Locus 3429

Sequence ID X_DroMel_CAF1
Location 9,157,965 – 9,158,095
Length 130
Max. P 0.956664
window5613 window5614 window5615 window5616

overview

Window 3

Location 9,157,965 – 9,158,059
Length 94
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 81.98
Mean single sequence MFE -30.04
Consensus MFE -21.63
Energy contribution -21.80
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 0.72
SVM decision value 0.84
SVM RNA-class probability 0.862783
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9157965 94 + 22224390
---------UGA-----CCUUAAACGCUUUUCCAAG-CAGGAAAUGCAUUUUCAUUUAGCAGCGGAAGUAGCUGCAAAUGAGCUUUUAGUUUUUCCUCACCUU----------CGGCAU
---------(((-----....((((((.(((((...-..))))).))...(((((((.(((((.......))))))))))))......))))....)))....----------...... ( -24.30)
>DroPse_CAF1 10439 104 + 1
--GG-----UGGCAAUGGCUUAAACGCUUUUCCAAG-CAGGAAAUGCAUUUUCAUUUAGCAGCGGAAGUAGCUGCAAAUGAGCUUUUAGUUUUUGCUCACCUUCACUCC-GGA------
--((-----((((((..(((.(((.((.(((((...-..))))).))...(((((((.(((((.......)))))))))))).))).)))..)))).))))........-...------ ( -35.60)
>DroSim_CAF1 1048 103 + 1
---------UGA-----CCUUAAACGCUUUUCCAAG-CAGGAAAUGCAUUUUCAUUUAGCAGCGGAAGUAGCUGCAAAUGAGCUUUUAGUUUUUCCUCACCUUUGCUCC-UGGCGGCGU
---------...-----......(((((...(((((-(((((((.((...(((((((.(((((.......))))))))))))......)).))))).......))))..-))).))))) ( -27.91)
>DroWil_CAF1 14648 112 + 1
GUUAUUCGAAAA-----ACUCAAACGCUUUUCCAAG-CAGGAAAUGCAUUUUCAUUUAGCAGCGGAAGUAACUGCAAAUGAGCUUUUAGUUUUUCCUCACUUUCUCUUCUUGACUGCG-
.......(((((-----(((.(((.((.(((((...-..))))).))...(((((((.(((((....)...))))))))))).))).)))))))).......................- ( -25.20)
>DroAna_CAF1 12832 103 + 1
--GC-----UGA-----CCUUAAACGCUUUUCCCAGCCAGGAAAUGCAUUUUCAUUUAGCAGCGGAAGUAGCUGCAAAUGAGCUUUUAGUUUUUGCUCACCUUUGCUCC-UGGCGG---
--..-----...-----...............((.(((((((...............(((.((....)).)))((((((((((...........)))))..))))))))-))))))--- ( -31.60)
>DroPer_CAF1 9596 104 + 1
--GG-----UGGCAAUGGCUUAAACGCUUUUCCAAG-CAGGAAAUGCAUUUUCAUUUAGCAGCGGAAGUAGCUGCAAAUGAGCUUUUAGUUUUUGCUCACCUUCACUCC-GGA------
--((-----((((((..(((.(((.((.(((((...-..))))).))...(((((((.(((((.......)))))))))))).))).)))..)))).))))........-...------ ( -35.60)
>consensus
__G______UGA_____CCUUAAACGCUUUUCCAAG_CAGGAAAUGCAUUUUCAUUUAGCAGCGGAAGUAGCUGCAAAUGAGCUUUUAGUUUUUCCUCACCUUCACUCC_UGACGG___
.....................((((((.(((((......))))).))...(((((((.(((((.......))))))))))))......))))........................... (-21.63 = -21.80 +   0.17)

