Locus 1941

Sequence ID 2R_DroMel_CAF1
Location 7,327,150 – 7,327,315
Length 165
Max. P 0.931693
window3207 window3208 window3209 window3210

overview

Window 7

Location 7,327,150 – 7,327,249
Length 99
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 80.07
Mean single sequence MFE -35.93
Consensus MFE -18.79
Energy contribution -20.57
Covariance contribution 1.78
Combinations/Pair 1.21
Mean z-score -2.39
Structure conservation index 0.52
SVM decision value 0.58
SVM RNA-class probability 0.789908
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7327150 99 + 20766785
--CAGUAACAGCAGGGAAGAUCACCUGGACAAUUCCGACAUGUUGCUAGCGGGCGAGAACGAAGUGAAGCCACAACAGCCACGCAAGUUACUGUGGACAGU
--(((((((((((((........)))(((....)))........))).(((((((....)...(((....)))....))).)))..)))))))........ ( -27.30)
>DroPse_CAF1 99022 83 + 1
GGCGGUGGCAGCAAGGAGAACCACAGGCA------------GUGGCUGCAGGGCGACAAUAAGUUG------CAGCAGCAGCACAAGCUCCUGCUGCCACU
...((((((((((.((((...(((.....------------)))(((((...(((((.....))))------).)))))........)))))))))))))) ( -42.50)
>DroSec_CAF1 122891 99 + 1
--CAGCAACAGCAGGGAAGAUCACCCGGAUAAUUCCGACAUGUUGCUGGCGGGCGAGAACGAAGUGAAGCCACAACAGCCACGCAAGUUGCUGUGGACAGU
--((((((((.(.(((.......)))(((....))))...))))))))...(((..............)))...(((((.((....)).)))))....... ( -34.04)
>DroSim_CAF1 127349 99 + 1
--CAGCAACAGCAGGGAAGAUCACCGGGAUAAUUCCGACAUGUUGCUGGCGGGCGAGAACGAAGUGAAGCCACUACAGCCACGCAAGUUGCUGUGGACAGU
--((((((((...((((..(((.....)))..))))....))))))))...(((..............))).(((((((.((....)).)))))))..... ( -37.64)
>DroEre_CAF1 122907 99 + 1
--CAGCCACAGCAGGGAAGAUCGCCCGGAUAAUUCGGACAUGUUGCUGGCGGGCGAGAACGAAGUGAAGCCACAACAGCCACGCAAGUUGCUGUGGACAGU
--..((((((((((((.......))).........((...(((((.((((..((.........))...))))))))).))((....)))))))))).)... ( -34.90)
>DroYak_CAF1 126719 99 + 1
--CAGCCACAGCAGGGAGGAUCGCCCGGAUAAUUCCGACAUGUUGCUGGCGGGCGAGAACGAAGUGAAGCCACAACUGCCACGCAAGUUGCUGUGGACAGU
--..(((((((((((.((..(((((((((....))).....((.....)))))))).......(((....)))..)).))((....)))))))))).)... ( -39.20)
>consensus
__CAGCAACAGCAGGGAAGAUCACCCGGAUAAUUCCGACAUGUUGCUGGCGGGCGAGAACGAAGUGAAGCCACAACAGCCACGCAAGUUGCUGUGGACAGU
..((((.(((...((((..(((.....)))..))))....))).))))...(((..............)))...(((((.((....)).)))))....... (-18.79 = -20.57 +   1.78)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,327,184 – 7,327,286
Length 102
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 83.99
Mean single sequence MFE -39.23
Consensus MFE -27.05
Energy contribution -29.67
Covariance contribution 2.61
Combinations/Pair 1.15
Mean z-score -2.42
Structure conservation index 0.69
SVM decision value 0.22
SVM RNA-class probability 0.640530
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7327184 102 + 20766785
GACAUGUUGCUAGCGGGCGAGAACGAAGUGAAGCCACAACAGCCACGCAAGUUACUGUGGACAGUGCAACCACCGCUCGCAACACGUGGCAGCACACUAGCA
.......((((((((........))..(((..(((((.((((..((....))..))))(..(.(((....))).)..).......)))))..))).)))))) ( -30.70)
