Locus 6339

Sequence ID 3R_DroMel_CAF1
Location 16,592,357 – 16,592,507
Length 150
Max. P 0.933096
window10337 window10338 window10339 window10340

overview

Window 7

Location 16,592,357 – 16,592,447
Length 90
Sequences 6
Columns 90
Reading direction forward
Mean pairwise identity 78.96
Mean single sequence MFE -22.88
Consensus MFE -13.44
Energy contribution -14.97
Covariance contribution 1.53
Combinations/Pair 1.06
Mean z-score -1.68
Structure conservation index 0.59
SVM decision value 0.21
SVM RNA-class probability 0.636023
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16592357 90 + 27905053
UAUACCCUUCCUCCCGAAUGCCAAUCAAGUCUGGCUGUCCUGCGAGCACUACAACUAGUUCUGCCAGCCGUCCUCGUCUUUAGAGGACGA
...............((..((((........))))..))..((..(((..((.....))..)))..))(((((((.......))))))). ( -23.90)
>DroSec_CAF1 148615 90 + 1
CAUCCCCUUCCUCCCGAAUGCCAAUCAAGUCUGGCUGUCCUGCGAACACUACAACUAGUUCUGCCAGCCGUCCUCGUCCUCAGAGGACGA
................................(((((....((((((..........)))).)))))))((((((.......)))))).. ( -22.20)
>DroSim_CAF1 153612 90 + 1
CAUCCCCUUCCUCCCGAAUGCCAAUCAAGUCUGGCUGUCCUGCGAACACUACAACUAGUUCUGCCAGCCGUCCUCGUCCUCAGAGGACGA
................................(((((....((((((..........)))).)))))))((((((.......)))))).. ( -22.20)
>DroEre_CAF1 152451 85 + 1
UAUCCCCUCCC-----CAUGCCAAUCAAGUCUGGCUGUCCUGCGAGCACUACAACUAGUUCUGCCAGCCGUCCUCGUCCUCAGAGGACGA
...........-----((.((((........))))))....((..(((..((.....))..)))..))(((((((.......))))))). ( -23.50)
>DroYak_CAF1 148099 85 + 1
UAUCCCCUCCC-----CAUGCCAAUCAAGUCUUGCUGUCCUGCGAGCACUACAACUAGUUUUGCCAGCCGUCCUCGUCCUCAGAGGACGA
...........-----.................((((....(((((.((((....)))))))))))))(((((((.......))))))). ( -21.70)
>DroAna_CAF1 145166 70 + 1
GACAG---UCAGCCAGUCGGCCAGGCCAGGCAGCCUGUCCUGC-----CUACAACUAGUUCUGUCAGUC------------GGAGGACAA
(((((---..(((.(((.(((.(((.((((...)))).)))))-----)....))).)))))))).(((------------....))).. ( -23.80)
>consensus
UAUCCCCUUCCUCCCGAAUGCCAAUCAAGUCUGGCUGUCCUGCGAGCACUACAACUAGUUCUGCCAGCCGUCCUCGUCCUCAGAGGACGA
................................(((((....(((...((((....))))..))))))))((((((.......)))))).. (-13.44 = -14.97 +   1.53)

