((((....)))))).......)))))))..-----...........))))))..... ( -30.44)
>DroSim_CAF1 87351 113 - 1
CUAUUUACUUCUCGAGUUCACAGUCCAAAGUGUGACCAUUAAAUAUUUUGGCAAAUAUCCUGGUGUAAUCACCAGCAGAAUGGCCAACGAG-----CAGCAUCCGAAGAGGAGGAGGA
.......((.((((.(.(((((.(....).))))).)..........(((((.......((((((....)))))).......)))))))))-----.))..(((.....)))...... ( -29.14)
>DroEre_CAF1 113863 110 - 1
CUAUUUACUAUUUGAGUUCACAGUCCAAAGUGUGACCAUUAAAUAUUUUGGCAAAUAUCCUGGUGUAAUCACCAGCAGAAUGGCCAAGGAG-----CAGCAUUUGAAGA---GGAGGA
((.((((.(((((((..(((((.(....).)))))...)))))))(((((((.......((((((....)))))).......)))))))..-----.......)))).)---)..... ( -25.74)
>DroYak_CAF1 87014 115 - 1
CUAUUUACUUUUCGAGUUCACAGUCCAAAGUGUGACCAUUAAAUAUUUUGGCAAAUAUCCUGGUGUAAUCACCAGCAGAAUGGCCAAGGAGCUGAGCUGCACCUGCAGA---GAAGGA
.......((((((.((((((...(((..((((....)))).......(((((.......((((((....)))))).......))))))))..))))))((....)).))---)))).. ( -33.44)
>consensus
CUAUUUACUUCUCGAGUUCACAGUCCAAAGUGUGACCAUUAAAUAUUUUGGCAAAUAUCCUGGUGUAAUCACCAGCAGAAUGGCCAAGGAG_____CAGCAUCUGAAGAGGAGGAGGA
.......((((((..(.(((((.(....).))))).)........(((((((.......((((((....)))))).......))))))).....................)))))).. (-24.12 = -25.16 +   1.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,630,264 – 11,630,372
Length 108
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 94.72
Mean single sequence MFE -18.47
Consensus MFE -17.08
Energy contribution -16.92
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -1.50
Structure conservation index 0.92
SVM decision value 1.53
SVM RNA-class probability 0.961327
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11630264 108 - 22407834
AUUUAAUCAAUCCUCUUAGCCAUCCCAUCCUAUUAACUUCUCGAGUUCACAGUCCAAAUUGUGACCAUUAAAUAUUUUGGCAAAUAUCCUGGUGUAAUCACCAGCAGA
..................((((.............((((...))))(((((((....))))))).............)))).......((((((....)))))).... ( -19.70)
>DroSec_CAF1 83595 108 - 1
AUUUAAUCAAUCCUCUUAGCUAUCCCAUCCUAUUUACUUCUCGAGUUCACAGUCCAAAGUGUGACCAUUAAAUAUUUUGGCAAAUAUCCUGGUGUAAUCACCAGCAGA
..................(((..............................(.(((((((((.........)))))))))).........((((....)))))))... ( -16.60)
>DroSim_CAF1 87385 108 - 1
AUAUAAUCAAUCCUCUUAGCCAUCCCAUCCUAUUUACUUCUCGAGUUCACAGUCCAAAGUGUGACCAUUAAAUAUUUUGGCAAAUAUCCUGGUGUAAUCACCAGCAGA
..................((((.............((((...))))(((((.(....).))))).............)))).......((((((....)))))).... ( -18.00)
>DroEre_CAF1 113894 108 - 1
AUUCAAUCAAUCAUCGCAGCCAUCCUAUCCUAUUUACUAUUUGAGUUCACAGUCCAAAGUGUGACCAUUAAAUAUUUUGGCAAAUAUCCUGGUGUAAUCACCAGCAGA
...............((.((((...............(((((((..(((((.(....).)))))...)))))))...))))........(((((....)))))))... ( -20.27)
>DroYak_CAF1 87050 108 - 1
AUUUAAUCAAUCUUCUUGGCCAUCCCAUCCUAUUUACUUUUCGAGUUCACAGUCCAAAGUGUGACCAUUAAAUAUUUUGGCAAAUAUCCUGGUGUAAUCACCAGCAGA
..................((((.............((((...))))(((((.(....).))))).............)))).......((((((....)))))).... ( -17.80)
>consensus
AUUUAAUCAAUCCUCUUAGCCAUCCCAUCCUAUUUACUUCUCGAGUUCACAGUCCAAAGUGUGACCAUUAAAUAUUUUGGCAAAUAUCCUGGUGUAAUCACCAGCAGA
..................((((.............(((.....)))(((((.(....).))))).............)))).......((((((....)))))).... (-17.08 = -16.92 +  -0.16)

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 11:06:48 2006