Locus 545

Sequence ID 2L_DroMel_CAF1
Location 1,686,488 – 1,686,685
Length 197
Max. P 0.949058
window879 window880 window881 window882

overview

Window 9

Location 1,686,488 – 1,686,608
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.31
Mean single sequence MFE -34.58
Consensus MFE -26.08
Energy contribution -26.32
Covariance contribution 0.25
Combinations/Pair 1.06
Mean z-score -3.00
Structure conservation index 0.75
SVM decision value 1.39
SVM RNA-class probability 0.949058
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1686488 120 - 22407834
CCAAGCAAAGCAGUUAACACAAAUACGGUUGACAGCCGGGCCAAAACGCUUCGCUGGGCAGCCGAAGAAAAAAUGUUGUGUUAAUGCAGUGCAAGUACAAAGAAUGUGUAUCUUGAAGAU
....(((..(((.(((((((((...((((((.((((..(((......)))..))))..))))))...........))))))))))))..)))(((((((.......)))).)))...... ( -37.14)
>DroSec_CAF1 5471 120 - 1
CCAAGCGAAGCAGUUAACACAAAUACGGUUGACAGUCGGGCCAAAACGCUUCGCUGGGCAGCCGAAGAAAAAAUGUUGUGUUAAUGCAGUGCAAGUACAAACAAUGUGUAUUUUGAAGAU
....(((..(((.(((((((((...((((((.((((..(((......)))..))))..))))))...........))))))))))))..)))(((((((.......)))))))....... ( -35.84)
>DroSim_CAF1 6455 120 - 1
CCAAGCAAAGCAGUUAACACAAAUACGGUUGACAGUCGGGCCAAAACGCUUCGCUGCGCAGCCGAAGAAAAAAUGUUGUGUUAAUGCAGUGCAAGUACAAACAAUGUGUAUCUUGAAGAU
....(((..(((.(((((((((...((((((.((((..(((......)))..))))..))))))...........))))))))))))..)))(((((((.......)))).)))...... ( -34.44)
>DroYak_CAF1 6624 105 - 1
CCAAGCAAAGCAGUUAACACAACAA---------------CUAAAACGCUUCGCUGGGCAGCCGAAGAAAAGCUGUUGUGUUGAUGCAGUGCAAGUACAAACAAUGUGUAUCUUGAAGAU
....(((..(((.(((((((((((.---------------((......(((((((....)).)))))...)).))))))))))))))..)))(((((((.......)))).)))...... ( -30.90)
>consensus
CCAAGCAAAGCAGUUAACACAAAUACGGUUGACAGUCGGGCCAAAACGCUUCGCUGGGCAGCCGAAGAAAAAAUGUUGUGUUAAUGCAGUGCAAGUACAAACAAUGUGUAUCUUGAAGAU
.((((((..(((.(((((((((....((((........))))......(((((((....)).)))))........))))))))))))..)))..(((((.......))))).)))..... (-26.08 = -26.32 +   0.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,686,528 – 1,686,648
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.31
Mean single sequence MFE -31.75
Consensus MFE -22.31
Energy contribution -23.00
Covariance contribution 0.69
Combinations/Pair 1.04
Mean z-score -1.80
Structure conservation index 0.70
SVM decision value 0.13
SVM RNA-class probability 0.599472
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1686528 120 - 22407834
UGCAGCGCCAUGAAACACAAAUGAGCUGCCAUCAAAAGGGCCAAGCAAAGCAGUUAACACAAAUACGGUUGACAGCCGGGCCAAAACGCUUCGCUGGGCAGCCGAAGAAAAAAUGUUGUG
.((((((((((.........))).((((((........)))..)))...))..............((((((.((((..(((......)))..))))..))))))..........))))). ( -33.50)
>DroSec_CAF1 5511 120 - 1
UGCAGCGCCAUGAAAAACAAAUGAGCUGCCAUCAAAAGGGCCAAGCGAAGCAGUUAACACAAAUACGGUUGACAGUCGGGCCAAAACGCUUCGCUGGGCAGCCGAAGAAAAAAUGUUGUG
.(((((..(((.........))).)))))........(((((.((((((((.((((((.(......)))))))....(........))))))))).)))..))................. ( -35.40)
>DroSim_CAF1 6495 120 - 1
UGCAGCGCCAUGAAAAACAAAUGAGCUGCCAUCAAAAGGGCCAAGCAAAGCAGUUAACACAAAUACGGUUGACAGUCGGGCCAAAACGCUUCGCUGCGCAGCCGAAGAAAAAAUGUUGUG
.((((((((((.........))).((((((........)))..)))...))..............((((((.((((..(((......)))..))))..))))))..........))))). ( -30.80)
>DroYak_CAF1 6664 105 - 1
UGCAGCUCCGUGAAAAACAAAUGAGCUGCCAUCAAAAGGGCCAAGCAAAGCAGUUAACACAACAA---------------CUAAAACGCUUCGCUGGGCAGCCGAAGAAAAGCUGUUGUG
((((((((..((.....))...)))))(((........)))...)))..........(((((((.---------------((......(((((((....)).)))))...)).))))))) ( -27.30)
>consensus
UGCAGCGCCAUGAAAAACAAAUGAGCUGCCAUCAAAAGGGCCAAGCAAAGCAGUUAACACAAAUACGGUUGACAGUCGGGCCAAAACGCUUCGCUGGGCAGCCGAAGAAAAAAUGUUGUG
