Locus 5740

Sequence ID 3R_DroMel_CAF1
Location 14,949,734 – 14,949,866
Length 132
Max. P 0.808410
window9403 window9404 window9405 window9406

overview

Window 3

Location 14,949,734 – 14,949,840
Length 106
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 83.53
Mean single sequence MFE -34.62
Consensus MFE -23.58
Energy contribution -23.38
Covariance contribution -0.19
Combinations/Pair 1.22
Mean z-score -1.84
Structure conservation index 0.68
SVM decision value -0.02
SVM RNA-class probability 0.524223
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14949734 106 + 27905053
UCUGUUCGCACUUCACCCAGAAUGCCUGGAAGAAGGAUUUGUGCUCGAACUGCUUCAAGUCCAAGGAUGAGCACAAGGCAGCCGCUGCA---GCAGCUGCCUCCAAAAU--
..........((((..((((.....))))..))))...(((((((((((....)))..(((....)))))))))))((((((.((....---)).))))))........-- ( -38.60)
>DroVir_CAF1 17 109 + 1
UUUGCUCGCACUUUACGCAGAAUGCGUGGAAAAAGGAUCUAUGCUCGAACUGUUUCAAGUCAAAGGAUGAGCAUAAAGCAGCCGCUGCUGCCGCAGCUGCCGCACAACA--
..((((((..((((((((((...(((((((.......))))))).....)))).....)).))))..))))))....((.((.(((((....))))).)).))......-- ( -35.80)
>DroWil_CAF1 83 106 + 1
UCUGUUCGCAUUUCACGCAAAACGCCUGGAAAAAGGAUUUGUGCUCGAAUUGCUUCAAGUCUAAGGAUGAGCACAAAGCAGCAGCUGCA---GCAGCCGCCGCCAAGAU--
.(((((.((.(((((.((.....)).)))))......((((((((((((....)))..(((....)))))))))))))))))))..((.---((....)).))......-- ( -28.80)
>DroYak_CAF1 14 106 + 1
UCUGUUCGCACUUCACCCAGAAUGCCUGGAAGAAGGACUUGUGCUCGAACUGCUUCAAGUCCAAGGACGAGCACAAAGCAGCCGCUGCA---GCAGCCGCCUCCAAACU--
.......((.((((..((((.....))))..))))...(((((((((((....)))..(((....))))))))))).)).((.((((..---.)))).)).........-- ( -34.80)
>DroAna_CAF1 14 106 + 1
UCUGUUCACACUUCACCCAGAAUGCCUGGAAAAAGGACCUGUGCUCCAACUGCUUCAAGUCGAAGGACGAGCAUAAGGCUGCCGCAGCA---GCAGCAGCUGCCAAGUC--
..(((((...((((..((((.....))))......(((.((.((.......))..)).)))))))...)))))...((((((.((....---)).))))))........-- ( -32.60)
>DroPer_CAF1 16 108 + 1
UUUGCUCACACUUUACGCAGAAUGCUUGGAAGAAGGAUCUGUGCUCCAACUGCUUCAAGUCCAAGGACGAGCACAAGGCAGCCGCAGCA---GCAGCCGCCUCCAAGCAGC
(((((...........))))).((((((((.........((((((((....)......(((....)))))))))).(((.((.((....---)).)).))))))))))).. ( -37.10)
>consensus
UCUGUUCGCACUUCACCCAGAAUGCCUGGAAAAAGGAUCUGUGCUCGAACUGCUUCAAGUCCAAGGACGAGCACAAAGCAGCCGCUGCA___GCAGCCGCCGCCAAACU__
..((((..................(((......)))...((((((((((....)))..(((....)))))))))).))))((.(((((....))))).))........... (-23.58 = -23.38 +  -0.19)

