Locus 872

Sequence ID X_DroMel_CAF1
Location 2,452,971 – 2,453,251
Length 280
Max. P 0.964553
window1415 window1416 window1417 window1418 window1419

overview

Window 5

Location 2,452,971 – 2,453,091
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -42.77
Consensus MFE -42.23
Energy contribution -42.23
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.99
SVM decision value 0.51
SVM RNA-class probability 0.762724
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2452971 120 - 22224390
CAUCGGAGACCCGAAAGCUGUCCGCCAAUGUGGUCAGCCAAUUGACCACGUUCUCGUUGGCAUAGGUGAUCAGGCCCUGGCCGAACGGGUGCUUGCCAUCCAGCACAAAGUUAAUGAUAC
..((((....))))..((((...((((((((((((((....))))))))(....)))))))...((((..(((((((((......)))).))))).))))))))................ ( -43.70)
>DroSec_CAF1 13428 120 - 1
CAUCGGAGACCCGAAAGCUGUCCGCCAAGGUGGUCAGCCAAUUGACCACGUUCUCGUUGGCAUAGGUGAUCAGGCCCUGGCCAAACGGGUGCUUGCCAUCCAGCACAAAGUUAAUGAUUC
..((((....))))..((((...(((((.((((((((....))))))))(....).)))))...((((..(((((((((......)))).))))).))))))))................ ( -42.30)
>DroSim_CAF1 15885 120 - 1
CAUCGGAGACCCGAAAGCUGUCCGCCAAGGUGGUCAGCCAAUUGACCACGUUCUCGUUGGCAUAGGUGAUCAGGCCCUGGCCAAACGGGUGCUUGCCAUCCAGCACAAAGUUAAUGAUUC
..((((....))))..((((...(((((.((((((((....))))))))(....).)))))...((((..(((((((((......)))).))))).))))))))................ ( -42.30)
>consensus
CAUCGGAGACCCGAAAGCUGUCCGCCAAGGUGGUCAGCCAAUUGACCACGUUCUCGUUGGCAUAGGUGAUCAGGCCCUGGCCAAACGGGUGCUUGCCAUCCAGCACAAAGUUAAUGAUUC
..((((....))))..((((...(((((.((((((((....))))))))(....).)))))...((((..(((((((((......)))).))))).))))))))................ (-42.23 = -42.23 +  -0.00) 

alignment

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secondary structure

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Window 6

Location 2,453,051 – 2,453,171
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -50.13
Consensus MFE -47.16
Energy contribution -46.50
Covariance contribution -0.66
Combinations/Pair 1.07
Mean z-score -2.34
Structure conservation index 0.94
SVM decision value 1.10
SVM RNA-class probability 0.915593
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2453051 120 + 22224390
UGGCUGACCACAUUGGCGGACAGCUUUCGGGUCUCCGAUGAUAUGGGCAAGCUGCGUCUGCAGUUCAAGCUCUUUCACAAGCCGCUCUUCAGCUGGAAGGGCAGUUAUGUGGUCACCCAG
(((.(((((((((.(((.........((((....))))(((...((((.((((((....))))))...))))..)))...)))(((((((.....)))))))....))))))))).))). ( -50.20)
>DroSec_CAF1 13508 120 + 1
UGGCUGACCACCUUGGCGGACAGCUUUCGGGUCUCCGAUGAUAUGGGCAAGCUGCGCCUGCAGUUCAAGCUCUUCCACAAGCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAG
(((.(((((((..((((((((.((..((((....))))......((((.......)))))).))))..(((((((((......(((....)))))))))))).)))).))))))).))). ( -50.10)
>DroSim_CAF1 15965 120 + 1
UGGCUGACCACCUUGGCGGACAGCUUUCGGGUCUCCGAUGAUAUGGGCAAGCUGCGCCUGCAGUUCAAGCUCUUCCACAAGCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAG
(((.(((((((..((((((((.((..((((....))))......((((.......)))))).))))..(((((((((......(((....)))))))))))).)))).))))))).))). ( -50.10)
>consensus
UGGCUGACCACCUUGGCGGACAGCUUUCGGGUCUCCGAUGAUAUGGGCAAGCUGCGCCUGCAGUUCAAGCUCUUCCACAAGCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAG
(((.(((((((..((((((((.((..((((....))))......((((.......)))))).))))..(((((((((......(((....)))))))))))).)))).))))))).))). (-47.16 = -46.50 +  -0.66) 