>DroPse_CAF1 99051 82 + 1
-----GUGGCUGCAGGGCGACAAUAAGUUG------CAGCAGCAGCACAAGCUCCUGCUGCCACUGCAGCCGCCG------ACA---GGCAGCACGCGAGUA
-----((((((((((((((((.....))).------.(((((.(((....))).)))))))).))))))))(((.------...---))).))((....)). ( -41.10)
>DroSec_CAF1 122925 102 + 1
GACAUGUUGCUGGCGGGCGAGAACGAAGUGAAGCCACAACAGCCACGCAAGUUGCUGUGGACAGUGCAACCACCGCUCGCAACACGUGGCAGCACGCUAGCA
.......((((((((.((.........(((....)))....((((((...(((((.((((............))))..))))).)))))).)).)))))))) ( -39.70)
>DroSim_CAF1 127383 102 + 1
GACAUGUUGCUGGCGGGCGAGAACGAAGUGAAGCCACUACAGCCACGCAAGUUGCUGUGGACAGUGCAACCACCGCUCGCAACACGUGGCAGCACGCUAGCA
.......((((((((.((......(.((((....)))).).((((((...(((((.((((............))))..))))).)))))).)).)))))))) ( -40.80)
>DroEre_CAF1 122941 102 + 1
GACAUGUUGCUGGCGGGCGAGAACGAAGUGAAGCCACAACAGCCACGCAAGUUGCUGUGGACAGUGCAACCACCGCUCGCAACACGUGGCAGCACGCCAGCA
.......((((((((.((.........(((....)))....((((((...(((((.((((............))))..))))).)))))).)).)))))))) ( -42.00)
>DroYak_CAF1 126753 102 + 1
GACAUGUUGCUGGCGGGCGAGAACGAAGUGAAGCCACAACUGCCACGCAAGUUGCUGUGGACAGUGCAACCACCGCUCGCAACACGUGGCAGCACGCCUGCA
............(((((((........(((....)))..((((((((...(((((.((((............))))..))))).))))))))..))))))). ( -41.10)
>consensus
GACAUGUUGCUGGCGGGCGAGAACGAAGUGAAGCCACAACAGCCACGCAAGUUGCUGUGGACAGUGCAACCACCGCUCGCAACACGUGGCAGCACGCUAGCA
........(((((((.((.........(((....)))....((((((...(((((.((((............))))..))))).)))))).)).))))))). (-27.05 = -29.67 +   2.61)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,327,212 – 7,327,315
Length 103
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 81.42
Mean single sequence MFE -36.42
Consensus MFE -26.81
Energy contribution -27.12
Covariance contribution 0.31
Combinations/Pair 1.27
Mean z-score -2.80
Structure conservation index 0.74
SVM decision value 1.21
SVM RNA-class probability 0.931693
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7327212 103 + 20766785
UGAAGCCACAACAGCCACGCAAGUUACUGUGGACAGUGCAACCACCGCUCGCAACACGUGGCAGCACACUAGCAACAUUGGUGGCAACACCAGAGCAGCAACA
....(((((.((((..((....))..))))(..(.(((....))).)..).......))))).........((..(.((((((....)))))).)..)).... ( -32.00)
>DroPse_CAF1 99074 88 + 1
UG------CAGCAGCAGCACAAGCUCCUGCUGCCACUGCAGCCGCCG------ACA---GGCAGCACGCGAGUACCUUCCGCGACGACGCCCAGGAGGAGACU
.(------((((((.(((....))).)))))))...(((.((.(((.------...---))).))..)))(((..((((((((....)))...)))))..))) ( -35.50)
>DroSec_CAF1 122953 103 + 1
UGAAGCCACAACAGCCACGCAAGUUGCUGUGGACAGUGCAACCACCGCUCGCAACACGUGGCAGCACGCUAGCAACAUUGGUGGCAACACCAGAGCAGCAACA
....(((((.(((((.((....)).)))))(..(.(((....))).)..).......))))).....(((.((....((((((....)))))).))))).... ( -38.30)
>DroSim_CAF1 127411 103 + 1
UGAAGCCACUACAGCCACGCAAGUUGCUGUGGACAGUGCAACCACCGCUCGCAACACGUGGCAGCACGCUAGCAACAUUGGUGGCAACACCAGAGCAGCAACA
...(((..(((((((.((....)).)))))))...((((..((((............))))..))))))).((..(.((((((....)))))).)..)).... ( -40.70)
>DroEre_CAF1 122969 103 + 1
