Locus 6393

Sequence ID 3R_DroMel_CAF1
Location 16,770,142 – 16,770,542
Length 400
Max. P 0.954673
window10418 window10419 window10420 window10421 window10422

overview

Window 8

Location 16,770,142 – 16,770,262
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.66
Mean single sequence MFE -30.03
Consensus MFE -23.92
Energy contribution -24.03
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.82
Structure conservation index 0.80
SVM decision value 0.29
SVM RNA-class probability 0.668661
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16770142 120 - 27905053
AAAACGCCUUUGGUGCAGCGUGGAAAACGGGAAACUUUUCCCUACCCGCCUAGAAAAACACUAAACAAAAGUUGAGUCGAGCAAAACAACAGAGGCAACAAACAUCGCGAAACAACAUUA
.....(((((((.(((((.((((.....(((((....)))))...))))))........(((.(((....))).)))...)))......)))))))........................ ( -26.50)
>DroSec_CAF1 2191 119 - 1
AAAACGCCUUUGGUGCGGCGUGGAAAGCGAGAAAGUUUUC-CUGCCCGCCUAGAAAAACACUAAACAAAAGUUGAGUCGAGCAAAACAACAGAGGCAACAAACAUCGCGAAACAACAUUA
.....((((((((((.((((.(((((((......))))))-))))))))).........(((.(((....))).))).............))))))........................ ( -31.80)
>DroSim_CAF1 3651 119 - 1
AAAACGCCUUUGGUGCGGCGUGGAAAGCGAGAAAGUUUUC-CUGCCCGCCUAGAAAAACACUAAACAAAAGUUGAGUCGAGCAAAACAACAGAGGCAACAAACAUCGCGAAACAACAUUA
.....((((((((((.((((.(((((((......))))))-))))))))).........(((.(((....))).))).............))))))........................ ( -31.80)
>consensus
AAAACGCCUUUGGUGCGGCGUGGAAAGCGAGAAAGUUUUC_CUGCCCGCCUAGAAAAACACUAAACAAAAGUUGAGUCGAGCAAAACAACAGAGGCAACAAACAUCGCGAAACAACAUUA
.....(((((((.(((((((.((.....((((....))))....)))))).........(((.(((....))).)))...)))......)))))))........................ (-23.92 = -24.03 +   0.11)

