Locus 4694

Sequence ID 3L_DroMel_CAF1
Location 13,235,219 – 13,235,346
Length 127
Max. P 0.965221
window7394 window7395 window7396 window7397

overview

Window 4

Location 13,235,219 – 13,235,312
Length 93
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 87.20
Mean single sequence MFE -20.95
Consensus MFE -16.98
Energy contribution -17.38
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.81
SVM decision value 1.31
SVM RNA-class probability 0.940428
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13235219 93 + 23771897
AGCCAAAAACUAGUUUAUGGUCAACGGUUUUUUU------UUUUUUCGGAUGCAUAAUUCGCUCAAAAUAGCUGACCAAAUGACUUUUAGUUCGGCUCA
((((...((((((.....(((((..((((..((.------((((..(((((.....)))))...)))).))..))))...))))).)))))).)))).. ( -20.00)
>DroSec_CAF1 28596 88 + 1
AGCCAAAAACUAGUUUAUGGUCAACGCAUU----------UUUUUUCGGAUGCAUAAUUCGCUCGAAAUAGCUGACCAAAUGACUU-UUAUUCGGCUCA
((((.......((((..((((((..(((((----------(......)))))).......(((......)))))))))...)))).-......)))).. ( -22.74)
>DroSim_CAF1 33561 89 + 1
AGCCAAAAACUAGUUUAUGGUCAACGCAUU----------UUUUUUCGGAUGCAUAAUUCGCUCGAAAUAGCUGACCAAAUGACUUUUUAUUCGGCUCA
((((((.((..((((..((((((..(((((----------(......)))))).......(((......)))))))))...))))..)).)).)))).. ( -22.40)
>DroEre_CAF1 18075 87 + 1
AGCCAAAAACUAGUUUAUGGUCAACGCUUUUUUUC------------GGAUGCAUAAUUCGCUCGAAAUAGCUGACCAAAUGACUUUUUGUUCAGCUCA
((((((((...((((..((((((..(((...((((------------((..((.......)))))))).)))))))))...)))))))))....))).. ( -20.10)
>DroYak_CAF1 28700 99 + 1
AGCCAAAAACUAGUUUAUGGUCAACGCUUUUUUUCUUCUUUUCUUUGGGAUGCAUAAUUCGCUCGAAAUAGCUGACCAAAUGACUUUUUGUUUAGCUCA
(((.(((....((((..((((((..(((...((((.((((......)))).((.......))..)))).)))))))))...)))).....))).))).. ( -19.50)
>consensus
AGCCAAAAACUAGUUUAUGGUCAACGCUUUUUUU______UUUUUUCGGAUGCAUAAUUCGCUCGAAAUAGCUGACCAAAUGACUUUUUGUUCGGCUCA
((((.((....((((..((((((........................((((.....))))(((......)))))))))...)))).....)).)))).. (-16.98 = -17.38 +   0.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,235,219 – 13,235,312
Length 93
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 87.20
Mean single sequence MFE -21.34
Consensus MFE -18.58
Energy contribution -18.22
Covariance contribution -0.36
Combinations/Pair 1.13
Mean z-score -1.97
Structure conservation index 0.87
SVM decision value 1.58
SVM RNA-class probability 0.965221
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13235219 93 - 23771897
UGAGCCGAACUAAAAGUCAUUUGGUCAGCUAUUUUGAGCGAAUUAUGCAUCCGAAAAAA------AAAAAAACCGUUGACCAUAAACUAGUUUUUGGCU
..(((((((..(..(((....((((((((..(((((((((.....))).))........------...))))..))))))))...)))..).))))))) ( -19.20)
>DroSec_CAF1 28596 88 - 1
UGAGCCGAAUAA-AAGUCAUUUGGUCAGCUAUUUCGAGCGAAUUAUGCAUCCGAAAAAA----------AAUGCGUUGACCAUAAACUAGUUUUUGGCU
..(((((((.(.-.(((....((((((((...(((....)))....((((.........----------.))))))))))))...)))..).))))))) ( -24.30)
