Locus 1811

Sequence ID 3L_DroMel_CAF1
Location 5,083,444 – 5,083,650
Length 206
Max. P 0.965228
window2817 window2818 window2819 window2820

overview

Window 7

Location 5,083,444 – 5,083,556
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.17
Mean single sequence MFE -28.20
Consensus MFE -28.44
Energy contribution -28.50
Covariance contribution 0.06
Combinations/Pair 1.09
Mean z-score -1.81
Structure conservation index 1.01
SVM decision value 1.58
SVM RNA-class probability 0.965228
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5083444 112 - 23771897
--------CCCACAGUUACUUAACAAUAUUUCUCAUUGUUGUUGAGACGUUGCAGGUGUUUGCUGAAGCAUAUCAAAAAUAUAUGUAUGUACGAGCAUAGCUGCGACUACGUCGACGAUU
--------......(((.((((((((((........))))))))))..((((((((((((((.((..((((((.......))))))...)))))))))..)))))))......))).... ( -30.30)
>DroSec_CAF1 289666 110 - 1
--------CC--CAGUUACUUAACAAUGUUUCUCAUUGUUGUUGAGACGUUGCAGGUGUUUGCUGAAGCAUAUCAAAAAUAUAUGUAUGUACGACCAUAGCUGCGACUACGUCGACGAUU
--------..--..(((.((((((((((........))))))))))..(((((((.((((((.((..((((((.......))))))...)))))..))).)))))))......))).... ( -25.30)
>DroSim_CAF1 310966 110 - 1
--------CC--CAGUUACUUAACAAUAUUUCUCAUUGUUGUUGAGACGUUGCAGGUGUUUGCUGAAGCAUAUCAAAAAUAUAUGUAUAUACGACCAUAGCUGCGACUACGUCGACGAUU
--------..--..(((.((((((((((........))))))))))..(((((((.((((((.....((((((.......)))))).....)))..))).)))))))......))).... ( -26.60)
>DroYak_CAF1 301186 118 - 1
CUCCCCUCAC--CAGUUACUUAACAAUAUUUCCCAUUGUUGUUGAGACGUUGCAGGUGUUUGCUGAAGCAUAUCAAAAAUAUAUGUAUAUACAAACAUAGCUGCGACUACGUCGACGACU
..........--..(((.((((((((((........))))))))))..((((((((((((((.....((((((.......)))))).....)))))))..)))))))......))).... ( -30.60)
>consensus
________CC__CAGUUACUUAACAAUAUUUCUCAUUGUUGUUGAGACGUUGCAGGUGUUUGCUGAAGCAUAUCAAAAAUAUAUGUAUAUACGACCAUAGCUGCGACUACGUCGACGAUU
..............(((.((((((((((........))))))))))..((((((((((((((.....((((((.......)))))).....)))))))..)))))))......))).... (-28.44 = -28.50 +   0.06)