alignment

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secondary structure

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Window 4

Location 14,949,734 – 14,949,840
Length 106
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 83.53
Mean single sequence MFE -41.82
Consensus MFE -28.17
Energy contribution -27.82
Covariance contribution -0.36
Combinations/Pair 1.29
Mean z-score -2.57
Structure conservation index 0.67
SVM decision value 0.36
SVM RNA-class probability 0.705352
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14949734 106 - 27905053
--AUUUUGGAGGCAGCUGC---UGCAGCGGCUGCCUUGUGCUCAUCCUUGGACUUGAAGCAGUUCGAGCACAAAUCCUUCUUCCAGGCAUUCUGGGUGAAGUGCGAACAGA
--..(((((((((((((((---....)))))))))))((((((......(((((......))))))))))).....((((.(((((.....))))).))))......)))) ( -42.90)
>DroVir_CAF1 17 109 - 1
--UGUUGUGCGGCAGCUGCGGCAGCAGCGGCUGCUUUAUGCUCAUCCUUUGACUUGAAACAGUUCGAGCAUAGAUCCUUUUUCCACGCAUUCUGCGUAAAGUGCGAGCAAA
--......(((((.(((((....))))).)))))....(((((...((.((.((((((....)))))))).))...........((((.....)))).......))))).. ( -37.90)
>DroWil_CAF1 83 106 - 1
--AUCUUGGCGGCGGCUGC---UGCAGCUGCUGCUUUGUGCUCAUCCUUAGACUUGAAGCAAUUCGAGCACAAAUCCUUUUUCCAGGCGUUUUGCGUGAAAUGCGAACAGA
--..((((((((((((((.---..))))))))))(((((((((.((....))...(((....)))))))))))).........)))).((((.((((...))))))))... ( -37.00)
>DroYak_CAF1 14 106 - 1
--AGUUUGGAGGCGGCUGC---UGCAGCGGCUGCUUUGUGCUCGUCCUUGGACUUGAAGCAGUUCGAGCACAAGUCCUUCUUCCAGGCAUUCUGGGUGAAGUGCGAACAGA
--.((((.(((((((((((---....)))))))))))(((((((((....)))..(((....)))))))))..(..((((.(((((.....))))).))))..)))))... ( -46.70)
>DroAna_CAF1 14 106 - 1
--GACUUGGCAGCUGCUGC---UGCUGCGGCAGCCUUAUGCUCGUCCUUCGACUUGAAGCAGUUGGAGCACAGGUCCUUUUUCCAGGCAUUCUGGGUGAAGUGUGAACAGA
--(((((((((((((((((---....))))))))....))).....((((((((......))))))))..))))))((((.(((((.....))))).))))((....)).. ( -40.10)
>DroPer_CAF1 16 108 - 1
GCUGCUUGGAGGCGGCUGC---UGCUGCGGCUGCCUUGUGCUCGUCCUUGGACUUGAAGCAGUUGGAGCACAGAUCCUUCUUCCAAGCAUUCUGCGUAAAGUGUGAGCAAA
(((((((((((((((((((---....)))))))))(((((((((((....)))......(....)))))))))........))))))).....((.....))...)))... ( -46.30)
>consensus
__AGCUUGGAGGCGGCUGC___UGCAGCGGCUGCCUUGUGCUCAUCCUUGGACUUGAAGCAGUUCGAGCACAAAUCCUUCUUCCAGGCAUUCUGCGUGAAGUGCGAACAGA
.....((((.(((((((((.......)))))))))((((((((.((....))...(((....))))))))))).........))))(((((........)))))....... (-28.17 = -27.82 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,949,774 – 14,949,866
Length 92
Sequences 6
Columns 92
Reading direction forward
Mean pairwise identity 82.25
Mean single sequence MFE -34.33
Consensus MFE -24.16
Energy contribution -25.25
Covariance contribution 1.09
Combinations/Pair 1.25
Mean z-score -2.26
Structure conservation index 0.70
SVM decision value 0.64
SVM RNA-class probability 0.808410
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14949774 92 + 27905053
GUGCUCGAACUGCUUCAAGUCCAAGGAUGAGCACAAGGCAGCCGCUGCAGCAGCUGCCUCCAAAAUGGGUGGCGGCCAUAAGCCGGACAAAG
(((((((((....)))..(((....))))))))).(((((((.((....)).)))))))......((..((((........))))..))... ( -35.90)
>DroSim_CAF1 54 92 + 1
GUGCUCGAACUGCUUCAAGUCCAAGGACGAGCACAAGGCAGCCGCUGCAGCAGCCGCCUCCAAAAUGGGUGGUGGCCAUAAGCCGGACAAGG
(((((((((....)))..(((....)))))))))..(((....((....)).((((((.((......)).)))))).....)))........ ( -36.90)
