Locus 4443

Sequence ID 3L_DroMel_CAF1
Location 12,948,165 – 12,948,324
Length 159
Max. P 0.982560
window6902 window6903 window6904 window6905

overview

Window 2

Location 12,948,165 – 12,948,284
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.35
Mean single sequence MFE -33.54
Consensus MFE -24.10
Energy contribution -24.90
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.72
SVM decision value 0.49
SVM RNA-class probability 0.756970
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12948165 119 + 23771897
UGGUUUUUGGGC-AGAGGUUGAGUUUCGCCGAAGACUUCUUGCAGAAAAGUGUCUGAGACGACAGUUUUAUUGCUGUCGGCAUGAAAACUUUACGCUUUUUGGCUUGUAAGCCCCUAAAA
...(((..((((-(((((((..(......)...))))))).((.(((((((((..(((.(((((((......)))))))...(....)))).))))))))).))......))))..))). ( -35.60)
>DroSec_CAF1 65388 105 + 1
UGGUUUUUGGGU-AGAG--------------AAGACUUCUUACAGAAAAGUGUCUGAGUCGACAGUUUUAUUGCUGUCGGCAUGAAAACUUUACGCUUUUUGGCUUGUAUGCCCCUAAAA
....((((((((-((((--------------.((((..(((......))).))))..(((((((((......))))))))).......)))))).......(((......))).)))))) ( -31.90)
>DroSim_CAF1 69742 105 + 1
UGGUUUUUGGGC-AGAG--------------AAGACUUCUUGCAGAAAAGUGUCUGAGUCGACAGUUUUAUUGCUGUCGGCAUGAAAACUUUACGCUUUUUGGCUUGUACUCCCCUAAAA
....(((((((.-.(((--------------(((....)))((.(((((((((....(((((((((......))))))))).(....)....))))))))).)).....))).))))))) ( -31.70)
>DroEre_CAF1 71466 113 + 1
UGGUUUUUGAGG--G-----AGGUGCUCCAGAAGACUUCUUGCAGAAAAGUGUCUGAGUAGACAGUUUUAUUGCUGUCGGCAUGAAAACUUUACGCAUUUUGGCUUGUAAGCCCCUAAAA
.........(((--(-----((((((....((((..(((.((((((......))).....((((((......)))))).))).)))..))))..)))))))((((....))))))).... ( -29.10)
>DroYak_CAF1 69183 120 + 1
CGCUUUUUGGGGUGGAGGUUAAGUGCCCAAGAAGACUUCUUGCAGAAAAGUGUCUGAGUCGACAGUUUUAUUGCUGUCGGCAUGAAAACUUUACACAUUUUGGCUUGUAAGCCCCUAAAA
....((((((((((((((((..(((((......((((.(..(((......)))..)))))((((((......)))))))))))...)))))).))).....((((....))))))))))) ( -39.40)
>consensus
UGGUUUUUGGGC_AGAG_____GU______GAAGACUUCUUGCAGAAAAGUGUCUGAGUCGACAGUUUUAUUGCUGUCGGCAUGAAAACUUUACGCUUUUUGGCUUGUAAGCCCCUAAAA
....(((((((.....................((((..(((......))).))))..(((((((((......)))))))))....................(((......)))))))))) (-24.10 = -24.90 +   0.80)

