Locus 5941

Sequence ID X_DroMel_CAF1
Location 15,333,485 – 15,333,630
Length 145
Max. P 0.976941
window9635 window9636 window9637

overview

Window 5

Location 15,333,485 – 15,333,590
Length 105
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 72.81
Mean single sequence MFE -30.18
Consensus MFE -9.89
Energy contribution -11.20
Covariance contribution 1.31
Combinations/Pair 1.15
Mean z-score -2.36
Structure conservation index 0.33
SVM decision value 0.96
SVM RNA-class probability 0.890557
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15333485 105 + 22224390
--CAGAAAGAGACGGGGCUAGUCGUAGAGUGACUUGGCUUAAACU----UGAGCUAACUUGAGUUAUUC-CUCGCUU------UUUUAGCCCCAUCUCGC--UUUUUUUUUCGUUUAAGC
--......((((.((((((((.((..(((((((((((((((....----)))))).....)))))))))-..))...------..)))))))).))))((--((............)))) ( -36.30)
>DroSec_CAF1 38168 85 + 1
--CAGAAAGAGACGGGGCUAGUCGCAGAGUGACUUGGCUUAAACU----UGAGCUAAGUUGAGUUAUUC-CUCGCUU------UU----------------------UUUUCGUUUAAGC
--.((((((((.((((((.....)).((((((((..(((((....----.....)))))..))))))))-)))))))------))----------------------))).......... ( -26.90)
>DroSim_CAF1 14849 84 + 1
--CAGAAAGAGACGGGGCUAGUCGCAGAGUGACUUGGCUUAAACU----UGAGCUAAGUUGAGUUAUUC-CUCGCUU------UU-----------------------UUUCGUUUAAGC
--..((((((((((((((.....)).((((((((..(((((....----.....)))))..))))))))-)))).))------))-----------------------))))........ ( -28.00)
>DroEre_CAF1 13897 104 + 1
--GCGAAAGAGACGGGGCUAGUCGCAGAGUGACUUGGCUUAAACU----UGAGCUAAGUUGAGUUAUUC-CUCGCUU------UUUUAGCCCCAUCUCGC---UUUUUUUUCGUUUAAGC
--((((((((((.((((((((....((((((((((((((((....----)))))))))))(((......-)))))))------).)))))))).))))..---.....))))))...... ( -39.41)
>DroYak_CAF1 14380 107 + 1
--GAGAGGGAGACGGAGCUAGUCGUAGAGUGACUUGGCUUUAACU----UGAGCUAACUUGAGUUAUUC-CUCGCCU------UUUUAGCCACAUCUCGCGCUUUUUUUUUCGUUUAAGC
--(((.(.((((.(..(((((.((..((((((((((((((.....----.))))).....)))))))))-..))...------..)))))..).)))).).)))................ ( -28.90)
>DroAna_CAF1 36312 111 + 1
GGCAGAAAGAGCCAGCGAUAGUC----AGAGACUUGGCUAGAAAAUAACUCAUCUCACCUGUGCUGUUAGCCCGCUUUUAGUUUUUUUUCCCCAUUU-----UUUUUGCUGCUUUUUAGC
.((..(((((((.((((((((((----((....)))))))(((((.................((((..((....))..))))...))))).......-----...)))))))))))).)) ( -21.55)
>consensus
__CAGAAAGAGACGGGGCUAGUCGCAGAGUGACUUGGCUUAAACU____UGAGCUAACUUGAGUUAUUC_CUCGCUU______UUUUAGCCCCAUCU______UUUUUUUUCGUUUAAGC
.........((((((((...((((.....))))((((((((........))))))))...................................................)))))))).... ( -9.89 = -11.20 +   1.31)