alignment

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secondary structure

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Window 9

Location 16,770,182 – 16,770,302
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.87
Mean single sequence MFE -33.53
Consensus MFE -30.33
Energy contribution -29.45
Covariance contribution -0.88
Combinations/Pair 1.14
Mean z-score -1.96
Structure conservation index 0.90
SVM decision value 0.46
SVM RNA-class probability 0.743232
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16770182 120 + 27905053
UCGACUCAACUUUUGUUUAGUGUUUUUCUAGGCGGGUAGGGAAAAGUUUCCCGUUUUCCACGCUGCACCAAAGGCGUUUUCCCUUUUUUCUCGCACGAAACUGUUGAGUGGCAAGUACAC
.(.(((((((....((((.((((.......((((((..(((((....))))).....)).)))).....(((((.(....))))))......)))).)))).))))))).)......... ( -32.90)
>DroSec_CAF1 2231 119 + 1
UCGACUCAACUUUUGUUUAGUGUUUUUCUAGGCGGGCAG-GAAAACUUUCUCGCUUUCCACGCCGCACCAAAGGCGUUUUUCCCUUUUUCUCACACAAAACUGUUGAGUGGCAAGUACAC
.(.(((((((....((((.((((.......((..(((..-(((....)))..)))..))(((((........)))))...............)))).)))).))))))).)......... ( -33.70)
>DroSim_CAF1 3691 119 + 1
UCGACUCAACUUUUGUUUAGUGUUUUUCUAGGCGGGCAG-GAAAACUUUCUCGCUUUCCACGCCGCACCAAAGGCGUUUUUCCCUUUUCCUCGCACAAAACUGUUGAGUGGCAAGUACAC
.(.(((((((....((((.((((.......((..(((..-(((....)))..)))..))(((((........)))))...............)))).)))).))))))).)......... ( -34.00)
>consensus
UCGACUCAACUUUUGUUUAGUGUUUUUCUAGGCGGGCAG_GAAAACUUUCUCGCUUUCCACGCCGCACCAAAGGCGUUUUUCCCUUUUUCUCGCACAAAACUGUUGAGUGGCAAGUACAC
.(.(((((((....((((.((((......(((((((.............)))))))...(((((........)))))...............)))).)))).))))))).)......... (-30.33 = -29.45 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,770,262 – 16,770,382
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.11
Mean single sequence MFE -32.70
Consensus MFE -27.62
Energy contribution -27.73
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.27
Structure conservation index 0.84
SVM decision value 0.60
SVM RNA-class probability 0.794228
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16770262 120 - 27905053
UGUGUGUUUGUGCUGGUGUUGAUGACUGCACAAAGCACACAAACUCGAAAAAAAGAACACACACACACGGCAACACUUCUGUGUACUUGCCACUCAACAGUUUCGUGCGAGAAAAAAGGG
((((((((((((((.((((........))))..))))).(......).......))))))))).....((((((((....))))...)))).(((.((......))..)))......... ( -32.20)
>DroSec_CAF1 2310 112 - 1
------UGUGUGCGGGUGUUGAUGACUGCACAAAGCACACAAACUCGAAAAAAAGAA--CACACACACGGCAACACUUCUGUGUACUUGCCACUCAACAGUUUUGUGUGAGAAAAAGGGA
------(((((((..((((........))))...)))))))................--..((((((.((((((((....))))...))))(((....)))..))))))........... ( -32.40)
>DroSim_CAF1 3770 112 - 1
UA----UGUGUGCGGGUGUUGAUGACUGCACAAAGCACACAAACUCGAAAAAA--AA--CACACACACGGCAACACUUCUGUGUACUUGCCACUCAACAGUUUUGUGCGAGGAAAAGGGA
..----(((((((..((((........))))...)))))))..((((....((--((--(........((((((((....))))...))))........)))))...))))......... ( -33.49)
>consensus
U_____UGUGUGCGGGUGUUGAUGACUGCACAAAGCACACAAACUCGAAAAAAAGAA__CACACACACGGCAACACUUCUGUGUACUUGCCACUCAACAGUUUUGUGCGAGAAAAAGGGA
......(((((((..((((........))))...)))))))..((((.....................((((((((....))))...)))).....((......)).))))......... (-27.62 = -27.73 +   0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,770,302 – 16,770,422
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.37
Mean single sequence MFE -37.35
Consensus MFE -31.83
Energy contribution -33.67
Covariance contribution 1.83
Combinations/Pair 1.00
Mean z-score -3.86
Structure conservation index 0.85
SVM decision value 1.45
SVM RNA-class probability 0.954673
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16770302 120 - 27905053
UAAUGUCCUUUCUAUUUACUAUCCACUGGCUGUGUGUGCGUGUGUGUUUGUGCUGGUGUUGAUGACUGCACAAAGCACACAAACUCGAAAAAAAGAACACACACACACGGCAACACUUCU
............................((((((((((.((((((((((((((.(((.......))))))).))))))......((........)))))).))))))))))......... ( -36.40)
>DroSec_CAF1 2350 112 - 1
UAAUGUCCUUUCUAUUUACUAUCCACUGGCUGUGUGUGUG------UGUGUGCGGGUGUUGAUGACUGCACAAAGCACACAAACUCGAAAAAAAGAA--CACACACACGGCAACACUUCU
............................((((((((((((------(((((((..((((........))))...))))))....((........)))--))))))))))))......... ( -38.90)
>DroSim_CAF1 3810 112 - 1
UAAUGUCCUUUCUAUUUACUAUCCACUGGCUGUGUGUGUGUA----UGUGUGCGGGUGUUGAUGACUGCACAAAGCACACAAACUCGAAAAAA--AA--CACACACACGGCAACACUUCU
............................(((((((((((((.----(((((((..((((........))))...)))))))............--.)--))))))))))))......... ( -36.74)
>consensus
UAAUGUCCUUUCUAUUUACUAUCCACUGGCUGUGUGUGUGU_____UGUGUGCGGGUGUUGAUGACUGCACAAAGCACACAAACUCGAAAAAAAGAA__CACACACACGGCAACACUUCU
............................((((((((((((((....(((((((..((((........))))...)))))))...((........)).))))))))))))))......... (-31.83 = -33.67 +   1.83)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,770,422 – 16,770,542
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -43.17
Consensus MFE -40.97
Energy contribution -41.63
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.95
SVM decision value 0.95
SVM RNA-class probability 0.889037
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16770422 120 + 27905053
AGUGGCGUUAAACAGACACUCGUGCAACAGCCGCAACAUGUGAAGUGGACCAGCGGGGAAGUGGCAAGCCAGGACAUCGGGUGGUUGGGUGUGAAAAAAAUGCAUGAGGCUGCGCCAUUG
(((((((.....(((...(((((((((((.((....(((.....)))(((((.(.((....(((....))).....)).).))))))).)))........)))))))).)))))))))). ( -40.90)
>DroSec_CAF1 2462 120 + 1
AGUGGCGUUAAACAGACACUCGUGCAACAGCCGCAACAUGUGAAGUGGACCAGCGGGGAAGUGGCACGCCAGGACAUCGGGUGGAUUGGUGGGGAAAAAAGGCAUGAGGCUGCGCCAUUG
(((((((.....(((...(((((((....(((((..(((.....)))..((....))...))))).((((((..(((...)))..))))))..........))))))).)))))))))). ( -44.30)
>DroSim_CAF1 3922 120 + 1
AGUGGCGUUAAACAGACACUCGUGCAACAGCCGCAACAUGUGAAGUGGACCAGCGGGGAAGUGGCACGCCAGGACAUCGGGUGGAUUGGUGGGGAAAAAAGGCAUGAGGCUGCGCCAUUG
(((((((.....(((...(((((((....(((((..(((.....)))..((....))...))))).((((((..(((...)))..))))))..........))))))).)))))))))). ( -44.30)
>consensus
AGUGGCGUUAAACAGACACUCGUGCAACAGCCGCAACAUGUGAAGUGGACCAGCGGGGAAGUGGCACGCCAGGACAUCGGGUGGAUUGGUGGGGAAAAAAGGCAUGAGGCUGCGCCAUUG
(((((((.....(((...(((((((....(((((..(((.....)))..((....))...))))).((((((..(((...)))..))))))..........))))))).)))))))))). (-40.97 = -41.63 +   0.67)

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 12:20:24 2006