alignment

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secondary structure

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Window 3

Location 12,948,165 – 12,948,284
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.35
Mean single sequence MFE -24.72
Consensus MFE -18.34
Energy contribution -18.06
Covariance contribution -0.28
Combinations/Pair 1.12
Mean z-score -1.52
Structure conservation index 0.74
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12948165 119 - 23771897
UUUUAGGGGCUUACAAGCCAAAAAGCGUAAAGUUUUCAUGCCGACAGCAAUAAAACUGUCGUCUCAGACACUUUUCUGCAAGAAGUCUUCGGCGAAACUCAACCUCU-GCCCAAAAACCA
......((((......((......))((..((((((...(((((..(((..((((.((((......)))).)))).))).((....)))))))))))))..))....-))))........ ( -27.70)
>DroSec_CAF1 65388 105 - 1
UUUUAGGGGCAUACAAGCCAAAAAGCGUAAAGUUUUCAUGCCGACAGCAAUAAAACUGUCGACUCAGACACUUUUCUGUAAGAAGUCUU--------------CUCU-ACCCAAAAACCA
((((.(((((......))).......(..(((.((((....((((((........))))))...((((......))))...)))).)))--------------..).-.)).)))).... ( -21.00)
>DroSim_CAF1 69742 105 - 1
UUUUAGGGGAGUACAAGCCAAAAAGCGUAAAGUUUUCAUGCCGACAGCAAUAAAACUGUCGACUCAGACACUUUUCUGCAAGAAGUCUU--------------CUCU-GCCCAAAAACCA
.....(((((((....((...(((((.....)))))...))((((((........))))))))))(((.((((((.....))))))..)--------------))..-.)))........ ( -23.50)
>DroEre_CAF1 71466 113 - 1
UUUUAGGGGCUUACAAGCCAAAAUGCGUAAAGUUUUCAUGCCGACAGCAAUAAAACUGUCUACUCAGACACUUUUCUGCAAGAAGUCUUCUGGAGCACCU-----C--CCUCAAAAACCA
(((((((((((....))))....((((((.((((((..(((.....)))..))))))...)))(((((.((((((.....))))))..))))).)))...-----.--))).)))).... ( -24.50)
>DroYak_CAF1 69183 120 - 1
UUUUAGGGGCUUACAAGCCAAAAUGUGUAAAGUUUUCAUGCCGACAGCAAUAAAACUGUCGACUCAGACACUUUUCUGCAAGAAGUCUUCUUGGGCACUUAACCUCCACCCCAAAAAGCG
.....((((.(((((..........))))).(((....(((((((((........)))))....((((......))))(((((.....)))))))))...))).....))))........ ( -26.90)
>consensus
UUUUAGGGGCUUACAAGCCAAAAAGCGUAAAGUUUUCAUGCCGACAGCAAUAAAACUGUCGACUCAGACACUUUUCUGCAAGAAGUCUUC______AC_____CUCU_CCCCAAAAACCA
.....(((........((......))...(((.((((.(((((((((........))))))....(((......)))))).)))).)))....................)))........ (-18.34 = -18.06 +  -0.28)

