Locus 5122

Sequence ID 2R_DroMel_CAF1
Location 16,657,394 – 16,657,569
Length 175
Max. P 0.724687
window8189 window8190 window8191

overview

Window 9

Location 16,657,394 – 16,657,514
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.42
Mean single sequence MFE -41.50
Consensus MFE -24.63
Energy contribution -26.05
Covariance contribution 1.42
Combinations/Pair 1.32
Mean z-score -1.80
Structure conservation index 0.59
SVM decision value 0.38
SVM RNA-class probability 0.711487
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16657394 120 - 20766785
CAAGGAGGAUGAGGUCAUCGAUCUCAAGGCAAAGAUUGCCCAACUUUUGGCCGUGAUGCCAGACAACUUGUGCAUGAACACUGGCCCACAUGGGCCGUCGAGCAGCAUUCUGCGCAUGAA
((((..(..(((((((...))))))).((((.....)))).....((((((......)))))))..))))..((((......(((((....))))).....((((....)))).)))).. ( -39.30)
>DroVir_CAF1 6863 120 - 1
CAAGGAGGAUGAGGUCAUUGAUCUCAAGGCCAAGAUAGCACAGCUGCUGGCUGUUAUGCCGGAUACACUGUGUCUGAACACGGGAGCACAUGGUCCCGGCGGAAGUAUGCUGCGCAUGAA
......((.(((((((...)))))))...))......((.((((((((..((((.....(((((((...)))))))....(((((.(....).))))))))).)))).)))).))..... ( -43.10)
>DroGri_CAF1 7271 120 - 1
CCAGGAUGAUGAGGUCAUUGAUCUCAAGGCCAAGAUAGCACAGUUGCUGGCAGUUAUGCCAGACUCAAUGUGCCUAAAUACAGGACCACAUGGUCCAGGCGGUAGCAUGCUGCGCAUGAA
.(((.(((.(((((((...)))))))..(((......(((((...(((((((....)))))).)....))))).........(((((....))))).))).....))).)))........ ( -44.90)
>DroWil_CAF1 6317 111 - 1
UAAGGAGGAUGAGGUCAUUGAUCUCAAGGCCAAAAUUGCCCAAUUGUUGGCUGUAAUGCCCGACAGCAUGUGCAUGAACACCGGUUC---------AGCUAGUAGCAUGUUGCGCAUGAA
...(..((.(((((((...))))))).((((((((((....)))).)))))).......))..)..(((((((((((((....))))---------)((.....))....)))))))).. ( -35.50)
>DroMoj_CAF1 6714 117 - 1
CAAGGAGGAUGAGGUCAUUGAUCUCAAGGCCAAGAUAGCCCAGCUGCUGGCUGUAAUGCCGGACACGCUGUGCCUAAACACGGGGCCGCAUGGU---AGCGGAAGCAUGCUGCGCAUGAA
.........(((((((...))))))).((((......((.(((((((((((......))))).)).)))).))((......)))))).((((((---((((......)))))).)))).. ( -44.70)
>DroAna_CAF1 5994 120 - 1
CAAGGAGGAAGAGGUCGUUGAUCUCAAGGCCAAGAUAGCGCAGCUACUGGCUGUAAUGCCGGACACACUGUGCAUGAACACGGGACCCCAUGGCCCGACCAGCAGCAUUCUGCGCAUGAA
............((((((((....)))(((((.....((((((...(((((......))))).....))))))........((....)).)))))))))).((((....))))....... ( -41.50)
>consensus
CAAGGAGGAUGAGGUCAUUGAUCUCAAGGCCAAGAUAGCCCAGCUGCUGGCUGUAAUGCCGGACACACUGUGCAUGAACACGGGACCACAUGGUCCAGCCAGAAGCAUGCUGCGCAUGAA
...((....(((((((...)))))))...))......((.((((..(((((......))))).......((((.((......(((((....)))))......)))))))))).))..... (-24.63 = -26.05 +   1.42)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,657,434 – 16,657,543
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.66
Mean single sequence MFE -35.60
Consensus MFE -20.87
Energy contribution -20.57
Covariance contribution -0.30
Combinations/Pair 1.26
Mean z-score -1.57
Structure conservation index 0.59
SVM decision value 0.41
SVM RNA-class probability 0.724687
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16657434 109 - 20766785
-----------AUAUCCACUCCCGCAGACCAUCGUCGCUCCAAGGAGGAUGAGGUCAUCGAUCUCAAGGCAAAGAUUGCCCAACUUUUGGCCGUGAUGCCAGACAACUUGUGCAUGAACA
-----------............(((((((.(((((.(((....))))))))))))...........((((.....)))).....((((((......)))))).......)))....... ( -30.80)
>DroVir_CAF1 6903 109 - 1
-----------UAUUUCUUGCUUCCAGGUCAUCGUCGGUCCAAGGAGGAUGAGGUCAUUGAUCUCAAGGCCAAGAUAGCACAGCUGCUGGCUGUUAUGCCGGAUACACUGUGUCUGAACA
-----------....((((((((..((((((.(.(((.(((.....)))))).)....))))))..))).)))))((((((((...(((((......))))).....))))).))).... ( -35.10)
>DroPse_CAF1 8189 119 - 1
CUAAUAAC-GAUUACGCUUUCAUUCAGACCAUCGUCGCUCCAAGGAGGAUGAGGUCAUCGAUCUCAAGGCCAAGAUUGCCCAACUUCUGGCCGUGAUGCCAGACACAAUGUGCAUGAACA
