Locus 1774

Sequence ID 2R_DroMel_CAF1
Location 6,632,423 – 6,632,521
Length 98
Max. P 0.961721
window2952 window2953

overview

Window 2

Location 6,632,423 – 6,632,521
Length 98
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 77.85
Mean single sequence MFE -23.50
Consensus MFE -11.77
Energy contribution -12.02
Covariance contribution 0.25
Combinations/Pair 1.14
Mean z-score -2.66
Structure conservation index 0.50
SVM decision value 1.53
SVM RNA-class probability 0.961721
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6632423 98 + 20766785
ACACUCUCUCGGCCAUU-UUGCGGAAGUUUCAACUCACCGCAAAAC-GCUCCAAAAUGAGCAGCCAAAUUGCGAGUUCCUUCCUUAAU-UG--CGCACUCGUA
..........(((..((-((((((.(((....)))..)))))))).-((((......)))).)))....(((((((.((.........-.)--.).))))))) ( -26.90)
>DroVir_CAF1 130290 87 + 1
UCUCCUUU----------UUGCGGGAGCUU-AAUUCACCGCAAAAU-CCUCG-AUAUGAGCAGCUAAAUUACGAGUUCCUUCCUUAAU-UG--CAAACAGGAA
..((((.(----------((((((((((((-........((.....-.(((.-....)))..))........))))))))........-.)--)))).)))). ( -18.19)
>DroGri_CAF1 131986 94 + 1
UCUCUCUUUCGA------UUGCGGAAAUUG-AACUCACCGCAAAAGCGCUCG-AAAUGAGCAGCGAAAUUAUGAGUUCCUUCCUUAAU-UGCACAAACAGCCA
.........(((------(((.((((...(-((((((..((....))((((.-....))))..........))))))).)))).))))-))............ ( -22.80)
>DroYak_CAF1 192429 98 + 1
ACACUCUCUCGGCCAUU-UUGCGGAAGUUUCAACUCACCGCAAAAC-GCUCCAAAAUGAGCAGCCAAAUUGCGAGUUCCUUCCUUAAU-UG--CGCACUCGUA
..........(((..((-((((((.(((....)))..)))))))).-((((......)))).)))....(((((((.((.........-.)--.).))))))) ( -26.90)
>DroMoj_CAF1 137209 87 + 1
UCACA-AU----------UUGCGGAAGCUU-AACUCACCGCAAAAU-GCUCA-AAAUGAGCAGCCAAAUUACGAAUUCCUUCCUUAAUUUG--CAAACUGGCG
.....-.(----------((((((.((...-..))..))))))).(-((((.-....)))))((((..((.((((((........))))))--.))..)))). ( -23.00)
>DroAna_CAF1 199004 96 + 1
--ACUCUCUCGGCCAUUUUUGCGGAAGCUUCAACUCACCGCAAAAC-GCUCG-AAAUGAGCAGCCAAAUUACGAGUUCCUUCCUUAAU-UG--CUCACUCGAA
--........(((...((((((((.((......))..)))))))).-((((.-....)))).)))......(((((............-..--...))))).. ( -23.23)
>consensus
UCACUCUCUCGG______UUGCGGAAGCUU_AACUCACCGCAAAAC_GCUCG_AAAUGAGCAGCCAAAUUACGAGUUCCUUCCUUAAU_UG__CAAACUCGAA
......................(((((....(((((...........((((......))))...........))))).))))).................... (-11.77 = -12.02 +   0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,632,423 – 6,632,521
Length 98
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 77.85
Mean single sequence MFE -28.54
Consensus MFE -15.93
Energy contribution -15.82
Covariance contribution -0.11
Combinations/Pair 1.25
Mean z-score -1.99
Structure conservation index 0.56
SVM decision value 0.72
SVM RNA-class probability 0.833439
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6632423 98 - 20766785
UACGAGUGCG--CA-AUUAAGGAAGGAACUCGCAAUUUGGCUGCUCAUUUUGGAGC-GUUUUGCGGUGAGUUGAAACUUCCGCAA-AAUGGCCGAGAGAGUGU
..(((((...--..-............)))))...(((((((((((......))))-(((((((((.((((....))))))))))-))))))))))....... ( -32.23)
>DroVir_CAF1 130290 87 - 1
UUCCUGUUUG--CA-AUUAAGGAAGGAACUCGUAAUUUAGCUGCUCAUAU-CGAGG-AUUUUGCGGUGAAUU-AAGCUCCCGCAA----------AAAGGAGA
(((((....(--((-.(((((..(.(....).)..))))).)))......-.....-.((((((((.((...-....))))))))----------))))))). ( -20.00)
>DroGri_CAF1 131986 94 - 1
UGGCUGUUUGUGCA-AUUAAGGAAGGAACUCAUAAUUUCGCUGCUCAUUU-CGAGCGCUUUUGCGGUGAGUU-CAAUUUCCGCAA------UCGAAAGAGAGA
..(((((....)))-.....((((.((((((((.........((((....-.))))((....)).)))))))-)...))))))..------((....)).... ( -27.80)
>DroYak_CAF1 192429 98 - 1
UACGAGUGCG--CA-AUUAAGGAAGGAACUCGCAAUUUGGCUGCUCAUUUUGGAGC-GUUUUGCGGUGAGUUGAAACUUCCGCAA-AAUGGCCGAGAGAGUGU
..(((((...--..-............)))))...(((((((((((......))))-(((((((((.((((....))))))))))-))))))))))....... ( -32.23)
>DroMoj_CAF1 137209 87 - 1
CGCCAGUUUG--CAAAUUAAGGAAGGAAUUCGUAAUUUGGCUGCUCAUUU-UGAGC-AUUUUGCGGUGAGUU-AAGCUUCCGCAA----------AU-UGUGA
.(((((.(((--(.((((........)))).)))).)))))(((((....-.))))-).(((((((.(((..-...)))))))))----------).-..... ( -27.80)
>DroAna_CAF1 199004 96 - 1
UUCGAGUGAG--CA-AUUAAGGAAGGAACUCGUAAUUUGGCUGCUCAUUU-CGAGC-GUUUUGCGGUGAGUUGAAGCUUCCGCAAAAAUGGCCGAGAGAGU--
(((...(((.--..-.))).)))....((((....(((((((((((....-.))))-.((((((((.((((....))))))))))))..))))))).))))-- ( -31.20)
>consensus
UACCAGUGUG__CA_AUUAAGGAAGGAACUCGUAAUUUGGCUGCUCAUUU_CGAGC_GUUUUGCGGUGAGUU_AAACUUCCGCAA______CCGAAAGAGUGA
....................(((((.(((((((.........((((......)))).........)))))))....)))))...................... (-15.93 = -15.82 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:51 2006