alignment

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secondary structure

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Window 6

Location 15,333,485 – 15,333,590
Length 105
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.81
Mean single sequence MFE -24.86
Consensus MFE -8.49
Energy contribution -8.93
Covariance contribution 0.45
Combinations/Pair 1.12
Mean z-score -1.99
Structure conservation index 0.34
SVM decision value 0.02
SVM RNA-class probability 0.542200
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15333485 105 - 22224390
GCUUAAACGAAAAAAAAA--GCGAGAUGGGGCUAAAA------AAGCGAG-GAAUAACUCAAGUUAGCUCA----AGUUUAAGCCAAGUCACUCUACGACUAGCCCCGUCUCUUUCUG--
((((............))--))((((((((((((...------......(-(...((((..((....))..----))))....))..(((.......)))))))))))))))......-- ( -32.80)
>DroSec_CAF1 38168 85 - 1
GCUUAAACGAAAA----------------------AA------AAGCGAG-GAAUAACUCAACUUAGCUCA----AGUUUAAGCCAAGUCACUCUGCGACUAGCCCCGUCUCUUUCUG--
((((((((.....----------------------..------(((.(((-......)))..)))......----.))))))))..((((.......)))).................-- ( -15.04)
>DroSim_CAF1 14849 84 - 1
GCUUAAACGAAA-----------------------AA------AAGCGAG-GAAUAACUCAACUUAGCUCA----AGUUUAAGCCAAGUCACUCUGCGACUAGCCCCGUCUCUUUCUG--
((((((((....-----------------------..------(((.(((-......)))..)))......----.))))))))..((((.......)))).................-- ( -14.62)
>DroEre_CAF1 13897 104 - 1
GCUUAAACGAAAAAAAA---GCGAGAUGGGGCUAAAA------AAGCGAG-GAAUAACUCAACUUAGCUCA----AGUUUAAGCCAAGUCACUCUGCGACUAGCCCCGUCUCUUUCGC--
((((...........))---))((((((((((((...------..(((((-......))).((((.(((..----......))).))))......))...))))))))))))......-- ( -35.10)
>DroYak_CAF1 14380 107 - 1
GCUUAAACGAAAAAAAAAGCGCGAGAUGUGGCUAAAA------AGGCGAG-GAAUAACUCAAGUUAGCUCA----AGUUAAAGCCAAGUCACUCUACGACUAGCUCCGUCUCCCUCUC--
((((............))))..((((((..((((...------.((((((-......)))...(((((...----.))))).)))..(((.......)))))))..))))))......-- ( -29.80)
>DroAna_CAF1 36312 111 - 1
GCUAAAAAGCAGCAAAAA-----AAAUGGGGAAAAAAAACUAAAAGCGGGCUAACAGCACAGGUGAGAUGAGUUAUUUUCUAGCCAAGUCUCU----GACUAUCGCUGGCUCUUUCUGCC
........((((.(((..-----...(((..........))).....((((...((((...(((.(((.((....)).))).))).((((...----))))...))))))))))))))). ( -21.80)
>consensus
GCUUAAACGAAAAAAAA______AGAUGGGGCUAAAA______AAGCGAG_GAAUAACUCAACUUAGCUCA____AGUUUAAGCCAAGUCACUCUGCGACUAGCCCCGUCUCUUUCUG__
((((((((............((........))...............(((.......)))................))))))))..((((.......))))................... ( -8.49 =  -8.93 +   0.45)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,333,523 – 15,333,630
Length 107
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 85.61
Mean single sequence MFE -22.98
Consensus MFE -18.84
Energy contribution -18.88
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -2.33
Structure conservation index 0.82
SVM decision value 1.78
SVM RNA-class probability 0.976941
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15333523 107 - 22224390
GGAGAUGUCAAGACGCGACAAAAGUCGAAAGUCAAGGCGGGCUUAAACGAAAAAAAAA--GCGAGAUGGGGCUAAAAAAGCGAGGAAUAACUCAAGUUAGCUCAAGUUU
.(((.((((..(((.((((....))))...)))..))))..)))..............--........(((((((......(((......)))...)))))))...... ( -24.90)
>DroSec_CAF1 38206 87 - 1
GGAGAUGUCAAGACGCGACAAAAGUCGAAAGUCAAGGCGGGCUUAAACGAAAA----------------------AAAAGCGAGGAAUAACUCAACUUAGCUCAAGUUU
.(((.((((..(((.((((....))))...)))..)))).((((.........----------------------..))))(((......))).......)))...... ( -19.70)
>DroSim_CAF1 14887 86 - 1
GGAGAUGUCAAGACGCGACAAAAGUCGAAAGUCAAGGCGGGCUUAAACGAAA-----------------------AAAAGCGAGGAAUAACUCAACUUAGCUCAAGUUU
.(((.((((..(((.((((....))))...)))..)))).((((........-----------------------..))))(((......))).......)))...... ( -19.80)
>DroEre_CAF1 13935 106 - 1
GGAGAUGUCAAGACGCGACAAAAGUCGAAAGUCAAGGCGGGCUUAAACGAAAAAAAA---GCGAGAUGGGGCUAAAAAAGCGAGGAAUAACUCAACUUAGCUCAAGUUU
.(((.((((..(((.((((....))))...)))..))))..))).............---..(((.(((((((.....)))(((......)))..)))).)))...... ( -25.70)
>DroYak_CAF1 14418 109 - 1
GGAGAUGUCAAGAUGCGACAAAAGUCGAAAGUCAAGGCGGGCUUAAACGAAAAAAAAAGCGCGAGAUGUGGCUAAAAAGGCGAGGAAUAACUCAAGUUAGCUCAAGUUA
.(((..(((......((((....))))..(((((...((.((((............)))).)).....))))).....)))(((......))).......)))...... ( -24.80)
>consensus
GGAGAUGUCAAGACGCGACAAAAGUCGAAAGUCAAGGCGGGCUUAAACGAAAAAAAA___GCGAGAUG_GGCUAAAAAAGCGAGGAAUAACUCAACUUAGCUCAAGUUU
......(((..(((.((((....))))...)))..)))(((((.................((........)).........(((......))).....)))))...... (-18.84 = -18.88 +   0.04)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:03 2006