Locus 1182

Sequence ID X_DroMel_CAF1
Location 3,521,214 – 3,521,459
Length 245
Max. P 0.925304
window1892 window1893 window1894 window1895

overview

Window 2

Location 3,521,214 – 3,521,319
Length 105
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 79.52
Mean single sequence MFE -24.03
Consensus MFE -14.94
Energy contribution -16.28
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.34
Structure conservation index 0.62
SVM decision value 1.17
SVM RNA-class probability 0.925304
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3521214 105 + 22224390
UCCGAUCAGUAAGUAAAUAAGUUUUGAACUAGGUUUGGGUAG----------UUGAUUUAAUUAGUCACCUUAAACAGUUCAAACAGUAUGAAAGCCUAGUAUAUACAUUUAUAU
............((((((..((((.(((((..((((((((..----------(((((...)))))..))).)))))))))))))).(((((...........))))))))))).. ( -17.50)
>DroSec_CAF1 29572 102 + 1
UCCGAUCAGUAAGUACAUACAUUUUGAACUGGGGUUGGGUAGCUUAUCAUAUUUGAUUUAAUUAGUUACCUUAAACAGUUCAAACAGU-------------GCAUACAUAUAACU
........(((.((((......(((((((((.....((((((((.((((....))))......))))))))....)))))))))..))-------------)).)))........ ( -27.30)
>DroSim_CAF1 30800 102 + 1
UCCGAUCAGUAAGUACAUACAUUUUGAACUGGGGUUGGGUAGCUUAUCAUAUUUGAUUUAAUUAGUUACCUUAAACAGUUCAAACAGU-------------GCAUACAUUUAACU
........(((.((((......(((((((((.....((((((((.((((....))))......))))))))....)))))))))..))-------------)).)))........ ( -27.30)
>consensus
UCCGAUCAGUAAGUACAUACAUUUUGAACUGGGGUUGGGUAGCUUAUCAUAUUUGAUUUAAUUAGUUACCUUAAACAGUUCAAACAGU_____________GCAUACAUUUAACU
......................(((((((((.....((((((((...................))))))))....)))))))))............................... (-14.94 = -16.28 +   1.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,521,279 – 3,521,398
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 79.94
Mean single sequence MFE -25.78
Consensus MFE -20.46
Energy contribution -20.53
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -1.62
Structure conservation index 0.79
SVM decision value 0.43
SVM RNA-class probability 0.733492
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3521279 119 - 22224390
CGUCGCUGACGUCAGCGGCGUAAUAAAGCAAUA-AAUUGCAAUGUUAACUGAAGGGAUUAAGACGGAAACCAUUAAUGUAAUAUAAAUGUAUAUACUAGGCUUUCAUACUGUUUGAACUG
((((((((....))))))))(((((..((((..-..))))..)))))..((((((.(((((...(....)..)))))(((((((....)))).)))....)))))).............. ( -26.10)
>DroSec_CAF1 29647 106 - 1
CGUCGCUGACGUCAGCGGCGUAACAGAGCAAUA-AAUUGCAAUGUUAACUCAAGGGAUUAAGACGGAAACCAUUAAUGUAAGUUAUAUGUAUGC-------------ACUGUUUGAACUG
((((((((....)))))))).(((((.(((...-...((((....(((((....(.(((((...(....)..))))).).)))))..)))))))-------------.)))))....... ( -27.60)
>DroSim_CAF1 30875 106 - 1
CGUCGCUGACGUCAGCGGCGUAACAGAGCAAUA-AAUUGCAAUGUUAACUCAAGGGAUUAAGACGGAAACCAUUAAUGUAAGUUAAAUGUAUGC-------------ACUGUUUGAACUG
((((((((....)))))))).(((((.(((...-...((((...((((((....(.(((((...(....)..))))).).)))))).)))))))-------------.)))))....... ( -29.20)
>DroYak_CAF1 28543 97 - 1
CGUCGCUGACGUCAGCGGCGUAACAAAGCAAAAAAAAUGCAAUGUUAACUGAAGGAAUUAAGACGGAAACCAUG--UGUAAAGG--------GG-------------AUUAUUACAAAUC
((((((((....))))))))(((((..(((.......)))..))))).................(....)....--(((((...--------..-------------....))))).... ( -20.20)
>consensus
CGUCGCUGACGUCAGCGGCGUAACAAAGCAAUA_AAUUGCAAUGUUAACUCAAGGGAUUAAGACGGAAACCAUUAAUGUAAGUUAAAUGUAUGC_____________ACUGUUUGAACUG
((((((((....))))))))(((((..((((.....))))..)))))......((..((......))..))................................................. (-20.46 = -20.53 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,521,319 – 3,521,420
Length 101
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.58