........-.....(((.........((((.(((((.(((....))))))))))))...........(((((.((..........))))))))))((((((.......)).))))..... ( -32.70)
>DroWil_CAF1 6348 109 - 1
-----------UUUUUCUUUUUUUAAGGUAAUCGCCGCUCUAAGGAGGAUGAGGUCAUUGAUCUCAAGGCCAAAAUUGCCCAAUUGUUGGCUGUAAUGCCCGACAGCAUGUGCAUGAACA
-----------...............((((((.(((.(((....)))..(((((((...))))))).)))....))))))....(((((((......).))))))((....))....... ( -27.30)
>DroMoj_CAF1 6751 109 - 1
-----------CUGUUUUGGCUUGCAGGUCAACGUCGGUCCAAGGAGGAUGAGGUCAUUGAUCUCAAGGCCAAGAUAGCCCAGCUGCUGGCUGUAAUGCCGGACACGCUGUGCCUAAACA
-----------.(((((((((((..((((((((.(((.(((.....)))))).))...))))))..)))))))))))((.(((((((((((......))))).)).)))).))....... ( -44.20)
>DroAna_CAF1 6034 116 - 1
CUAAUGGUUCCUUGUC----CUGGCAGACCAUCGUCGCUCCAAGGAGGAAGAGGUCGUUGAUCUCAAGGCCAAGAUAGCGCAGCUACUGGCUGUAAUGCCGGACACACUGUGCAUGAACA
......((((..((((----.((((.((((.((.((.(((....))))).)))))).(((....))).)))).))))((((((...(((((......))))).....))))))..)))). ( -43.50)
>consensus
___________UUAUUCUUUCUUGCAGACCAUCGUCGCUCCAAGGAGGAUGAGGUCAUUGAUCUCAAGGCCAAGAUAGCCCAACUGCUGGCUGUAAUGCCGGACACACUGUGCAUGAACA
.................................(((..(((.....)))(((((((...))))))).))).......((.(((...(((((......))))).....))).))....... (-20.87 = -20.57 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,657,474 – 16,657,569
Length 95
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 77.52
Mean single sequence MFE -24.93
Consensus MFE -17.49
Energy contribution -17.30
Covariance contribution -0.19
Combinations/Pair 1.17
Mean z-score -1.14
Structure conservation index 0.70
SVM decision value 0.26
SVM RNA-class probability 0.658531
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16657474 95 - 20766785
UGUUUUAAUG--U-UGAUAGCUAGUUGAU----------AUAUCCACUCCCGCAGACCAUCGUCGCUCCAAGGAGGAUGAGGUCAUCGAUCUCAAGGCAAAGAUUGCC
((((((.(.(--(-((((.((.(((.((.----------...)).)))...)).((((.(((((.(((....)))))))))))))))))).).))))))......... ( -26.20)
>DroVir_CAF1 6943 92 - 1
--UCAGAAUGAUUGUAAUAAACA----AC----------UAUUUCUUGCUUCCAGGUCAUCGUCGGUCCAAGGAGGAUGAGGUCAUUGAUCUCAAGGCCAAGAUAGCA
--...(((((.((((.....)))----).----------)))))..((((((..((((.......((((.....))))((((((...))))))..))))..)).)))) ( -22.20)
>DroSec_CAF1 5983 105 - 1
CAUUUAAAUG--U-UGAUAGCUAGUUGAUUUCUAAUGCAAUAUCCACUCACGCAGACCAUCGUCGCUCCAAGGAGGAUGAGGUCAUCGAUCUCAAGGCAAAGAUUGCC
.........(--(-((((.((.(((.(((............))).)))...)).((((.(((((.(((....)))))))))))))))))).....((((.....)))) ( -26.70)
>DroSim_CAF1 6008 105 - 1
AGUUUAAAUG--U-UGAUAGCUAGUUGAUUUCUAAUGCAAUAUCCACUCACGCAGACCAUCGUCGCUCCAAGGAGGAUGAGGUCAUCGAUCUCAAGGCAAAGAUUGCC
.........(--(-((((.((.(((.(((............))).)))...)).((((.(((((.(((....)))))))))))))))))).....((((.....)))) ( -26.70)
>DroEre_CAF1 6053 102 - 1
-GU-UUAAUG--U-A-AAAGCUGGUUGAUUUCUAAUUCAUUAUUCACUUCCUCAGACCAUCGUCGCUCCAAGGAGGAUGAGGUCAUUGAUCUCAAGGCAAAGAUUGCC
-..-....((--.-.-.(((.(((.(((........)))....))))))...))((((.(((((.(((....)))))))))))).(((....)))((((.....)))) ( -23.20)
>DroYak_CAF1 6034 101 - 1
-GU-UUAAUG--U-A-AAAGA-AGUUGAUUUUAAAUUCAUUAUUUACUUCCUCAGACCAUCGUCGCUCCAAGGAGGAUGAGGUCAUUGAUCUCAAGGCAAAGAUUGCC
-..-(((((.--.-.-...((-(((.(((............))).)))))....((((.(((((.(((....)))))))))))))))))......((((.....)))) ( -24.60)
>consensus
_GUUUUAAUG__U_UGAUAGCUAGUUGAUUUCUAAU_CAAUAUCCACUCCCGCAGACCAUCGUCGCUCCAAGGAGGAUGAGGUCAUCGAUCUCAAGGCAAAGAUUGCC
......................................................((((.(((((.(((....))))))))))))..((((((........)))))).. (-17.49 = -17.30 +  -0.19)

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 11:37:06 2006