alignment

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secondary structure

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Window 8

Location 16,592,357 – 16,592,447
Length 90
Sequences 6
Columns 90
Reading direction reverse
Mean pairwise identity 78.96
Mean single sequence MFE -28.78
Consensus MFE -21.51
Energy contribution -22.65
Covariance contribution 1.14
Combinations/Pair 1.17
Mean z-score -1.23
Structure conservation index 0.75
SVM decision value 0.40
SVM RNA-class probability 0.719562
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16592357 90 - 27905053
UCGUCCUCUAAAGACGAGGACGGCUGGCAGAACUAGUUGUAGUGCUCGCAGGACAGCCAGACUUGAUUGGCAUUCGGGAGGAAGGGUAUA
.(((((((.......)))))))(((((.....)))))....((((((........(((((......))))).(((....))).)))))). ( -28.40)
>DroSec_CAF1 148615 90 - 1
UCGUCCUCUGAGGACGAGGACGGCUGGCAGAACUAGUUGUAGUGUUCGCAGGACAGCCAGACUUGAUUGGCAUUCGGGAGGAAGGGGAUG
.((((((((..(((((...((((((((.....))))))))..)))))........(((((......))))).(((....))))))))))) ( -31.10)
>DroSim_CAF1 153612 90 - 1
UCGUCCUCUGAGGACGAGGACGGCUGGCAGAACUAGUUGUAGUGUUCGCAGGACAGCCAGACUUGAUUGGCAUUCGGGAGGAAGGGGAUG
.((((((((..(((((...((((((((.....))))))))..)))))........(((((......))))).(((....))))))))))) ( -31.10)
>DroEre_CAF1 152451 85 - 1
UCGUCCUCUGAGGACGAGGACGGCUGGCAGAACUAGUUGUAGUGCUCGCAGGACAGCCAGACUUGAUUGGCAUG-----GGGAGGGGAUA
..(((((.((((.((....((((((((.....)))))))).)).)))).))))).(((((......)))))...-----........... ( -30.60)
>DroYak_CAF1 148099 85 - 1
UCGUCCUCUGAGGACGAGGACGGCUGGCAAAACUAGUUGUAGUGCUCGCAGGACAGCAAGACUUGAUUGGCAUG-----GGGAGGGGAUA
.(((((((.......)))))))((..((((..((.(((((..((....))..))))).))..))).)..))...-----........... ( -26.30)
>DroAna_CAF1 145166 70 - 1
UUGUCCUCC------------GACUGACAGAACUAGUUGUAG-----GCAGGACAGGCUGCCUGGCCUGGCCGACUGGCUGA---CUGUC
..(((....------------))).(((((..(((((((..(-----.((((.((((...)))).)))).))))))))....---))))) ( -25.20)
>consensus
UCGUCCUCUGAGGACGAGGACGGCUGGCAGAACUAGUUGUAGUGCUCGCAGGACAGCCAGACUUGAUUGGCAUUCGGGAGGAAGGGGAUA
..(((((.((((.((....((((((((.....)))))))).)).)))).))))).(((((......)))))................... (-21.51 = -22.65 +   1.14)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,592,415 – 16,592,507
Length 92
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 79.75
Mean single sequence MFE -27.70
Consensus MFE -15.10
Energy contribution -14.49
Covariance contribution -0.61
Combinations/Pair 1.24
Mean z-score -2.73
Structure conservation index 0.54
SVM decision value 1.23
SVM RNA-class probability 0.933096
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16592415 92 + 27905053
UUCUGCCAGCCGUCCUCGUCUUUAGAGGACGACGACAGCAAAGGCAGUAAC--AGCGGCAGCAAAUAAUUUUGUAAUUCAAUUGUUGUCCUUCU
..(((((.((.(((.((((((.....)))))).))).))...)))))....--((.((((((((..((((....))))...))))))))))... ( -30.00)
>DroPse_CAF1 150390 80 + 1
UUCUUCAAGUC------------AGACGAGGACGUGGACGUGGACGACGAC--AGCAGCAGCAAAUAAUUUUGUAAUUCAAUUGUUGUCGUUCU
........(((------------..(((....))).)))..((((((((((--((.....(((((....))))).......)))))))))))). ( -22.60)
>DroSim_CAF1 153670 94 + 1
UUCUGCCAGCCGUCCUCGUCCUCAGAGGACGACGACAGCAAAGGCAGUAACACAGCGGCAGCAAAUAAUUUUGUAAUUCAAUUGUUGUCCUUCU
