Locus 5819

Sequence ID X_DroMel_CAF1
Location 15,066,234 – 15,066,370
Length 136
Max. P 0.969128
window9442 window9443 window9444 window9445

overview

Window 2

Location 15,066,234 – 15,066,340
Length 106
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.06
Mean single sequence MFE -21.57
Consensus MFE -16.23
Energy contribution -15.90
Covariance contribution -0.33
Combinations/Pair 1.13
Mean z-score -2.24
Structure conservation index 0.75
SVM decision value 1.60
SVM RNA-class probability 0.966692
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15066234 106 + 22224390
-----CACUCGCGGUGUAAGCACACCAUCGCACCA---------UUCGCCCCAACCCACCCUUUGGCUCAGUCAUGCUCUGCGAAUUUUUCGCACAUUCCUACCCCUUUCUUUUCCAUCU
-----...(((((((((....)))))...(((..(---------((.(..((((........))))..))))..)))...)))).................................... ( -16.90)
>DroEre_CAF1 18364 111 + 1
ACUCGCACUCGCGGGGUAAGAACCACCUCGCACCAC--------CUCGCACC-ACCCACUUUGCAGCCCAGUCAUGCUCUGCGAAUUUUUCGCACAGUUCUACCCCUUCCUUUUCCAUGU
....((....))((((((.((((......((.....--------...))...-......(((((((..((....))..)))))))...........)))))))))).............. ( -25.70)
>DroYak_CAF1 20794 114 + 1
-----CACUCGCGGGGUAAGCACCACCUCGCACCACUUGCGCCACUUGCACC-ACCCACUUUUCAGCCCAGUCAUGCUCUGCGAAUUUUUCGCACAUUUCUACCCCUUUCUUUUUCAUAU
-----.......((((((.(((......((((.....)))).....)))...-...........(((........))).(((((.....)))))......)))))).............. ( -22.10)
>consensus
_____CACUCGCGGGGUAAGCACCACCUCGCACCAC________CUCGCACC_ACCCACUUUUCAGCCCAGUCAUGCUCUGCGAAUUUUUCGCACAUUUCUACCCCUUUCUUUUCCAUAU
..........(((((((.......))))))).................................(((........))).(((((.....))))).......................... (-16.23 = -15.90 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,066,234 – 15,066,340
Length 106
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.06
Mean single sequence MFE -32.97
Consensus MFE -22.64
Energy contribution -22.87
Covariance contribution 0.22
Combinations/Pair 1.04
Mean z-score -2.26
Structure conservation index 0.69
SVM decision value 1.38
SVM RNA-class probability 0.948335
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15066234 106 - 22224390
AGAUGGAAAAGAAAGGGGUAGGAAUGUGCGAAAAAUUCGCAGAGCAUGACUGAGCCAAAGGGUGGGUUGGGGCGAA---------UGGUGCGAUGGUGUGCUUACACCGCGAGUG-----
..............(.(((.......(((((.....)))))((((((..((.((((........)))).))(((..---------...)))......))))))..))).).....----- ( -24.80)
>DroEre_CAF1 18364 111 - 1
ACAUGGAAAAGGAAGGGGUAGAACUGUGCGAAAAAUUCGCAGAGCAUGACUGGGCUGCAAAGUGGGU-GGUGCGAG--------GUGGUGCGAGGUGGUUCUUACCCCGCGAGUGCGAGU
..............((((((((((..(((((.....))))...((((.((((.((..(.......).-.)).)..)--------)).))))...)..)))).))))))((....)).... ( -37.30)
>DroYak_CAF1 20794 114 - 1
AUAUGAAAAAGAAAGGGGUAGAAAUGUGCGAAAAAUUCGCAGAGCAUGACUGGGCUGAAAAGUGGGU-GGUGCAAGUGGCGCAAGUGGUGCGAGGUGGUGCUUACCCCGCGAGUG-----
..............(((((((....(..(.(....((((((..((((.(((.(.((....))).)))-.))))...(.((....)).))))))).).)..)))))))).......----- ( -36.80)
>consensus
ACAUGGAAAAGAAAGGGGUAGAAAUGUGCGAAAAAUUCGCAGAGCAUGACUGGGCUGAAAAGUGGGU_GGUGCGAG________GUGGUGCGAGGUGGUGCUUACCCCGCGAGUG_____
..............(((((((...(.(((((.....))))).)((((.((...(((....)))..((....))...........)).))))..........)))))))............ (-22.64 = -22.87 +   0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,066,264 – 15,066,370
Length 106
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 87.34
Mean single sequence MFE -28.04
Consensus MFE -20.18
Energy contribution -20.34
Covariance contribution 0.16
Combinations/Pair 1.16
Mean z-score -2.93
Structure conservation index 0.72
SVM decision value 1.60
SVM RNA-class probability 0.967006
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15066264 106 + 22224390