alignment

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secondary structure

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Window 4

Location 12,948,204 – 12,948,324
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.92
Mean single sequence MFE -31.54
Consensus MFE -28.94
Energy contribution -29.82
Covariance contribution 0.88
Combinations/Pair 1.06
Mean z-score -1.69
Structure conservation index 0.92
SVM decision value 1.92
SVM RNA-class probability 0.982560
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12948204 120 + 23771897
UGCAGAAAAGUGUCUGAGACGACAGUUUUAUUGCUGUCGGCAUGAAAACUUUACGCUUUUUGGCUUGUAAGCCCCUAAAAGGCUUAUAAUGUAAUUAGAUUUGUCGUCGCCUUUGUUAUG
.((((((((((((..(((.(((((((......)))))))...(....)))).)))))))))((((((((((((.......)))))))))........(((.....))))))..))).... ( -33.70)
>DroSec_CAF1 65413 120 + 1
UACAGAAAAGUGUCUGAGUCGACAGUUUUAUUGCUGUCGGCAUGAAAACUUUACGCUUUUUGGCUUGUAUGCCCCUAAAAGGCUUAUAAUGUAAUUAGAUUUGUCGUCGCCUUUGUUAUG
....(((((((((....(((((((((......))))))))).(....)....)))))))))((((((((.(((.......))).)))))........(((.....))))))......... ( -31.00)
>DroSim_CAF1 69767 120 + 1
UGCAGAAAAGUGUCUGAGUCGACAGUUUUAUUGCUGUCGGCAUGAAAACUUUACGCUUUUUGGCUUGUACUCCCCUAAAAGGCUUAUAAUGUAAUUAGAUUUGUCGUCGCCUUUGUUAUG
.((.(((((((((....(((((((((......))))))))).(....)....))))))))).)).............((((((...((((...))))(((.....)))))))))...... ( -29.40)
>DroEre_CAF1 71499 120 + 1
UGCAGAAAAGUGUCUGAGUAGACAGUUUUAUUGCUGUCGGCAUGAAAACUUUACGCAUUUUGGCUUGUAAGCCCCUAAAAGGCUUAUAAUGUAAUUAGAUUUGUCACCGCCUUUGUUUUG
..((((......))))....((((((......))))))(((.((((((((((((((......))(((((((((.......))))))))).))))..)).))).)))..)))......... ( -29.20)
>DroYak_CAF1 69223 120 + 1
UGCAGAAAAGUGUCUGAGUCGACAGUUUUAUUGCUGUCGGCAUGAAAACUUUACACAUUUUGGCUUGUAAGCCCCUAAAAGGCUUAUAAUGUAAUUAGAUUUGUCGUCGCCUUUGUUAUU
.((((((((((((.((((((((((((......))))))))).(....)..))).)))))))((((((((((((.......)))))))))........(((.....))))))))))).... ( -34.40)
>consensus
UGCAGAAAAGUGUCUGAGUCGACAGUUUUAUUGCUGUCGGCAUGAAAACUUUACGCUUUUUGGCUUGUAAGCCCCUAAAAGGCUUAUAAUGUAAUUAGAUUUGUCGUCGCCUUUGUUAUG
.((((((((((......(((((((((......)))))))))......))))).........((((((((((((.......)))))))))........(((.....))))))))))).... (-28.94 = -29.82 +   0.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,948,204 – 12,948,324
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.92
Mean single sequence MFE -25.52
Consensus MFE -22.12
Energy contribution -22.60
Covariance contribution 0.48
Combinations/Pair 1.07
Mean z-score -1.86
Structure conservation index 0.87
SVM decision value 1.65
SVM RNA-class probability 0.969891
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12948204 120 - 23771897
CAUAACAAAGGCGACGACAAAUCUAAUUACAUUAUAAGCCUUUUAGGGGCUUACAAGCCAAAAAGCGUAAAGUUUUCAUGCCGACAGCAAUAAAACUGUCGUCUCAGACACUUUUCUGCA
..........((((((((........((((....(((((((.....)))))))...((......))))))((((((..(((.....)))..))))))))))))..(((......))))). ( -29.20)
>DroSec_CAF1 65413 120 - 1
CAUAACAAAGGCGACGACAAAUCUAAUUACAUUAUAAGCCUUUUAGGGGCAUACAAGCCAAAAAGCGUAAAGUUUUCAUGCCGACAGCAAUAAAACUGUCGACUCAGACACUUUUCUGUA
.........(((((.(((...................((((.....))))......((......)).....))).))..)))(((((........)))))....((((......)))).. ( -22.30)
>DroSim_CAF1 69767 120 - 1
CAUAACAAAGGCGACGACAAAUCUAAUUACAUUAUAAGCCUUUUAGGGGAGUACAAGCCAAAAAGCGUAAAGUUUUCAUGCCGACAGCAAUAAAACUGUCGACUCAGACACUUUUCUGCA
......((((((.........................))))))(((..((((....((...(((((.....)))))...))((((((........))))))........))))..))).. ( -24.81)
>DroEre_CAF1 71499 120 - 1
CAAAACAAAGGCGGUGACAAAUCUAAUUACAUUAUAAGCCUUUUAGGGGCUUACAAGCCAAAAUGCGUAAAGUUUUCAUGCCGACAGCAAUAAAACUGUCUACUCAGACACUUUUCUGCA
.........((((....)........((((....(((((((.....)))))))...((......)))))).........)))....(((..((((.(((((....))))).)))).))). ( -27.20)
>DroYak_CAF1 69223 120 - 1
AAUAACAAAGGCGACGACAAAUCUAAUUACAUUAUAAGCCUUUUAGGGGCUUACAAGCCAAAAUGUGUAAAGUUUUCAUGCCGACAGCAAUAAAACUGUCGACUCAGACACUUUUCUGCA
.........(((...((....))...........(((((((.....)))))))...)))....(((..(((((.((...(.((((((........)))))).)...)).)))))...))) ( -24.10)
>consensus
CAUAACAAAGGCGACGACAAAUCUAAUUACAUUAUAAGCCUUUUAGGGGCUUACAAGCCAAAAAGCGUAAAGUUUUCAUGCCGACAGCAAUAAAACUGUCGACUCAGACACUUUUCUGCA
.........((((....)................(((((((.....)))))))...))).....(((.(((((.((...(.((((((........)))))).)...)).)))))..))). (-22.12 = -22.60 +   0.48)

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 11:23:01 2006