>DroEre_CAF1 12601 92 + 1
GUGCUCCAACUGCUUCAAGUCCAAGGACGAGCACAAGGCAGCCGCUGCAGCAGCCGCCUCCAAACUGGGUGGCGGCCAUAAGCCAGACAAAG
(((((((....)......(((....)))))))))..(((....((....)).((((((.((......)).)))))).....)))........ ( -34.90)
>DroWil_CAF1 123 92 + 1
GUGCUCGAAUUGCUUCAAGUCUAAGGAUGAGCACAAAGCAGCAGCUGCAGCAGCCGCCGCCAAGAUGGGCACAACACAAAAGUCAGAUGGCC
(((((((...(((((...(((....))))))))....((.((.((((...)))).)).)).....))))))).........(((....))). ( -25.40)
>DroYak_CAF1 54 92 + 1
GUGCUCGAACUGCUUCAAGUCCAAGGACGAGCACAAAGCAGCCGCUGCAGCAGCCGCCUCCAAACUGGGCAGCGGCCAUAAGCCAGACAAAG
(((((((((....)))..(((....)))))))))......((((((((.((....))..((.....))))))))))................ ( -34.40)
>DroAna_CAF1 54 89 + 1
GUGCUCCAACUGCUUCAAGUCGAAGGACGAGCAUAAGGCUGCCGCAGCAGCAGCAGCUGCCAAGUC---UGGCGGCAGCAAAGCGGACAUUC
(((.(((...(((((...(((....))))))))....((((((((.(((((....)))))((....---)))))))))).....)))))).. ( -38.50)
>consensus
GUGCUCGAACUGCUUCAAGUCCAAGGACGAGCACAAGGCAGCCGCUGCAGCAGCCGCCUCCAAAAUGGGUGGCGGCCAUAAGCCAGACAAAG
(((((((((....)))..(((....)))))))))...((((...))))....((((((.((......)).))))))................ (-24.16 = -25.25 +   1.09)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,949,774 – 14,949,866
Length 92
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 82.25
Mean single sequence MFE -35.78
Consensus MFE -27.37
Energy contribution -28.57
Covariance contribution 1.20
Combinations/Pair 1.19
Mean z-score -1.74
Structure conservation index 0.76
SVM decision value 0.43
SVM RNA-class probability 0.733974
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14949774 92 - 27905053
CUUUGUCCGGCUUAUGGCCGCCACCCAUUUUGGAGGCAGCUGCUGCAGCGGCUGCCUUGUGCUCAUCCUUGGACUUGAAGCAGUUCGAGCAC
.......((((.....))))............(((((((((((....)))))))))))((((((......(((((......))))))))))) ( -36.90)
>DroSim_CAF1 54 92 - 1
CCUUGUCCGGCUUAUGGCCACCACCCAUUUUGGAGGCGGCUGCUGCAGCGGCUGCCUUGUGCUCGUCCUUGGACUUGAAGCAGUUCGAGCAC
........(((.....))).............(((((((((((....)))))))))))(((((((((....)))..(((....))))))))) ( -38.10)
>DroEre_CAF1 12601 92 - 1
CUUUGUCUGGCUUAUGGCCGCCACCCAGUUUGGAGGCGGCUGCUGCAGCGGCUGCCUUGUGCUCGUCCUUGGACUUGAAGCAGUUGGAGCAC
..(((..((((........))))..)))....(((((((((((....)))))))))))(((((((((....)))......(....))))))) ( -38.00)
>DroWil_CAF1 123 92 - 1
GGCCAUCUGACUUUUGUGUUGUGCCCAUCUUGGCGGCGGCUGCUGCAGCUGCUGCUUUGUGCUCAUCCUUAGACUUGAAGCAAUUCGAGCAC
((.(((..(((......)))))).)).....(((((((((((...)))))))))))..((((((.((....))...(((....))))))))) ( -31.70)
>DroYak_CAF1 54 92 - 1
CUUUGUCUGGCUUAUGGCCGCUGCCCAGUUUGGAGGCGGCUGCUGCAGCGGCUGCUUUGUGCUCGUCCUUGGACUUGAAGCAGUUCGAGCAC
........(((....(((((((((.(((((.......)))))..))))))))))))..(((((((((....)))..(((....))))))))) ( -35.20)
>DroAna_CAF1 54 89 - 1
GAAUGUCCGCUUUGCUGCCGCCA---GACUUGGCAGCUGCUGCUGCUGCGGCAGCCUUAUGCUCGUCCUUCGACUUGAAGCAGUUGGAGCAC
........((...((((((((..---.....((((((....)))))))))))))).....))..((.((((((((......)))))))).)) ( -34.81)
>consensus
CUUUGUCCGGCUUAUGGCCGCCACCCAUUUUGGAGGCGGCUGCUGCAGCGGCUGCCUUGUGCUCGUCCUUGGACUUGAAGCAGUUCGAGCAC
........(((.....))).............(((((((((((....)))))))))))(((((((((....)))..(((....))))))))) (-27.37 = -28.57 +   1.20)

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 12:03:32 2006