alignment

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secondary structure

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dotplot

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Window 7

Location 2,453,051 – 2,453,171
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -50.50
Consensus MFE -47.20
Energy contribution -47.87
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.86
Structure conservation index 0.93
SVM decision value 1.57
SVM RNA-class probability 0.964553
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2453051 120 - 22224390
CUGGGUGACCACAUAACUGCCCUUCCAGCUGAAGAGCGGCUUGUGAAAGAGCUUGAACUGCAGACGCAGCUUGCCCAUAUCAUCGGAGACCCGAAAGCUGUCCGCCAAUGUGGUCAGCCA
..((.(((((((((..((((..(((..(((....)))(((((......))))).)))..))))..(((((((..........((((....)))))))))))......))))))))).)). ( -44.10)
>DroSec_CAF1 13508 120 - 1
CUGGGUGACCACAUAGCUGCCCUUCCAGCUGAAGAGCGGCUUGUGGAAGAGCUUGAACUGCAGGCGCAGCUUGCCCAUAUCAUCGGAGACCCGAAAGCUGUCCGCCAAGGUGGUCAGCCA
.((((..((((((.((((((.((((.....)))).)))))))))))..(.(((((.....))))).)...)..)))).....((((....))))..((((.((((....)))).)))).. ( -53.70)
>DroSim_CAF1 15965 120 - 1
CUGGGUGACCACAUAGCUGCCCUUCCAGCUGAAGAGCGGCUUGUGGAAGAGCUUGAACUGCAGGCGCAGCUUGCCCAUAUCAUCGGAGACCCGAAAGCUGUCCGCCAAGGUGGUCAGCCA
.((((..((((((.((((((.((((.....)))).)))))))))))..(.(((((.....))))).)...)..)))).....((((....))))..((((.((((....)))).)))).. ( -53.70)
>consensus
CUGGGUGACCACAUAGCUGCCCUUCCAGCUGAAGAGCGGCUUGUGGAAGAGCUUGAACUGCAGGCGCAGCUUGCCCAUAUCAUCGGAGACCCGAAAGCUGUCCGCCAAGGUGGUCAGCCA
.((((..((((((.((((((.((((.....)))).)))))))))))...........((((....)))).)..)))).....((((....))))..((((.((((....)))).)))).. (-47.20 = -47.87 +   0.67) 

alignment

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secondary structure

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dotplot

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Window 8

Location 2,453,091 – 2,453,211
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.61
Mean single sequence MFE -37.37
Consensus MFE -36.41
Energy contribution -35.97
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.29
Structure conservation index 0.97
SVM decision value 0.02
SVM RNA-class probability 0.542796
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2453091 120 + 22224390
AUAUGGGCAAGCUGCGUCUGCAGUUCAAGCUCUUUCACAAGCCGCUCUUCAGCUGGAAGGGCAGUUAUGUGGUCACCCAGGUGAGUAAUUUCCAAUUUCCUCCAUUUCGUUCGCUCGAUU
...(((((.((((((....))))))..(((....((((((((.(((((((.....))))))).))).)))))((((....))))........................))).)))))... ( -33.10)
>DroSec_CAF1 13548 112 + 1
AUAUGGGCAAGCUGCGCCUGCAGUUCAAGCUCUUCCACAAGCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAGGUGAGUAAUU-------CCCUCCGUUUCGUU-GCUCGAUU
...((((((((((((....)))))..((((....((((((((.(((((((.....))))))).))).)))))((((....))))......-------......))))..))-)))))... ( -39.50)
>DroSim_CAF1 16005 112 + 1
AUAUGGGCAAGCUGCGCCUGCAGUUCAAGCUCUUCCACAAGCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAGGUGAGUAAUU-------CCCUCCGUUUCGUU-GCUCGAUU
...((((((((((((....)))))..((((....((((((((.(((((((.....))))))).))).)))))((((....))))......-------......))))..))-)))))... ( -39.50)
>consensus
AUAUGGGCAAGCUGCGCCUGCAGUUCAAGCUCUUCCACAAGCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAGGUGAGUAAUU_______CCCUCCGUUUCGUU_GCUCGAUU
....((((.((((((....))))))...))))..((((((((.(((((((.....))))))).))).)))))((((....))))......................(((......))).. (-36.41 = -35.97 +  -0.44) 

alignment

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secondary structure

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Window 9

Location 2,453,131 – 2,453,251
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.34
Mean single sequence MFE -42.37
Consensus MFE -36.56
Energy contribution -35.90
Covariance contribution -0.66
Combinations/Pair 1.09
Mean z-score -1.66
Structure conservation index 0.86
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2453131 120 + 22224390
GCCGCUCUUCAGCUGGAAGGGCAGUUAUGUGGUCACCCAGGUGAGUAAUUUCCAAUUUCCUCCAUUUCGUUCGCUCGAUUUGUCGUCGAAUGAGUGGGCCUUUGGGGAAUUCCGCAAACA
...(((((((.....))))))).(((.(((((((((....))))....(..((((.....((((((.((((((..(((....))).))))))))))))...))))..)...)))))))). ( -43.10)
>DroSec_CAF1 13588 112 + 1
GCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAGGUGAGUAAUU-------CCCUCCGUUUCGUU-GCUCGAUUUGUGGGCGAAUGAGUGGGCCUUUGGGGAAUUCCACUCACU
((.(((((((.....))))))).))....(((....)))(((((((((((-------((((((..((((((-(((((.....))))).))))))..)).....))))))))..))))))) ( -42.00)
>DroSim_CAF1 16045 112 + 1
GCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAGGUGAGUAAUU-------CCCUCCGUUUCGUU-GCUCGAUUUGUGGGCGAAUGAGUGGGCCUUUGGGGAAUUCCACUCACU
((.(((((((.....))))))).))....(((....)))(((((((((((-------((((((..((((((-(((((.....))))).))))))..)).....))))))))..))))))) ( -42.00)
>consensus
GCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAGGUGAGUAAUU_______CCCUCCGUUUCGUU_GCUCGAUUUGUGGGCGAAUGAGUGGGCCUUUGGGGAAUUCCACUCACU
((.(((((((.....))))))).))...((((((((....))))...............(((((....(((.((((.(((((....))))))))).)))...)))))....))))..... (-36.56 = -35.90 +  -0.66) 

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 09:55:58 2006