Locus 372

Sequence ID 3R_DroMel_CAF1
Location 1,422,404 – 1,422,533
Length 129
Max. P 0.955976
window618 window619 window620

overview

Window 8

Location 1,422,404 – 1,422,506
Length 102
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 80.48
Mean single sequence MFE -23.93
Consensus MFE -17.89
Energy contribution -17.83
Covariance contribution -0.05
Combinations/Pair 1.20
Mean z-score -1.65
Structure conservation index 0.75
SVM decision value 0.64
SVM RNA-class probability 0.809259
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1422404 102 - 27905053
CGUAAUUGCAAGAGAAAUUUGGGUUUUUUGCUUGCCUCGUUGAUUUCCA-UUCACUGAACAACGUAGGCCAAUGAAAACCUGGACAAU----AUAAAUAUUCAAAUU
.................((..(((((((.....(((((((((..(((..-......)))))))).))))....)))))))..))....----............... ( -21.90)
>DroVir_CAF1 3951 105 - 1
CAAAAUUGCAAGAGC-AUUUGGGUUUUUUGCUUGCCUCGUUGUUUUUAAAACCAUAGAACAACGCAGGCCAAUGAAAACCUGGACAUUCGAUG-GAAUAUUUCCUGC
.......(((.(((.-.((..(((((((.....(((((((((((((.........))))))))).))))....)))))))..))..)))...(-((.....)))))) ( -31.30)
>DroGri_CAF1 4286 106 - 1
CAAAAUUGCAAAAGC-AAUUGGGUUUUUUGCUUGCCUCGUUGUUUUAUCAAUCAAUAAACAAUGCAGGCCAAUGAAAACCUGGACAAAGGAUAUAAAUAAUUGUAGC
...((((((....))-))))((((((((.....((((((((((((...........)))))))).))))....)))))))).......................... ( -25.30)
>DroSec_CAF1 4299 102 - 1
CGUAAUUGCAAGAGAAAUUUGGGUUUUUUGCUUGCCUCGUUGCUUUCGA-UUCACUGAACAACGUAGGCCAAUGAAAACCUGGACAAU----AUAAGUAUUCAAAUU
.................((..(((((((.....(((((((((..((((.-.....))))))))).))))....)))))))..))....----............... ( -23.20)
>DroEre_CAF1 4490 99 - 1
CGUAAUUGCAAGAGAAAUUUGUGUUUUUUGCUUGCCACGUUGCUUUCAA-UUUACUGAACAGCGUAGGCCAAUGAAAACCUGGACAAC----AUA-GUAUAUAAA--
.((....((((((((........))))))))..(((((((((..((((.-.....)))))))))).)))..............))...----...-.........-- ( -19.10)
>DroYak_CAF1 4901 101 - 1
CGUAAUUGCAAGAGAAAUUUGGGUUUUUUGCUUGCCUCGUUGCUUUCGA-UUCACUGAACAACGUAGGCCAAUGAAAACCUGAACAAU----AUA-GUAUUAAAACG
.................((..(((((((.....(((((((((..((((.-.....))))))))).))))....)))))))..))....----...-........... ( -22.80)
>consensus
CGUAAUUGCAAGAGAAAUUUGGGUUUUUUGCUUGCCUCGUUGCUUUCAA_UUCACUGAACAACGUAGGCCAAUGAAAACCUGGACAAU____AUAAAUAUUUAAAGC
.................((..(((((((.....(((((((((.((...........)).))))).))))....)))))))..))....................... (-17.89 = -17.83 +  -0.05) 

