Locus 7700

Sequence ID X_DroMel_CAF1
Location 19,197,204 – 19,197,424
Length 220
Max. P 0.923327
window12627 window12628 window12629 window12630

overview

Window 7

Location 19,197,204 – 19,197,305
Length 101
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.37
Mean single sequence MFE -28.67
Consensus MFE -25.27
Energy contribution -25.53
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.88
SVM decision value 0.94
SVM RNA-class probability 0.885195
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19197204 101 + 22224390
-----------UACAUGCAUAUGUGAUGUGGCCUUAUCAAAUGCAUGA--------UACCGGCUGCCAAGCAAGGCUUGUAAUUUUUAAAUUAGAAUUACGUGAUGUGCCUGCUAAAUUG
-----------..(((((((...(((((......))))).))))))).--------....(((.(((......)))..((((((((......)))))))).......))).......... ( -27.00)
>DroSec_CAF1 18720 112 + 1
UACCACAUACAUACAUGCAUAUGUGAUGUGGCCUUAUCAAAUGCAUGA--------UACCGGCUGCCAAGCAAGGCUUGUAAUUUUUAAAUUAGAAUUACGUGAUGUGCCUGCUAAAUCG
...((((((((((......))))).)))))(((.(((((......)))--------))..))).....((((.(((.(((((((((......)))))))))......)))))))...... ( -28.90)
>DroEre_CAF1 16207 109 + 1
-----------UACAUGCAUAUGUGAUGGGGCCUUAUCAAAUGCAUGAUACCAUGAUACCGGCUGCCAAGCAAGGCUUGUAAUUUUUAAAUUAGAAUUACGUGAUGUGCCUGCUAAAUUG
-----------..(((((((...((((((....)))))).)))))))...((........))......((((.(((.(((((((((......)))))))))......)))))))...... ( -27.40)
>DroYak_CAF1 16093 109 + 1
-----------UGCAUGCAUAUGCGAUGGGGCCUUAUCAAAUGCAUGAUACCAUGAUACCGGCUGCCAAGCAAGGCUUGUAAUUUUUAAAUUAGAAUUACGUGAUGUGCCUGCUAAAUCG
-----------.(((.((((((((....(((((((........((((....))))......(((....))))))))))((((((((......)))))))))).)))))).)))....... ( -31.40)
>consensus
___________UACAUGCAUAUGUGAUGGGGCCUUAUCAAAUGCAUGA________UACCGGCUGCCAAGCAAGGCUUGUAAUUUUUAAAUUAGAAUUACGUGAUGUGCCUGCUAAAUCG
.............(((((((...(((((......))))).))))))).............(((.(((......)))..((((((((......)))))))).......))).......... (-25.27 = -25.53 +   0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,197,204 – 19,197,305
Length 101
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.37
Mean single sequence MFE -26.08
Consensus MFE -23.36
Energy contribution -23.18
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -1.89
Structure conservation index 0.90
SVM decision value 1.15
SVM RNA-class probability 0.923327
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19197204 101 - 22224390
CAAUUUAGCAGGCACAUCACGUAAUUCUAAUUUAAAAAUUACAAGCCUUGCUUGGCAGCCGGUA--------UCAUGCAUUUGAUAAGGCCACAUCACAUAUGCAUGUA-----------
.......((.(((.......((((((..........))))))..(((......))).))).)).--------.(((((((.((((........))))...)))))))..----------- ( -23.40)
>DroSec_CAF1 18720 112 - 1
CGAUUUAGCAGGCACAUCACGUAAUUCUAAUUUAAAAAUUACAAGCCUUGCUUGGCAGCCGGUA--------UCAUGCAUUUGAUAAGGCCACAUCACAUAUGCAUGUAUGUAUGUGGUA
..........(((.......((((((..........))))))..(((......))).)))..((--------(((......)))))..(((((((.((((((....))))))))))))). ( -30.90)
>DroEre_CAF1 16207 109 - 1
CAAUUUAGCAGGCACAUCACGUAAUUCUAAUUUAAAAAUUACAAGCCUUGCUUGGCAGCCGGUAUCAUGGUAUCAUGCAUUUGAUAAGGCCCCAUCACAUAUGCAUGUA-----------
..........(((.......((((((..........))))))..(((......))).)))(((((....)))))((((((.((((........))))...))))))...----------- ( -24.10)
>DroYak_CAF1 16093 109 - 1
CGAUUUAGCAGGCACAUCACGUAAUUCUAAUUUAAAAAUUACAAGCCUUGCUUGGCAGCCGGUAUCAUGGUAUCAUGCAUUUGAUAAGGCCCCAUCGCAUAUGCAUGCA-----------
.......((.(((.......((((((..........))))))..(((......))).)))(((((....)))))((((((.((....(....)....)).)))))))).----------- ( -25.90)
>consensus
CAAUUUAGCAGGCACAUCACGUAAUUCUAAUUUAAAAAUUACAAGCCUUGCUUGGCAGCCGGUA________UCAUGCAUUUGAUAAGGCCACAUCACAUAUGCAUGUA___________
.......((.(((.......((((((..........))))))..(((......))).))).))..........(((((((.((((........))))...)))))))............. (-23.36 = -23.18 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,197,233 – 19,197,345
