Locus 6820

Sequence ID 3R_DroMel_CAF1
Location 18,032,455 – 18,032,607
Length 152
Max. P 0.742090
window11071 window11072 window11073

overview

Window 1

Location 18,032,455 – 18,032,551
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 92.92
Mean single sequence MFE -27.44
Consensus MFE -22.76
Energy contribution -23.00
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.45
Structure conservation index 0.83
SVM decision value 0.41
SVM RNA-class probability 0.726250
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18032455 96 + 27905053
CGUUGGCUUCAUCCAGCUUGAAUGCUUUCUCUGGCUGGUAAGUUCUGGCCAAGUUCUGGCGAAGGAACAAAACUAUUUCCUAAGCUGCUUAGCAAA
.....(((.....((((((...((((..((.((((..(......)..))))))....)))).(((((.........)))))))))))...)))... ( -26.80)
>DroSec_CAF1 75047 96 + 1
CGUUGGCUUCAUCCAGCUUGAAUGCUUUCUCUGGCUGGUUAGUUGUGGCCAAGUUCUGGCGCAGGAACAAAACUAUUUCCUAAGCUGCUUAGCAAA
..((((((.((.((((((.(((....)))...)))))).....)).))))))(((..((((((((((.........)))))..)).))).)))... ( -28.70)
>DroSim_CAF1 76968 96 + 1
CGUUGGCUUCAUCCAGCUUGAAUGCUUUCUCUGGCUGGUUAGUUCUGGCCAAGUUCUGGCGCAGGAACAAUACUAUUUCCUAAGCUGCUUAGCAAA
..((((((....((((((.(((....)))...))))))........))))))(((..((((((((((.........)))))..)).))).)))... ( -27.00)
>DroEre_CAF1 76945 93 + 1
CGUUGGCUUCAUCCAGCUCGAAUGCUUU---UGGCUGGUUAGUUCUGGCCAAGUUCUGGCGAAGGAACGUAACUAUUUCCUAAGCUGCUUAGACAA
..((((((....(((((.((((....))---)))))))........))))))(((..((((.(((((.........)))))....))))..))).. ( -26.40)
>DroYak_CAF1 78749 96 + 1
CGUUGGCUUCAUCCAGCUUGAAUGCUUUCUCCGACUGGUUAGUUCUGGCCAAGUUCUGGUGAAGGAACGUAACUAUUUCCUAAGCUGCUUAGCCAA
..((((((.....(((((((......(((.(((((((((((....))))).))))..)).)))((((.........)))))))))))...)))))) ( -28.30)
>consensus
CGUUGGCUUCAUCCAGCUUGAAUGCUUUCUCUGGCUGGUUAGUUCUGGCCAAGUUCUGGCGAAGGAACAAAACUAUUUCCUAAGCUGCUUAGCAAA
..((((((....((((((.(((....)))...))))))........)))))).....(((..(((((.........)))))..))).......... (-22.76 = -23.00 +   0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,032,517 – 18,032,607
Length 90
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 82.18
Mean single sequence MFE -19.73
Consensus MFE -13.53
Energy contribution -14.62
Covariance contribution 1.08
Combinations/Pair 1.04
Mean z-score -1.68
Structure conservation index 0.69
SVM decision value 0.18
SVM RNA-class probability 0.622697
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18032517 90 + 27905053
AGGAACAAAACUAUUUCCUAAGCUGCUUAGCAAAAUGUCUAAUGCCUUGCUUAGACAAUUGCUUAAAGGAA---GAACUAGCGUAGUGAAAU----U
(((((.........)))))..(((((..(((((..(((((((.((...))))))))).)))))...((...---...))...))))).....----. ( -19.20)
>DroSec_CAF1 75109 93 + 1
AGGAACAAAACUAUUUCCUAAGCUGCUUAGCAAAAUGUCUAAUGCCUUGCUUAGACAAUUGCUAAAAGGAAGAAGAACUAGCGUAGAGAAAU----U
............((((((((.(((..(((((((..(((((((.((...))))))))).))))))).((.........))))).))).)))))----. ( -21.00)
>DroSim_CAF1 77030 93 + 1
AGGAACAAUACUAUUUCCUAAGCUGCUUAGCAAAAUGUCUAAUGCCUUGCUUAGACAAUUGCUAAAAGGAAGAAGAACUAGCGUAGAGAAAU----U
............((((((((.(((..(((((((..(((((((.((...))))))))).))))))).((.........))))).))).)))))----. ( -21.00)