alignment

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secondary structure

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dotplot

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Window 9

Location 1,422,436 – 1,422,533
Length 97
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 75.78
Mean single sequence MFE -22.51
Consensus MFE -13.92
Energy contribution -14.36
Covariance contribution 0.45
Combinations/Pair 1.12
Mean z-score -1.61
Structure conservation index 0.62
SVM decision value 0.74
SVM RNA-class probability 0.837908
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1422436 97 + 27905053
UGGCCUACGUUGUUCAGU----G-AA-UGGAAAUCAACGAGGCAAGCAAAAAACCCAAAUUUCUCUUGCAAUUACGUACCAGAAUCA---AGCUAUU-U--AAGACAAG
..((((.(((((((((..----.-..-))))...))))))))).................((((..(((......)))..))))...---.......-.--........ ( -16.20)
>DroVir_CAF1 3986 99 + 1
UGGCCUGCGUUGUUCUAU----G-GUUUUAAAAACAACGAGGCAAGCAAAAAACCCAAAU-GCUCUUGCAAUUUUGUACAAUGAAAA---UGCCACA-CAAAAGGCAAA
..((((.(((((((....----.-........)))))))))))............(((((-((....)))..))))...........---((((...-.....)))).. ( -21.42)
>DroPse_CAF1 5144 99 + 1
UGGCCUACGUUGCUCUGGUU-UU-CU-UUUUGAGCAACAAGGCAAGCAAAAAACCCAAAU-GCUCUUGCAAUUUUGUACAAUGAAAG---UGCCAUC-C--AGGACAAG
((.(((..(((((((.((..-..-))-....)))))))..((((...........(((((-((....)))..))))...........---))))...-.--))).)).. ( -23.55)
>DroGri_CAF1 4322 98 + 1
UGGCCUGCAUUGUUUAUU----G-AUUGAUAAAACAACGAGGCAAGCAAAAAACCCAAUU-GCUUUUGCAAUUUUGUACAAUGUAAGAAGUGCCAC-----AUGGCAAA
..((((.(.(((((((((----.-...))).)))))).)))))..(((....((..((((-((....))))))..))....)))......((((..-----..)))).. ( -21.80)
>DroMoj_CAF1 5650 101 + 1
UGGCCUUCAUUGUUUAUU----GUAUUUUCAAAACAACGAGGCAAGCAAAAAACCCAAAU-GCUAUUGCAAUUUUGUACAAUGAAAG---AGCCACGUCAAAAGGCAAA
(((((((((((((...((----(......))).((((....(((((((...........)-)))..)))....)))))))))).)))---.)))).(((....)))... ( -21.90)
>DroPer_CAF1 4811 100 + 1
UGGCCUACGUUGCUCUGGUUUUU-CU-UUUGGAGCAACGAGGCAAGCAAAAAACCCAAAU-GCUCUUGCAAUUUUGUACAAUGAAAG---UGCCAUC-C--AGGACAAG
..((((.((((((((..(.....-..-.)..))))))))))))...........((...(-((....))).....((((.......)---)))....-.--.))..... ( -30.20)
>consensus
UGGCCUACGUUGUUCAGU____G_AU_UUUAAAACAACGAGGCAAGCAAAAAACCCAAAU_GCUCUUGCAAUUUUGUACAAUGAAAG___UGCCACC_C__AAGACAAA
..((((.((((((((................))))))))))))..((((................))))........................................ (-13.92 = -14.36 +   0.45) 

alignment

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secondary structure

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dotplot

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Window 0

Location 1,422,436 – 1,422,533
Length 97
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 75.78
Mean single sequence MFE -24.46
Consensus MFE -19.62
Energy contribution -18.62
Covariance contribution -1.00
Combinations/Pair 1.32
Mean z-score -1.55
Structure conservation index 0.80
SVM decision value 1.46
SVM RNA-class probability 0.955976
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1422436 97 - 27905053
CUUGUCUU--A-AAUAGCU---UGAUUCUGGUACGUAAUUGCAAGAGAAAUUUGGGUUUUUUGCUUGCCUCGUUGAUUUCCA-UU-C----ACUGAACAACGUAGGCCA
.......(--(-((.((((---..(((((.(((......))).))))....)..)))).))))...(((((((((..(((..-..-.----...)))))))).)))).. ( -18.30)
>DroVir_CAF1 3986 99 - 1
UUUGCCUUUUG-UGUGGCA---UUUUCAUUGUACAAAAUUGCAAGAGC-AUUUGGGUUUUUUGCUUGCCUCGUUGUUUUUAAAAC-C----AUAGAACAACGCAGGCCA
.((((.(((((-((..(..---......)..)))))))..))))((((-(...........)))))(((((((((((((......-.----..))))))))).)))).. ( -28.00)
>DroPse_CAF1 5144 99 - 1
CUUGUCCU--G-GAUGGCA---CUUUCAUUGUACAAAAUUGCAAGAGC-AUUUGGGUUUUUUGCUUGCCUUGUUGCUCAAAA-AG-AA-AACCAGAGCAACGUAGGCCA
.....((.--.-((((...---..(((.(((((......)))))))))-)))..))..........((((((((((((....-..-..-.....)))))))).)))).. ( -26.42)
>DroGri_CAF1 4322 98 - 1
UUUGCCAU-----GUGGCACUUCUUACAUUGUACAAAAUUGCAAAAGC-AAUUGGGUUUUUUGCUUGCCUCGUUGUUUUAUCAAU-C----AAUAAACAAUGCAGGCCA
..((((..-----..)))).......((....((..((((((....))-))))..))....))...((((((((((((.......-.----...)))))))).)))).. ( -24.60)
>DroMoj_CAF1 5650 101 - 1
UUUGCCUUUUGACGUGGCU---CUUUCAUUGUACAAAAUUGCAAUAGC-AUUUGGGUUUUUUGCUUGCCUCGUUGUUUUGAAAAUAC----AAUAAACAAUGAAGGCCA
...((((((.((((.(((.---.....((((((......))))))(((-(...........)))).))).))))((((.........----...))))...)))))).. ( -21.50)
>DroPer_CAF1 4811 100 - 1
CUUGUCCU--G-GAUGGCA---CUUUCAUUGUACAAAAUUGCAAGAGC-AUUUGGGUUUUUUGCUUGCCUCGUUGCUCCAAA-AG-AAAAACCAGAGCAACGUAGGCCA
.....((.--.-((((...---..(((.(((((......)))))))))-)))..))..........((((((((((((....-..-........)))))))).)))).. ( -27.94)
>consensus
CUUGCCUU__G_GAUGGCA___CUUUCAUUGUACAAAAUUGCAAGAGC_AUUUGGGUUUUUUGCUUGCCUCGUUGUUUUAAA_AU_C____ACAGAACAACGUAGGCCA
...(((.........)))......................(((((((..........)))))))..((((((((((((................)))))))).)))).. (-19.62 = -18.62 +  -1.00) 

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 09:41:40 2006