alignment

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secondary structure

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Window 8

Location 5,083,524 – 5,083,623
Length 99
Sequences 3
Columns 99
Reading direction forward
Mean pairwise identity 94.58
Mean single sequence MFE -31.10
Consensus MFE -26.47
Energy contribution -26.37
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.24
Structure conservation index 0.85
SVM decision value 0.36
SVM RNA-class probability 0.706336
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5083524 99 + 23771897
AACAAUGAGAAAUAUUGUUAAGUAACUGUGGGGGGGGGGGGGGCUGAGAAUAGUGGAUGCAGUUUUUGGUGCAUUAGCGGAGUGCGUUACCCCCGGCUC
(((((((.....)))))))........((.(((((.....(.((..(((((.((....)).)))))..)).)..(((((.....)))))))))).)).. ( -29.90)
>DroSec_CAF1 289746 96 + 1
AACAAUGAGAAACAUUGUUAAGUAACUG--GG-GGAGGGGGUACUGAGAGUAGUGGAUGCAGUUUUUGGUGCAUUAGCGGAGUGCGUUACCCCCGGCUC
(((((((.....)))))))......(((--((-((.....((((..((((..((....))..))))..))))..(((((.....))))))))))))... ( -32.80)
>DroSim_CAF1 311046 97 + 1
AACAAUGAGAAAUAUUGUUAAGUAACUG--GGGGGAGGGGGUACUGAGAGUAGUGGAUGCAGUUUUUGGUGCAUUAGCGGAGUGCGUUACCCCCGGCUC
(((((((.....)))))))......(((--((((......((((..((((..((....))..))))..))))..(((((.....))))))))))))... ( -30.60)
>consensus
AACAAUGAGAAAUAUUGUUAAGUAACUG__GGGGGAGGGGGUACUGAGAGUAGUGGAUGCAGUUUUUGGUGCAUUAGCGGAGUGCGUUACCCCCGGCUC
(((((((.....))))))).................(((((((.((......((.((((((.(....).)))))).))......)).)))))))..... (-26.47 = -26.37 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,083,524 – 5,083,623
Length 99
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 94.58
Mean single sequence MFE -20.60
Consensus MFE -17.80
Energy contribution -18.47
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.83
Structure conservation index 0.86
SVM decision value 1.07
SVM RNA-class probability 0.910323
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5083524 99 - 23771897
GAGCCGGGGGUAACGCACUCCGCUAAUGCACCAAAAACUGCAUCCACUAUUCUCAGCCCCCCCCCCCCCCACAGUUACUUAACAAUAUUUCUCAUUGUU
(((..((((((...((.....))..(((((........)))))............))))))............(((....))).......)))...... ( -18.70)
>DroSec_CAF1 289746 96 - 1
GAGCCGGGGGUAACGCACUCCGCUAAUGCACCAAAAACUGCAUCCACUACUCUCAGUACCCCCUCC-CC--CAGUUACUUAACAAUGUUUCUCAUUGUU
.....(((((((..((.....))..(((((........))))).............)))))))...-..--.........(((((((.....))))))) ( -23.00)
>DroSim_CAF1 311046 97 - 1
GAGCCGGGGGUAACGCACUCCGCUAAUGCACCAAAAACUGCAUCCACUACUCUCAGUACCCCCUCCCCC--CAGUUACUUAACAAUAUUUCUCAUUGUU
(((..(((((((..((.....))..(((((........))))).............)))))))......--..(((....))).......)))...... ( -20.10)
>consensus
GAGCCGGGGGUAACGCACUCCGCUAAUGCACCAAAAACUGCAUCCACUACUCUCAGUACCCCCUCCCCC__CAGUUACUUAACAAUAUUUCUCAUUGUU
(((..(((((((..((.....))..(((((........))))).............)))))))..........(((....))).......)))...... (-17.80 = -18.47 +   0.67)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,083,556 – 5,083,650
Length 94
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.18
Mean single sequence MFE -28.40
Consensus MFE -22.25
Energy contribution -22.50
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.78
SVM decision value 1.13
SVM RNA-class probability 0.920429
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5083556 94 - 23771897
ACCCAAAAC-------------GAGGAGCAGAUGGAGCAGGAGCCGG-GGGUAACGCACUCCGCUAAUGCACCAAAAACUGCAUCCACUAUUCUCAGCCCCCC------CCCCC------
.........-------------..(((((((.(((.(((..(((.((-((........)))))))..))).)))....)))).))).................------.....------ ( -27.30)
>DroSec_CAF1 289776 93 - 1
ACCCAAAAC-------------GAGGAGCAGAUGGAGCAGGAGCCGG-GGGUAACGCACUCCGCUAAUGCACCAAAAACUGCAUCCACUACUCUCAGUACCCC------CUCC-------
.........-------------((((.((((.(((.(((..(((.((-((........)))))))..))).)))....))))....(((......)))....)------))).------- ( -28.70)
>DroSim_CAF1 311076 94 - 1
ACCCACAAC-------------GAGGAGCAGAUGGAGCAGGAGCCGG-GGGUAACGCACUCCGCUAAUGCACCAAAAACUGCAUCCACUACUCUCAGUACCCC------CUCCC------
.........-------------((((.((((.(((.(((..(((.((-((........)))))))..))).)))....))))....(((......)))....)------)))..------ ( -28.70)
>DroYak_CAF1 301304 120 - 1
ACCCAAAACGAGGACCCCAAACGAGGAGCAGAUGCAGCAGGAGCUGGAGGGUAACGCACUCCGCUAAUGCACCAAAAACUGCAUCCACUACUCUCAGACCACCCCUCCCCUCCCCCUCCA
.........((((...((......)).((....))....((((..((((((....((.....))..(((((........)))))..................)))))).)))).)))).. ( -28.90)
>consensus
ACCCAAAAC_____________GAGGAGCAGAUGGAGCAGGAGCCGG_GGGUAACGCACUCCGCUAAUGCACCAAAAACUGCAUCCACUACUCUCAGUACCCC______CUCCC______
........................(((((((.(((.(((..(((.((.((........)))))))..))).)))....)))).))).................................. (-22.25 = -22.50 +   0.25)

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 10:17:14 2006