Mean single sequence MFE -32.77
Consensus MFE -26.46
Energy contribution -26.78
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -1.88
Structure conservation index 0.81
SVM decision value 0.77
SVM RNA-class probability 0.844981
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3521319 101 - 22224390
CCUCUG------------------CUUGCAGCGCUGCCGGCGUCGCUGACGUCAGCGGCGUAAUAAAGCAAUA-AAUUGCAAUGUUAACUGAAGGGAUUAAGACGGAAACCAUUAAUGUA
((((..------------------...((((((((((.((((((...)))))).)))))))......((((..-..))))..))).....).))).(((((...(....)..)))))... ( -30.40)
>DroSec_CAF1 29674 101 - 1
CCUCUG------------------CUUGCAGCGCUGCCGGCGUCGCUGACGUCAGCGGCGUAACAGAGCAAUA-AAUUGCAAUGUUAACUCAAGGGAUUAAGACGGAAACCAUUAAUGUA
((..((------------------......(((((((.((((((...)))))).)))))))((((..((((..-..))))..))))....))..))(((((...(....)..)))))... ( -32.40)
>DroSim_CAF1 30902 101 - 1
CCUCUG------------------CUUGCAGCGCUGCCGGCGUCGCUGACGUCAGCGGCGUAACAGAGCAAUA-AAUUGCAAUGUUAACUCAAGGGAUUAAGACGGAAACCAUUAAUGUA
((..((------------------......(((((((.((((((...)))))).)))))))((((..((((..-..))))..))))....))..))(((((...(....)..)))))... ( -32.40)
>DroYak_CAF1 28562 118 - 1
CCUCUGAUAACGUCGACUGCGACGCUUGCAGCACUGCCGGCGUCGCUGACGUCAGCGGCGUAACAAAGCAAAAAAAAUGCAAUGUUAACUGAAGGAAUUAAGACGGAAACCAUG--UGUA
(((((((...(((((...((((((((.(((....))).)))))))))))))))))(((..(((((..(((.......)))..))))).))).))).........(....)....--.... ( -35.90)
>consensus
CCUCUG__________________CUUGCAGCGCUGCCGGCGUCGCUGACGUCAGCGGCGUAACAAAGCAAUA_AAUUGCAAUGUUAACUCAAGGGAUUAAGACGGAAACCAUUAAUGUA
(((((.........................(((((((.((((((...)))))).)))))))((((..((((.....))))..))))..............))).)).............. (-26.46 = -26.78 +   0.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,521,359 – 3,521,459
Length 100
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.42
Mean single sequence MFE -32.52
Consensus MFE -23.45
Energy contribution -24.45
Covariance contribution 1.00
Combinations/Pair 1.04
Mean z-score -1.57
Structure conservation index 0.72
SVM decision value 0.10
SVM RNA-class probability 0.584041
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3521359 100 - 22224390
GUACAAAACCG-CCCCAUAAAAUGAGACCCUGUUACAACGCCUCUG------------------CUUGCAGCGCUGCCGGCGUCGCUGACGUCAGCGGCGUAAUAAAGCAAUA-AAUUGC
...........-...........(((...............)))((------------------(((...(((((((.((((((...)))))).)))))))....)))))...-...... ( -26.26)
>DroSec_CAF1 29714 101 - 1
UUCCUAGACCCCCCCCAUAAAAUGAGACUGUGUUACAACGCCUCUG------------------CUUGCAGCGCUGCCGGCGUCGCUGACGUCAGCGGCGUAACAGAGCAAUA-AAUUGC
.........................(.((.((((((.........(------------------((.(((....))).)))(((((((....))))))))))))).)))....-...... ( -29.80)
>DroSim_CAF1 30942 100 - 1
UUCCUAGACCC-CCCCAUAAAAUGAGACUCUGUUACAACGCCUCUG------------------CUUGCAGCGCUGCCGGCGUCGCUGACGUCAGCGGCGUAACAGAGCAAUA-AAUUGC
...........-.............(.(((((((((.........(------------------((.(((....))).)))(((((((....)))))))))))))))))....-...... ( -33.90)
>DroYak_CAF1 28600 117 - 1
UUCCUGAGC---CCCCAUAAAGAGAGACUGUGUUACAACGCCUCUGAUAACGUCGACUGCGACGCUUGCAGCACUGCCGGCGUCGCUGACGUCAGCGGCGUAACAAAGCAAAAAAAAUGC
.........---.............(.((.((((...(((((.((((...(((((...((((((((.(((....))).))))))))))))))))).))))))))).)))........... ( -40.10)
>consensus
UUCCUAAACCC_CCCCAUAAAAUGAGACUCUGUUACAACGCCUCUG__________________CUUGCAGCGCUGCCGGCGUCGCUGACGUCAGCGGCGUAACAAAGCAAUA_AAUUGC
.........................(.((.((((((...(((........(((((....)))))...(((....))).)))(((((((....))))))))))))).)))........... (-23.45 = -24.45 +   1.00)

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 10:03:14 2006