Locus 725

Sequence ID X_DroMel_CAF1
Location 1,986,716 – 1,986,875
Length 159
Max. P 0.854686
window1166 window1167 window1168

overview

Window 6

Location 1,986,716 – 1,986,836
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.64
Mean single sequence MFE -45.58
Consensus MFE -40.54
Energy contribution -42.23
Covariance contribution 1.69
Combinations/Pair 1.07
Mean z-score -1.34
Structure conservation index 0.89
SVM decision value -0.04
SVM RNA-class probability 0.512472
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1986716 120 + 22224390
GCACCGUCUGGGGCGAUUGAUUGUGGUUUGUGGGAAUGCAGGUCGCGUAAUUUCCGCCAGCGAAUCCCGCUUGGCCACCGAUCAUUUGCUUGGCGUUUUGAGUCGUGGUGGUAAGCAUCU
(((((..(..((((((.(((((((((((.((((((.(((.((.((.(......))))).)))..))))))..))))).)))))).))))))(((.......)))..)..)))..)).... ( -43.10)
>DroSec_CAF1 20254 120 + 1
GCACCGUUUGGGGCGAUUGGUUGUGAUUCGUGGGAAUGCAGGUGGCGUAAUUUCCGCCAGCGAAUCCCGCUUGACCACCGAUCAUUUGCUUGGCAUUUUGAGUAGUGGUGGUAAGCAUCU
((.((.....))))(((((((.((.(...((((((.(((.(((((........))))).)))..)))))).).)).)))))))...((((((.((((.........)))).))))))... ( -43.70)
>DroEre_CAF1 9846 120 + 1
GCACCGUCUGGGGCGAUUGGUUGUGGUUUGUGGGAAUGCAAGUGGCAUAAUUGCCGCCGGCGAAUCCCGCUUGGCCUCCGAUCAUUUGCUUGGCGUUUUGCGUCGUGGUGGUAAGCAUCU
(((((..(..((((((.((((((.((((.((((((.(((..((((((....))))))..)))..))))))..))))..)))))).))))))((((.....))))..)..)))..)).... ( -51.20)
>DroYak_CAF1 20568 120 + 1
GCACCGUCUGGGGCGAUUGGUUGUGGUUCGUGGGAAUACAUGUGGCGUAAUUGCCGCCGGCGAAUCCCGCUUGGCCACCGAUCAUUUGCUUGGCGUUCUGAGUCGUGGUGGUAAGCAUCU
(((((..(..((((((.(((((((((((.((((((......((((((....)))))).......))))))..))))).)))))).))))))(((.......)))..)..)))..)).... ( -44.32)
>consensus
GCACCGUCUGGGGCGAUUGGUUGUGGUUCGUGGGAAUGCAGGUGGCGUAAUUGCCGCCAGCGAAUCCCGCUUGGCCACCGAUCAUUUGCUUGGCGUUUUGAGUCGUGGUGGUAAGCAUCU
.(((((....((((((.(((((((((((.((((((.(((.(((((((....))))))).)))..))))))..))))).)))))).))))))(((.......))).))))).......... (-40.54 = -42.23 +   1.69)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,986,756 – 1,986,875
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.91
Mean single sequence MFE -51.55
Consensus MFE -41.31
Energy contribution -43.38
Covariance contribution 2.06
Combinations/Pair 1.07
Mean z-score -1.90
Structure conservation index 0.80
SVM decision value 0.53
SVM RNA-class probability 0.769974
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1986756 119 + 22224390
GGUCGCGUAAUUUCCGCCAGCGAAUCCCGCUUGGCCACCGAUCAUUUGCUUGGCGUUUUGAGUCGUGGUGGUAAGCAUCUGGG-GGCCGUUGCCUUGGAAUGGCUUGCCGGCGGUGAUCA
(((((((......)((((.((((.(((((((((.((((((.(((..(((...)))...)))....)))))))))))....)))-)((((((.(....))))))))))).)))))))))). ( -47.20)
>DroSec_CAF1 20294 119 + 1
GGUGGCGUAAUUUCCGCCAGCGAAUCCCGCUUGACCACCGAUCAUUUGCUUGGCAUUUUGAGUAGUGGUGGUAAGCAUCUGGG-GGCCGUUGCCCUGGAACGGCUUGCCGGCGGUGAUCA