>DroEre_CAF1 77004 90 + 1
AGGAACGUAACUAUUUCCUAAGCUGCUUAGACAAAUGUCUAAUGCCUUGCUUAGACAAUUGCUAAAAGGAA---GAUUUAGCGCCGAGUAAU----A
.((..............((((((.((((((((....)))))).))...))))))......((((((.....---..)))))).)).......----. ( -22.60)
>DroYak_CAF1 78811 89 + 1
AGGAACGUAACUAUUUCCUAAGCUGCUUAGCCAAAUGUCUAAUGCUUUGCUUAGACAAUUGCUAAAAGGAA---GAUUUAGAA-AGAGAAAU----U
..........(((..((.....((..(((((.((.(((((((.((...))))))))).)))))))..))..---))..)))..-........----. ( -16.90)
>DroAna_CAF1 71691 89 + 1
AGGAA-----CUAUUUCCUAAGCUGCUUACGGAGCUGUGUAAUGCCCUGCUUAGACAAUUGUUAAAGGGAGAA-AAUUCA--AAAGGGAAACUAACU
(((((-----....))))).((((.(....).))))((......((((.(((.(((....))).)))(((...-..))).--..))))......)). ( -17.70)
>consensus
AGGAACAAAACUAUUUCCUAAGCUGCUUAGCAAAAUGUCUAAUGCCUUGCUUAGACAAUUGCUAAAAGGAA___GAACUAGCGUAGAGAAAU____U
(((((.........)))))...((..(((((((..(((((((.((...))))))))).)))))))..))............................ (-13.53 = -14.62 +   1.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,032,517 – 18,032,607
Length 90
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 82.18
Mean single sequence MFE -20.30
Consensus MFE -13.84
Energy contribution -13.90
Covariance contribution 0.06
Combinations/Pair 1.18
Mean z-score -2.06
Structure conservation index 0.68
SVM decision value 0.45
SVM RNA-class probability 0.742090
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18032517 90 - 27905053
A----AUUUCACUACGCUAGUUC---UUCCUUUAAGCAAUUGUCUAAGCAAGGCAUUAGACAUUUUGCUAAGCAGCUUAGGAAAUAGUUUUGUUCCU
.----(((((.(((.(((.(((.---........(((((.(((((((((...)).)))))))..))))).)))))).))))))))............ ( -20.40)
>DroSec_CAF1 75109 93 - 1
A----AUUUCUCUACGCUAGUUCUUCUUCCUUUUAGCAAUUGUCUAAGCAAGGCAUUAGACAUUUUGCUAAGCAGCUUAGGAAAUAGUUUUGUUCCU
.----(((((.(((.(((.((...........(((((((.(((((((((...)).)))))))..)))))))))))).))))))))............ ( -22.90)
>DroSim_CAF1 77030 93 - 1
A----AUUUCUCUACGCUAGUUCUUCUUCCUUUUAGCAAUUGUCUAAGCAAGGCAUUAGACAUUUUGCUAAGCAGCUUAGGAAAUAGUAUUGUUCCU
.----(((((.(((.(((.((...........(((((((.(((((((((...)).)))))))..)))))))))))).))))))))............ ( -22.90)
>DroEre_CAF1 77004 90 - 1
U----AUUACUCGGCGCUAAAUC---UUCCUUUUAGCAAUUGUCUAAGCAAGGCAUUAGACAUUUGUCUAAGCAGCUUAGGAAAUAGUUACGUUCCU
.----.......(((((((((..---.....)))))).(((..((((((...((.((((((....)))))))).))))))..))).)))........ ( -24.00)
>DroYak_CAF1 78811 89 - 1
A----AUUUCUCU-UUCUAAAUC---UUCCUUUUAGCAAUUGUCUAAGCAAAGCAUUAGACAUUUGGCUAAGCAGCUUAGGAAAUAGUUACGUUCCU
.----........-.........---(((((((((((...(((((((((...)).)))))))....))))))......))))).............. ( -17.40)
>DroAna_CAF1 71691 89 - 1
AGUUAGUUUCCCUUU--UGAAUU-UUCUCCCUUUAACAAUUGUCUAAGCAGGGCAUUACACAGCUCCGUAAGCAGCUUAGGAAAUAG-----UUCCU
.....((((((....--......-................(((((.....)))))......((((.(....).))))..))))))..-----..... ( -14.20)
>consensus
A____AUUUCUCUACGCUAAAUC___UUCCUUUUAGCAAUUGUCUAAGCAAGGCAUUAGACAUUUUGCUAAGCAGCUUAGGAAAUAGUUUUGUUCCU
.....(((((.....(((((............)))))......((((((...((.((((........)))))).)))))))))))............ (-13.84 = -13.90 +   0.06)

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 12:30:47 2006