..(((((.((.(((.((((((.....)))))).))).))...)))))......((.((((((((..((((....))))...))))))))))... ( -32.30)
>DroEre_CAF1 152504 92 + 1
UUCUGCCAGCCGUCCUCGUCCUCAGAGGACGACGACAGCAAAGGCAGUAAG--AGCAGCAGCAAAUAAUUUUGUAAUUCAAUUGUUGUCCUUCU
..(((((.((.(((.((((((.....)))))).))).))...))))).(((--..((((((((((....)))))........)))))..))).. ( -32.50)
>DroYak_CAF1 148152 92 + 1
UUUUGCCAGCCGUCCUCGUCCUCAGAGGACGACGACAGCAGAAGCAGUAAC--AGCAGCAGCAAAUAAUUUUGUAAUUCAAUUGUUGUCCUUCU
........(.(((((((.......))))))).)((((((((..((.((...--.)).)).(((((....))))).......))))))))..... ( -26.20)
>DroPer_CAF1 157725 80 + 1
UUCUUCAAGUC------------AGACGAGGACGAGGACGUGGACGACGAC--AGCAGCAGCAAAUAAUUUUGUAAUUCAAUUGUUGUCGUUCU
.(((((..(((------------.......))))))))...((((((((((--((.....(((((....))))).......)))))))))))). ( -22.60)
>consensus
UUCUGCCAGCCGUCCUCGUCCUCAGAGGACGACGACAGCAAAGGCAGUAAC__AGCAGCAGCAAAUAAUUUUGUAAUUCAAUUGUUGUCCUUCU
........................(((((((((((........((((.......((....))........)))).......))))))))))).. (-15.10 = -14.49 +  -0.61)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,592,415 – 16,592,507
Length 92
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 79.75
Mean single sequence MFE -26.70
Consensus MFE -15.71
Energy contribution -18.63
Covariance contribution 2.92
Combinations/Pair 1.22
Mean z-score -2.17
Structure conservation index 0.59
SVM decision value 0.77
SVM RNA-class probability 0.846596
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16592415 92 - 27905053
AGAAGGACAACAAUUGAAUUACAAAAUUAUUUGCUGCCGCU--GUUACUGCCUUUGCUGUCGUCGUCCUCUAAAGACGAGGACGGCUGGCAGAA
....((.((.(((...((((....))))..))).))))...--....(((((...((((((.(((((.......))))).)))))).))))).. ( -32.90)
>DroPse_CAF1 150390 80 - 1
AGAACGACAACAAUUGAAUUACAAAAUUAUUUGCUGCUGCU--GUCGUCGUCCACGUCCACGUCCUCGUCU------------GACUUGAAGAA
.(.(((((.(((.(((.....)))........((....)))--)).))))).)..(((.(((....)))..------------)))........ ( -12.70)
>DroSim_CAF1 153670 94 - 1
AGAAGGACAACAAUUGAAUUACAAAAUUAUUUGCUGCCGCUGUGUUACUGCCUUUGCUGUCGUCGUCCUCUGAGGACGAGGACGGCUGGCAGAA
....((.((.(((...((((....))))..))).)))).........(((((...((((((.((((((.....)))))).)))))).))))).. ( -37.20)
>DroEre_CAF1 152504 92 - 1
AGAAGGACAACAAUUGAAUUACAAAAUUAUUUGCUGCUGCU--CUUACUGCCUUUGCUGUCGUCGUCCUCUGAGGACGAGGACGGCUGGCAGAA
(((.((.((.(((...((((....))))..))).))))..)--))..(((((...((((((.((((((.....)))))).)))))).))))).. ( -36.10)
>DroYak_CAF1 148152 92 - 1
AGAAGGACAACAAUUGAAUUACAAAAUUAUUUGCUGCUGCU--GUUACUGCUUCUGCUGUCGUCGUCCUCUGAGGACGAGGACGGCUGGCAAAA
....((.((.(((...((((....))))..))).))))...--.....((((...((((((.((((((.....)))))).)))))).))))... ( -29.40)
>DroPer_CAF1 157725 80 - 1
AGAACGACAACAAUUGAAUUACAAAAUUAUUUGCUGCUGCU--GUCGUCGUCCACGUCCUCGUCCUCGUCU------------GACUUGAAGAA
.(.(((((.(((.(((.....)))........((....)))--)).))))).)..(((..((....))...------------)))........ ( -11.90)
>consensus
AGAAGGACAACAAUUGAAUUACAAAAUUAUUUGCUGCUGCU__GUUACUGCCUUUGCUGUCGUCGUCCUCUGAGGACGAGGACGGCUGGCAGAA
....((.((.(((...((((....))))..))).)))).........(((((...((((((.(((((.......))))).)))))).))))).. (-15.71 = -18.63 +   2.92)

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 12:19:06 2006