alignment

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secondary structure

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Window 4

Location 9,157,965 – 9,158,059
Length 94
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 81.98
Mean single sequence MFE -31.32
Consensus MFE -24.58
Energy contribution -24.30
Covariance contribution -0.28
Combinations/Pair 1.08
Mean z-score -2.91
Structure conservation index 0.78
SVM decision value 1.28
SVM RNA-class probability 0.939881
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9157965 94 - 22224390
AUGCCG----------AAGGUGAGGAAAAACUAAAAGCUCAUUUGCAGCUACUUCCGCUGCUAAAUGAAAAUGCAUUUCCUG-CUUGGAAAAGCGUUUAAGG-----UCA---------
..(((.----------..(((........)))......(((((((((((.......))))).))))))((((((.(((((..-...))))).))))))..))-----)..--------- ( -27.00)
>DroPse_CAF1 10439 104 - 1
------UCC-GGAGUGAAGGUGAGCAAAAACUAAAAGCUCAUUUGCAGCUACUUCCGCUGCUAAAUGAAAAUGCAUUUCCUG-CUUGGAAAAGCGUUUAAGCCAUUGCCA-----CC--
------...-........((((.((((...........(((((((((((.......))))).))))))((((((.(((((..-...))))).))))))......))))))-----))-- ( -33.60)
>DroSim_CAF1 1048 103 - 1
ACGCCGCCA-GGAGCAAAGGUGAGGAAAAACUAAAAGCUCAUUUGCAGCUACUUCCGCUGCUAAAUGAAAAUGCAUUUCCUG-CUUGGAAAAGCGUUUAAGG-----UCA---------
..((((((.-........))))((......))....))(((((((((((.......))))).))))))((((((.(((((..-...))))).))))))....-----...--------- ( -28.60)
>DroWil_CAF1 14648 112 - 1
-CGCAGUCAAGAAGAGAAAGUGAGGAAAAACUAAAAGCUCAUUUGCAGUUACUUCCGCUGCUAAAUGAAAAUGCAUUUCCUG-CUUGGAAAAGCGUUUGAGU-----UUUUCGAAUAAC
-(((..((.......))..)))..((((((((......(((((((((((.......))))).))))))((((((.(((((..-...))))).)))))).)))-----)))))....... ( -31.90)
>DroAna_CAF1 12832 103 - 1
---CCGCCA-GGAGCAAAGGUGAGCAAAAACUAAAAGCUCAUUUGCAGCUACUUCCGCUGCUAAAUGAAAAUGCAUUUCCUGGCUGGGAAAAGCGUUUAAGG-----UCA-----GC--
---((((((-((((((.((((((((...........))))))))(((((.......)))))..........)))...))))))).))...............-----...-----..-- ( -33.20)
>DroPer_CAF1 9596 104 - 1
------UCC-GGAGUGAAGGUGAGCAAAAACUAAAAGCUCAUUUGCAGCUACUUCCGCUGCUAAAUGAAAAUGCAUUUCCUG-CUUGGAAAAGCGUUUAAGCCAUUGCCA-----CC--
------...-........((((.((((...........(((((((((((.......))))).))))))((((((.(((((..-...))))).))))))......))))))-----))-- ( -33.60)
>consensus
___CCGUCA_GGAGCGAAGGUGAGCAAAAACUAAAAGCUCAUUUGCAGCUACUUCCGCUGCUAAAUGAAAAUGCAUUUCCUG_CUUGGAAAAGCGUUUAAGG_____UCA______C__
..................(((........)))......(((((((((((.......))))).))))))((((((.(((((......))))).))))))..................... (-24.58 = -24.30 +  -0.28)