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.70
Mean single sequence MFE -31.93
Consensus MFE -30.05
Energy contribution -29.43
Covariance contribution -0.62
Combinations/Pair 1.09
Mean z-score -1.30
Structure conservation index 0.94
SVM decision value 0.04
SVM RNA-class probability 0.554041
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19197233 112 + 22224390
AUGCAUGA--------UACCGGCUGCCAAGCAAGGCUUGUAAUUUUUAAAUUAGAAUUACGUGAUGUGCCUGCUAAAUUGAGAUUAUUGAACGGUCGGAGAGCCAGGCAAGUGGCUAAGA
........--------..(((((((...((((.(((.(((((((((......)))))))))......)))))))...(..(.....)..).)))))))..(((((......))))).... ( -30.60)
>DroSec_CAF1 18760 112 + 1
AUGCAUGA--------UACCGGCUGCCAAGCAAGGCUUGUAAUUUUUAAAUUAGAAUUACGUGAUGUGCCUGCUAAAUCGAGUUUAUUGAACGGUCGGAGAGCUAGGCAAGUGGCUACGA
........--------..(((((((...((((.(((.(((((((((......)))))))))......)))))))...((((.....)))).)))))))..(((((......))))).... ( -30.50)
>DroEre_CAF1 16236 120 + 1
AUGCAUGAUACCAUGAUACCGGCUGCCAAGCAAGGCUUGUAAUUUUUAAAUUAGAAUUACGUGAUGUGCCUGCUAAAUUGGGAUUAUUGAACGGUCGGAGAGCUAGGCAAGUGGCUACGA
...((((....))))...((((((((((((((.(((.(((((((((......)))))))))......)))))))....)))..........)))))))..(((((......))))).... ( -30.90)
>DroYak_CAF1 16122 120 + 1
AUGCAUGAUACCAUGAUACCGGCUGCCAAGCAAGGCUUGUAAUUUUUAAAUUAGAAUUACGUGAUGUGCCUGCUAAAUCGAGAUUAUUGAACGGUCGGAGAGCUAGCCAAGUGGCUAAGA
...((((....))))...(((((((...((((.(((.(((((((((......)))))))))......)))))))...((((.....)))).))))))).....(((((....)))))... ( -35.70)
>consensus
AUGCAUGA________UACCGGCUGCCAAGCAAGGCUUGUAAUUUUUAAAUUAGAAUUACGUGAUGUGCCUGCUAAAUCGAGAUUAUUGAACGGUCGGAGAGCUAGGCAAGUGGCUAAGA
..................(((((((...((((.(((.(((((((((......)))))))))......)))))))...((((.....)))).)))))))..(((((......))))).... (-30.05 = -29.43 +  -0.62)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,197,305 – 19,197,424
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.09
Mean single sequence MFE -35.62
Consensus MFE -28.15
Energy contribution -28.78
Covariance contribution 0.63
Combinations/Pair 1.07
Mean z-score -1.60
Structure conservation index 0.79
SVM decision value 0.15
SVM RNA-class probability 0.608964
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19197305 119 + 22224390
AGAUUAUUGAACGGUCGGAGAGCCAGGCAAGUGGCUAAGAAAAUGUUGUUUAGAACCAGGUCGAGAAGUAUGGGACAUUCUGGGCCAGAGCAACA-GCUUUCCAGCCACGAAAACAUUGC
............(((.(((((((..(((.....))).......((((((((.(..(((((((...........)))...))))..).))))))))-))))))).)))............. ( -33.90)
>DroSec_CAF1 18832 118 + 1
AGUUUAUUGAACGGUCGGAGAGCUAGGCAAGUGGCUACGAAAAUGUUGUUUAGAACCAGGUCGAGAAGUAUGAGACGUUCUGGGCCAGAGCAACA-GCUUUCCAGCCACGAAAACAUUG-
.((((.(((...(((.((((((((.(((.....)))........(((((((.(..((((..((............))..))))..).))))))))-))))))).))).)))))))....- ( -36.40)
>DroEre_CAF1 16316 119 + 1
GGAUUAUUGAACGGUCGGAGAGCUAGGCAAGUGGCUACGAAAAUGUUGUUUAGAGCCAGGUCGAGAAGUAUGGGACUUAC-GGGCCAGAGCAACAAGCUUUCCUGCCACGGAAACACUUC
............(((.((((((((.(((.....))).......((((((((.(.(((.((((...........))))...-.)))).)))))))))))))))).)))..(....)..... ( -37.60)
>DroYak_CAF1 16202 119 + 1
AGAUUAUUGAACGGUCGGAGAGCUAGCCAAGUGGCUAAGAAAAUGUUGUUUAGAACCAGGUCGAGAAGUAUGGCACUUUC-GGGCCAAAGCAACAAGCUUUCUUGCCACGAAAACAUUUC
............(((.((((((((((((....)))))......((((((((.......((((..(((((.....))))).-.)))).)))))))).))))))).)))............. ( -34.60)
>consensus
AGAUUAUUGAACGGUCGGAGAGCUAGGCAAGUGGCUAAGAAAAUGUUGUUUAGAACCAGGUCGAGAAGUAUGGGACUUUC_GGGCCAGAGCAACA_GCUUUCCAGCCACGAAAACAUUGC
............(((.((((((((((.(....).)))......((((((((.(..(((((((...........)))...))))..).)))))))).))))))).)))............. (-28.15 = -28.78 +   0.63)

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 12:45:23 2006