UGAAGCCACAACAGCCACGCAAGUUGCUGUGGACAGUGCAACCACCGCUCGCAACACGUGGCAGCACGCCAGCAACACUGAUGGCGACACCAAUGCAGCAGCU
....(((((.(((((.((....)).)))))(..(.(((....))).)..).......))))).((((((((.((....)).))))).......)))....... ( -32.91)
>DroYak_CAF1 126781 103 + 1
UGAAGCCACAACUGCCACGCAAGUUGCUGUGGACAGUGCAACCACCGCUCGCAACACGUGGCAGCACGCCUGCAACAUUGGUGGCAACACCAGCGCAGCAACU
...........((((((((...(((((.((((............))))..))))).))))))))...((.(((....((((((....)))))).))))).... ( -39.10)
>consensus
UGAAGCCACAACAGCCACGCAAGUUGCUGUGGACAGUGCAACCACCGCUCGCAACACGUGGCAGCACGCUAGCAACAUUGGUGGCAACACCAGAGCAGCAACA
..........(((((.((....)).)))))((...((((..((((............))))..)))).)).((..(.((((((....)))))).)..)).... (-26.81 = -27.12 +   0.31)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,327,212 – 7,327,315
Length 103
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 81.42
Mean single sequence MFE -42.04
Consensus MFE -28.86
Energy contribution -30.07
Covariance contribution 1.20
Combinations/Pair 1.25
Mean z-score -1.94
Structure conservation index 0.69
SVM decision value 0.56
SVM RNA-class probability 0.780597
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7327212 103 - 20766785
UGUUGCUGCUCUGGUGUUGCCACCAAUGUUGCUAGUGUGCUGCCACGUGUUGCGAGCGGUGGUUGCACUGUCCACAGUAACUUGCGUGGCUGUUGUGGCUUCA
....((..(.........((((((((.((((((.((((((.(((((.(((.....)))))))).)))).....))))))))))).)))))....)..)).... ( -35.52)
>DroPse_CAF1 99074 88 - 1
AGUCUCCUCCUGGGCGUCGUCGCGGAAGGUACUCGCGUGCUGCC---UGU------CGGCGGCUGCAGUGGCAGCAGGAGCUUGUGCUGCUGCUG------CA
.((((......))))((((((((((..(((((....)))))..)---)).------))))))).((((..((((((.(....).))))))..)))------). ( -44.70)
>DroSec_CAF1 122953 103 - 1
UGUUGCUGCUCUGGUGUUGCCACCAAUGUUGCUAGCGUGCUGCCACGUGUUGCGAGCGGUGGUUGCACUGUCCACAGCAACUUGCGUGGCUGUUGUGGCUUCA
.(((((((....(((((.((((((....((((..(((((....)))))...))))..)))))).))))).....)))))))....(.((((.....)))).). ( -40.10)
>DroSim_CAF1 127411 103 - 1
UGUUGCUGCUCUGGUGUUGCCACCAAUGUUGCUAGCGUGCUGCCACGUGUUGCGAGCGGUGGUUGCACUGUCCACAGCAACUUGCGUGGCUGUAGUGGCUUCA
.((..((((...(((((.((((((....((((..(((((....)))))...))))..)))))).)))))(.((((.((.....))))))).))))..)).... ( -42.90)
>DroEre_CAF1 122969 103 - 1
AGCUGCUGCAUUGGUGUCGCCAUCAGUGUUGCUGGCGUGCUGCCACGUGUUGCGAGCGGUGGUUGCACUGUCCACAGCAACUUGCGUGGCUGUUGUGGCUUCA
.(((((.(((((((((....))))))))).)).)))((((.(((((.(((.....)))))))).)))).(.((((((((.((.....)).))))))))).... ( -43.70)
>DroYak_CAF1 126781 103 - 1
AGUUGCUGCGCUGGUGUUGCCACCAAUGUUGCAGGCGUGCUGCCACGUGUUGCGAGCGGUGGUUGCACUGUCCACAGCAACUUGCGUGGCAGUUGUGGCUUCA
...(((.(((.(((((....))))).))).)))(((..(((((((((((((((..((((((....)))))).....)))))..))))))))))....)))... ( -45.30)
>consensus
AGUUGCUGCUCUGGUGUUGCCACCAAUGUUGCUAGCGUGCUGCCACGUGUUGCGAGCGGUGGUUGCACUGUCCACAGCAACUUGCGUGGCUGUUGUGGCUUCA
....(((((...(((((.((((((....((((..(((((....)))))...))))..)))))).)))))....(((((.((....)).))))).))))).... (-28.86 = -30.07 +   1.20)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:54 2006