>DroSim_CAF1 33561 89 - 1
UGAGCCGAAUAAAAAGUCAUUUGGUCAGCUAUUUCGAGCGAAUUAUGCAUCCGAAAAAA----------AAUGCGUUGACCAUAAACUAGUUUUUGGCU
..(((((((.((..(((....((((((((...(((....)))....((((.........----------.))))))))))))...)))..))))))))) ( -23.80)
>DroEre_CAF1 18075 87 - 1
UGAGCUGAACAAAAAGUCAUUUGGUCAGCUAUUUCGAGCGAAUUAUGCAUCC------------GAAAAAAAGCGUUGACCAUAAACUAGUUUUUGGCU
..(((..((.((..(((....((((((((..(((((.(((.....)))...)------------))))......))))))))...)))..))))..))) ( -20.30)
>DroYak_CAF1 28700 99 - 1
UGAGCUAAACAAAAAGUCAUUUGGUCAGCUAUUUCGAGCGAAUUAUGCAUCCCAAAGAAAAGAAGAAAAAAAGCGUUGACCAUAAACUAGUUUUUGGCU
..(((((((.((..(((....((((((((........(((.....))).((.....))................))))))))...)))..))))))))) ( -19.10)
>consensus
UGAGCCGAACAAAAAGUCAUUUGGUCAGCUAUUUCGAGCGAAUUAUGCAUCCGAAAAAA______AAAAAAAGCGUUGACCAUAAACUAGUUUUUGGCU
..(((((((.....(((....((((((((...(((....)))....((........................))))))))))...)))....))))))) (-18.58 = -18.22 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,235,250 – 13,235,346
Length 96
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 78.96
Mean single sequence MFE -21.37
Consensus MFE -12.33
Energy contribution -12.69
Covariance contribution 0.36
Combinations/Pair 1.20
Mean z-score -1.87
Structure conservation index 0.58
SVM decision value 0.45
SVM RNA-class probability 0.740124
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13235250 96 + 23771897
UUU--------UUUUUU-------CGGAUGCAUAAUUCGCUCAAAAUAGCUGACCAAAUGACUUUUA---GUUCGGCUCACUCAUUUUGAGCUCAUAACAAAUGAGAGCAAAGU
(((--------(.((((-------(((((.....))))((((((((((((((((.(((.....))).---).)))))).....)))))))))...........))))).)))). ( -20.80)
>DroSec_CAF1 28626 92 + 1
-----------UUUUUU-------CGGAUGCAUAAUUCGCUCGAAAUAGCUGACCAAAUGACUU-UU---AUUCGGCUCACUCAUUUCGAGCUCAUAACAAAUGAGAGCAAAGU
-----------......-------....(((.......(((((((((((.(((((.(((((...-))---))).)).))))).)))))))))((((.....))))..))).... ( -22.60)
>DroSim_CAF1 33591 93 + 1
-----------UUUUUU-------CGGAUGCAUAAUUCGCUCGAAAUAGCUGACCAAAUGACUUUUU---AUUCGGCUCACUCAUUUCGAGCUCAUAACAAAUGAGAGCAAGAU
-----------......-------....(((.......(((((((((((.(((((.(((((....))---))).)).))))).)))))))))((((.....))))..))).... ( -23.40)
>DroEre_CAF1 18106 90 + 1
UUUC---------------------GGAUGCAUAAUUCGCUCGAAAUAGCUGACCAAAUGACUUUUU---GUUCAGCUCACUCAUUUUGUGCUCAUAACAAAUGAGAGCACAGU
((((---------------------((..((.......)))))))).((((((.((((......)))---).))))))........((((((((...........)))))))). ( -24.40)
>DroYak_CAF1 28731 102 + 1
UUUCUU--CUUUUCUUU-------GGGAUGCAUAAUUCGCUCGAAAUAGCUGACCAAAUGACUUUUU---GUUUAGCUCACUCAUUUUGUGCUCAUAACAAAUGAGAGCAAAGU
......--.....((((-------.((((.....))))((((.....((((((.((((......)))---).))))))...((((((.((.......)))))))))))))))). ( -21.10)
>DroAna_CAF1 114825 107 + 1
UUUCAGCUUUUUUCUUUAUACACACAUAUGCAUAAUUCUCCCGAACUAGCUGACCAAAUGACUUUUUCGAGUUCGGCUUAA-------AUGCUCAUAAUAAAUGAGAGCAAAGU