alignment

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secondary structure

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Window 5

Location 9,157,989 – 9,158,095
Length 106
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 81.30
Mean single sequence MFE -34.48
Consensus MFE -27.64
Energy contribution -28.03
Covariance contribution 0.39
Combinations/Pair 1.04
Mean z-score -2.24
Structure conservation index 0.80
SVM decision value 1.47
SVM RNA-class probability 0.956664
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9157989 106 + 22224390
GGAAAUGCAUUUUCAUUUAGCAGCGGAAGUAGCUGCAAAUGAGCUUUUAGUUUUUCCUCACCUU---------CGGCAUUCUCGUGCGUCCGCAUUUCCGGUCCACCGUCCACCU----
((((((((...(((((((.(((((.......)))))))))))).....................---------..((((....))))....))))))))((....))........---- ( -31.70)
>DroSim_CAF1 1072 119 + 1
GGAAAUGCAUUUUCAUUUAGCAGCGGAAGUAGCUGCAAAUGAGCUUUUAGUUUUUCCUCACCUUUGCUCCUGGCGGCGUUGUCGUGCGUCCGCAUUUCCGGUCCACCGUCCACCUGGUC
((((((((....((((((.(((((.......)))))))))))(((...(((..............)))...)))(((((......))))).))))))))((....))(.((....)).) ( -37.04)
>DroAna_CAF1 12859 101 + 1
GGAAAUGCAUUUUCAUUUAGCAGCGGAAGUAGCUGCAAAUGAGCUUUUAGUUUUUGCUCACCUUUGCUCCUGGCGG--------------CGCAUUUCCGGUCCGCCGUUAUCCU----
((((((((....((((((.(((((.......)))))))))))(((.((((.....((........))..)))).))--------------)))))))))((....))........---- ( -34.70)
>consensus
GGAAAUGCAUUUUCAUUUAGCAGCGGAAGUAGCUGCAAAUGAGCUUUUAGUUUUUCCUCACCUUUGCUCCUGGCGGC_UU_UCGUGCGUCCGCAUUUCCGGUCCACCGUCCACCU____
((((((((...(((((((.(((((.......))))))))))))................................(((......)))....))))))))((....))............ (-27.64 = -28.03 +   0.39)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,157,989 – 9,158,095
Length 106
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 81.30
Mean single sequence MFE -31.60
Consensus MFE -26.31
Energy contribution -26.87
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -1.50
Structure conservation index 0.83
SVM decision value 0.45
SVM RNA-class probability 0.741834
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9157989 106 - 22224390
----AGGUGGACGGUGGACCGGAAAUGCGGACGCACGAGAAUGCCG---------AAGGUGAGGAAAAACUAAAAGCUCAUUUGCAGCUACUUCCGCUGCUAAAUGAAAAUGCAUUUCC
----.(((.........)))(((((((((...((...((....((.---------.......)).....))....))(((((((((((.......))))).))))))...))))))))) ( -28.90)
>DroSim_CAF1 1072 119 - 1
GACCAGGUGGACGGUGGACCGGAAAUGCGGACGCACGACAACGCCGCCAGGAGCAAAGGUGAGGAAAAACUAAAAGCUCAUUUGCAGCUACUUCCGCUGCUAAAUGAAAAUGCAUUUCC
..((.(((((.(((((..(((......))).))).))......))))).)).(((..(((........)))......(((((((((((.......))))).))))))...)))...... ( -33.80)
>DroAna_CAF1 12859 101 - 1
----AGGAUAACGGCGGACCGGAAAUGCG--------------CCGCCAGGAGCAAAGGUGAGCAAAAACUAAAAGCUCAUUUGCAGCUACUUCCGCUGCUAAAUGAAAAUGCAUUUCC
----........((....))(((((((((--------------(((((.........)))).)).............(((((((((((.......))))).))))))....)))))))) ( -32.10)
>consensus
____AGGUGGACGGUGGACCGGAAAUGCGGACGCACGA_AA_GCCGCCAGGAGCAAAGGUGAGGAAAAACUAAAAGCUCAUUUGCAGCUACUUCCGCUGCUAAAUGAAAAUGCAUUUCC
............((....))(((((((((............((((............))))................(((((((((((.......))))).))))))...))))))))) (-26.31 = -26.87 +   0.56)

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 10:59:15 2006