.(((((..(((.........))).)))))........(((((.(((.((((.((....))......((((........)))).....)))).))).)))..))................. (-22.31 = -23.00 +   0.69)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,686,568 – 1,686,685
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.03
Mean single sequence MFE -28.55
Consensus MFE -23.69
Energy contribution -24.44
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.42
Structure conservation index 0.83
SVM decision value 0.07
SVM RNA-class probability 0.568886
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1686568 117 + 22407834
CCCGGCUGUCAACCGUAUUUGUGUUAACUGCUUUGCUUGGCCCUUUUGAUGGCAGCUCAUUUGUGUUUCAUGGCGCUGCAUUUCAAGUUGGCUGCACUUUCCUGCAUAGCUAAUUAC---
...(((.((.(((((....)).))).)).)))..(((.((((..(((((..(((((.(...((.....))..).)))))...)))))..))))(((......)))..))).......--- ( -29.70)
>DroSec_CAF1 5551 116 + 1
CCCGACUGUCAACCGUAUUUGUGUUAACUGCUUCGCUUGGCCCUUUUGAUGGCAGCUCAUUUGUUUUUCAUGGCGCUGCAUUUCA-GUUGGCUGCAUAUUCCUGCAUAGCUAAUUAC---
.(((((((((((.((.....((....)).....)).)))))......((..(((((.(...((.....))..).)))))...)))-))))).((((......))))...........--- ( -26.30)
>DroSim_CAF1 6535 116 + 1
CCCGACUGUCAACCGUAUUUGUGUUAACUGCUUUGCUUGGCCCUUUUGAUGGCAGCUCAUUUGUUUUUCAUGGCGCUGCAUUUCA-GUUGGCUGCACUUUCCUGCAUAGCUAAUUAC---
.(((((((((((.((.....((....)).....)).)))))......((..(((((.(...((.....))..).)))))...)))-))))).((((......))))...........--- ( -24.50)
>DroYak_CAF1 6704 105 + 1
---------------UUGUUGUGUUAACUGCUUUGCUUGGCCCUUUUGAUGGCAGCUCAUUUGUUUUUCACGGAGCUGCAUUUCAAGUUGGCUGCAUUUUCCUGCAUAGCUAAUUACCAC
---------------..(((((((.........(((..((((..(((((..(((((((...((.....))..)))))))...)))))..))))))).......))))))).......... ( -33.69)
>consensus
CCCGACUGUCAACCGUAUUUGUGUUAACUGCUUUGCUUGGCCCUUUUGAUGGCAGCUCAUUUGUUUUUCAUGGCGCUGCAUUUCA_GUUGGCUGCACUUUCCUGCAUAGCUAAUUAC___
..................((((((.........(((..((((..(((((..(((((.(...((.....))..).)))))...)))))..))))))).......))))))........... (-23.69 = -24.44 +   0.75)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,686,568 – 1,686,685
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.03
Mean single sequence MFE -29.25
Consensus MFE -23.34
Energy contribution -23.15
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.17
Structure conservation index 0.80
SVM decision value 1.13
SVM RNA-class probability 0.919679
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1686568 117 - 22407834
---GUAAUUAGCUAUGCAGGAAAGUGCAGCCAACUUGAAAUGCAGCGCCAUGAAACACAAAUGAGCUGCCAUCAAAAGGGCCAAGCAAAGCAGUUAACACAAAUACGGUUGACAGCCGGG
---.......(((.((((......))))(((...((((...(((((..(((.........))).)))))..))))...)))..)))...((.((((((.(......))))))).)).... ( -29.90)
>DroSec_CAF1 5551 116 - 1
---GUAAUUAGCUAUGCAGGAAUAUGCAGCCAAC-UGAAAUGCAGCGCCAUGAAAAACAAAUGAGCUGCCAUCAAAAGGGCCAAGCGAAGCAGUUAACACAAAUACGGUUGACAGUCGGG
---.......(((.((((......))))(((...-(((...(((((..(((.........))).)))))..)))....)))..)))......((((((.(......)))))))....... ( -27.80)
>DroSim_CAF1 6535 116 - 1
---GUAAUUAGCUAUGCAGGAAAGUGCAGCCAAC-UGAAAUGCAGCGCCAUGAAAAACAAAUGAGCUGCCAUCAAAAGGGCCAAGCAAAGCAGUUAACACAAAUACGGUUGACAGUCGGG
---.......(((.((((......))))(((...-(((...(((((..(((.........))).)))))..)))....)))..)))......((((((.(......)))))))....... ( -26.90)
>DroYak_CAF1 6704 105 - 1
GUGGUAAUUAGCUAUGCAGGAAAAUGCAGCCAACUUGAAAUGCAGCUCCGUGAAAAACAAAUGAGCUGCCAUCAAAAGGGCCAAGCAAAGCAGUUAACACAACAA---------------
(((.(((((.(((.((((......))))(((...((((...(((((((..((.....))...)))))))..))))...))).......)))))))).))).....--------------- ( -32.40)
>consensus
___GUAAUUAGCUAUGCAGGAAAAUGCAGCCAAC_UGAAAUGCAGCGCCAUGAAAAACAAAUGAGCUGCCAUCAAAAGGGCCAAGCAAAGCAGUUAACACAAAUACGGUUGACAGUCGGG
....(((((.(((.((((......))))(((....(((...(((((..(((.........))).)))))..)))....))).......))))))))........................ (-23.34 = -23.15 +  -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 09:38:59 2006