.....(((((.(((((.............((((.......(((((((......................))))))).....-------))))...........))))).))))) ( -15.90)
>consensus
UUU________UUUUUU_______CGGAUGCAUAAUUCGCUCGAAAUAGCUGACCAAAUGACUUUUU___GUUCGGCUCACUCAUUUUGAGCUCAUAACAAAUGAGAGCAAAGU
............................(((..........((((((((((((...................)))))).....))))))..(((((.....))))).))).... (-12.33 = -12.69 +   0.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,235,250 – 13,235,346
Length 96
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 78.96
Mean single sequence MFE -23.87
Consensus MFE -12.59
Energy contribution -12.92
Covariance contribution 0.33
Combinations/Pair 1.15
Mean z-score -2.16
Structure conservation index 0.53
SVM decision value 0.57
SVM RNA-class probability 0.784762
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13235250 96 - 23771897
ACUUUGCUCUCAUUUGUUAUGAGCUCAAAAUGAGUGAGCCGAAC---UAAAAGUCAUUUGGUCAGCUAUUUUGAGCGAAUUAUGCAUCCG-------AAAAAA--------AAA
....(((..((((.....))))(((((((((.(((..((((((.---.........))))))..)))))))))))).......)))....-------......--------... ( -23.10)
>DroSec_CAF1 28626 92 - 1
ACUUUGCUCUCAUUUGUUAUGAGCUCGAAAUGAGUGAGCCGAAU---AA-AAGUCAUUUGGUCAGCUAUUUCGAGCGAAUUAUGCAUCCG-------AAAAAA-----------
....(((..((((.....))))(((((((((.(((..(((((((---..-.....)))))))..)))))))))))).......)))....-------......----------- ( -26.80)
>DroSim_CAF1 33591 93 - 1
AUCUUGCUCUCAUUUGUUAUGAGCUCGAAAUGAGUGAGCCGAAU---AAAAAGUCAUUUGGUCAGCUAUUUCGAGCGAAUUAUGCAUCCG-------AAAAAA-----------
....(((..((((.....))))(((((((((.(((..(((((((---........)))))))..)))))))))))).......)))....-------......----------- ( -27.10)
>DroEre_CAF1 18106 90 - 1
ACUGUGCUCUCAUUUGUUAUGAGCACAAAAUGAGUGAGCUGAAC---AAAAAGUCAUUUGGUCAGCUAUUUCGAGCGAAUUAUGCAUCC---------------------GAAA
..(((((((...........)))))))...((((..((((((.(---(((......)))).))))))..)))).(((.....)))....---------------------.... ( -23.40)
>DroYak_CAF1 28731 102 - 1
ACUUUGCUCUCAUUUGUUAUGAGCACAAAAUGAGUGAGCUAAAC---AAAAAGUCAUUUGGUCAGCUAUUUCGAGCGAAUUAUGCAUCCC-------AAAGAAAAG--AAGAAA
..((((((((((((..((.((....)).))..)))))(((...(---(((......))))...)))......)))))))...........-------.........--...... ( -18.90)
>DroAna_CAF1 114825 107 - 1
ACUUUGCUCUCAUUUAUUAUGAGCAU-------UUAAGCCGAACUCGAAAAAGUCAUUUGGUCAGCUAGUUCGGGAGAAUUAUGCAUAUGUGUGUAUAAAGAAAAAAGCUGAAA
....(((((...........))))).-------.....(((((..(......)...)))))((((((..(((....)))((((((((....)))))))).......)))))).. ( -23.90)
>consensus
ACUUUGCUCUCAUUUGUUAUGAGCACAAAAUGAGUGAGCCGAAC___AAAAAGUCAUUUGGUCAGCUAUUUCGAGCGAAUUAUGCAUCCG_______AAAAAA________AAA
..(((((((((((.....))))..........(((..((((((.............))))))..))).....)))))))................................... (-12.59 = -12.92 +   0.33)

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 11:30:57 2006