(.(((((.......))))).)((.(((((((..(((((...(((..(((...)))...)))...)))))(((((((.((..((-(.......)))..))...)))))))))))).)))). ( -51.20)
>DroEre_CAF1 9886 119 + 1
AGUGGCAUAAUUGCCGCCGGCGAAUCCCGCUUGGCCUCCGAUCAUUUGCUUGGCGUUUUGCGUCGUGGUGGUAAGCAUCUGGG-UGCCGUUGCCUUGGAAGGGCUUACCGGCAGUGAUCA
...((((....))))(((((((.....))).))))....(((((((.(((.((((.....)))).....(((((((.((..((-.((....))))..))...))))))))))))))))). ( -49.70)
>DroYak_CAF1 20608 120 + 1
UGUGGCGUAAUUGCCGCCGGCGAAUCCCGCUUGGCCACCGAUCAUUUGCUUGGCGUUCUGAGUCGUGGUGGUAAGCAUCUGGGGGGCCGUUGCCCUGGAAGGGCUUGCCGGCGGUGAUCA
.........((..((((((((((..((((((((.((((((.(((..(((...)))...)))....))))))))))).((..(((........)))..)).))).))))))))))..)).. ( -58.10)
>consensus
GGUGGCGUAAUUGCCGCCAGCGAAUCCCGCUUGGCCACCGAUCAUUUGCUUGGCGUUUUGAGUCGUGGUGGUAAGCAUCUGGG_GGCCGUUGCCCUGGAAGGGCUUGCCGGCGGUGAUCA
.........((((((((((((((..(((((((.(((((((.(((..(((...)))...)))....)))))))))))....)))..((((((.(....))))))))))))))))))))).. (-41.31 = -43.38 +   2.06)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,986,756 – 1,986,875
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.91
Mean single sequence MFE -41.23
Consensus MFE -35.29
Energy contribution -34.73
Covariance contribution -0.56
Combinations/Pair 1.14
Mean z-score -1.85
Structure conservation index 0.86
SVM decision value 0.80
SVM RNA-class probability 0.854686
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1986756 119 - 22224390
UGAUCACCGCCGGCAAGCCAUUCCAAGGCAACGGCC-CCCAGAUGCUUACCACCACGACUCAAAACGCCAAGCAAAUGAUCGGUGGCCAAGCGGGAUUCGCUGGCGGAAAUUACGCGACC
((((..((((((((..(((.......)))...((..-(((....((((.(((((..((.(((....((...))...))))))))))..)))))))..))))))))))..))))....... ( -38.10)
>DroSec_CAF1 20294 119 - 1
UGAUCACCGCCGGCAAGCCGUUCCAGGGCAACGGCC-CCCAGAUGCUUACCACCACUACUCAAAAUGCCAAGCAAAUGAUCGGUGGUCAAGCGGGAUUCGCUGGCGGAAAUUACGCCACC
((((..((((((((..(((((((....).)))))).-(((....((((((((((.....(((...(((...)))..)))..)))))).)))))))....))))))))..))))....... ( -45.10)
>DroEre_CAF1 9886 119 - 1
UGAUCACUGCCGGUAAGCCCUUCCAAGGCAACGGCA-CCCAGAUGCUUACCACCACGACGCAAAACGCCAAGCAAAUGAUCGGAGGCCAAGCGGGAUUCGCCGGCGGCAAUUAUGCCACU
........(((((..(((((......(....)(((.-.((.(((((((..(.....)..((.....)).))))).....))))..)))....))).))..)))))((((....))))... ( -36.20)
>DroYak_CAF1 20608 120 - 1
UGAUCACCGCCGGCAAGCCCUUCCAGGGCAACGGCCCCCCAGAUGCUUACCACCACGACUCAGAACGCCAAGCAAAUGAUCGGUGGCCAAGCGGGAUUCGCCGGCGGCAAUUACGCCACA
((((..((((((((...(((.....((((....)))).......((((.(((((..((.(((....((...))...))))))))))..)))))))....))))))))..))))....... ( -45.50)
>consensus
UGAUCACCGCCGGCAAGCCCUUCCAAGGCAACGGCC_CCCAGAUGCUUACCACCACGACUCAAAACGCCAAGCAAAUGAUCGGUGGCCAAGCGGGAUUCGCCGGCGGAAAUUACGCCACC
((((..((((((((..(((.......)))...((((.((((..(((((.....................)))))..))...)).))))...........))))))))..))))....... (-35.29 = -34.73 +  -0.56)

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 09:52:10 2006