----UUCGCCCCAACCCACCCUUUGGCUCAGUCAUGCUCUGCGAAUUUUUCGCACAUUCCUACCCCUUUCUUUUCCAUCUGAUAC-------CUUAGGAUGUGCUGGGGCAUGUGCA
----...((((((.........((.((..((.....))..)).))......((((((.((((......((..........))...-------..))))))))))))))))....... ( -28.10)
>DroSec_CAF1 27483 105 + 1
----UUCGCCCC-ACCCACCCUUUAGCCCAGUCAUGCUCUGCGAAUUUUUCGCACAUUCCUACCCCUUUCUUUUCCAUCUGAUAC-------CUUAGGGUGUGCUGGGGCAUGUGCA
----...(((((-(.(((((((..(((........))).(((((.....)))))...............................-------...)))))).).))))))....... ( -29.60)
>DroSim_CAF1 13841 105 + 1
----UUCGCCCC-ACCCACCCUUUAGCCCAGUCAUGCUCUGCGAAUUUUUCGCACAUUCCUACCCCUUUCUUUUCCAUCUGAUAC-------CUUAGGGUGUGCUGGGGCAUGUGCA
----...(((((-(.(((((((..(((........))).(((((.....)))))...............................-------...)))))).).))))))....... ( -29.60)
>DroEre_CAF1 18400 105 + 1
----CUCGCACC-ACCCACUUUGCAGCCCAGUCAUGCUCUGCGAAUUUUUCGCACAGUUCUACCCCUUCCUUUUCCAUGUGAUAC-------CUUAGGAUGUGCUGGGGCAUAUGCA
----...(((..-.((((.(((((((..((....))..)))))))......(((((.(((((.....(((........).))...-------..)))))))))))))).....))). ( -26.70)
>DroYak_CAF1 20829 116 + 1
GCCACUUGCACC-ACCCACUUUUCAGCCCAGUCAUGCUCUGCGAAUUUUUCGCACAUUUCUACCCCUUUCUUUUUCAUAUGAUACCAUAUACCAUAGGGUGUACUGGGGCAUAUGCA
((....(((...-.....((....))((((((.(((((((((((.....)))).......................(((((....))))).....))))))))))))))))...)). ( -26.20)
>consensus
____UUCGCCCC_ACCCACCCUUUAGCCCAGUCAUGCUCUGCGAAUUUUUCGCACAUUCCUACCCCUUUCUUUUCCAUCUGAUAC_______CUUAGGGUGUGCUGGGGCAUGUGCA
.......(((((....((((((..(((........))).(((((.....))))).........................................))))))....)))))....... (-20.18 = -20.34 +   0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,066,264 – 15,066,370
Length 106
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 87.34
Mean single sequence MFE -34.90
Consensus MFE -25.16
Energy contribution -25.68
Covariance contribution 0.52
Combinations/Pair 1.17
Mean z-score -2.95
Structure conservation index 0.72
SVM decision value 1.64
SVM RNA-class probability 0.969128
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15066264 106 - 22224390
UGCACAUGCCCCAGCACAUCCUAAG-------GUAUCAGAUGGAAAAGAAAGGGGUAGGAAUGUGCGAAAAAUUCGCAGAGCAUGACUGAGCCAAAGGGUGGGUUGGGGCGAA----
......(((((((((.((((((...-------...((.....)).......((..(((..((((((((.....))))...))))..)))..))..)))))).)))))))))..---- ( -38.80)
>DroSec_CAF1 27483 105 - 1
UGCACAUGCCCCAGCACACCCUAAG-------GUAUCAGAUGGAAAAGAAAGGGGUAGGAAUGUGCGAAAAAUUCGCAGAGCAUGACUGGGCUAAAGGGUGGGU-GGGGCGAA----
......(((((((.(.((((((..(-------((.((.....))...........(((..((((((((.....))))...))))..))).)))..))))))).)-))))))..---- ( -36.90)
>DroSim_CAF1 13841 105 - 1
UGCACAUGCCCCAGCACACCCUAAG-------GUAUCAGAUGGAAAAGAAAGGGGUAGGAAUGUGCGAAAAAUUCGCAGAGCAUGACUGGGCUAAAGGGUGGGU-GGGGCGAA----
......(((((((.(.((((((..(-------((.((.....))...........(((..((((((((.....))))...))))..))).)))..))))))).)-))))))..---- ( -36.90)
>DroEre_CAF1 18400 105 - 1
UGCAUAUGCCCCAGCACAUCCUAAG-------GUAUCACAUGGAAAAGGAAGGGGUAGAACUGUGCGAAAAAUUCGCAGAGCAUGACUGGGCUGCAAAGUGGGU-GGUGCGAG----
......((((((..(...(((...(-------......)..)))....)..))))))....(.(((((.....))))).)((((.(((.(.((....))).)))-.))))...---- ( -28.70)
>DroYak_CAF1 20829 116 - 1
UGCAUAUGCCCCAGUACACCCUAUGGUAUAUGGUAUCAUAUGAAAAAGAAAGGGGUAGAAAUGUGCGAAAAAUUCGCAGAGCAUGACUGGGCUGAAAAGUGGGU-GGUGCAAGUGGC
.((((.((((((.....(((....)))(((((....)))))..........))))))...))))((((.....))))...((((.(((.(.((....))).)))-.))))....... ( -33.20)
>consensus
UGCACAUGCCCCAGCACACCCUAAG_______GUAUCAGAUGGAAAAGAAAGGGGUAGGAAUGUGCGAAAAAUUCGCAGAGCAUGACUGGGCUAAAGGGUGGGU_GGGGCGAA____
......((((((.((.((((((.............((....))........((..(((..((((((((.....))))...))))..)))..))..)))))).)).))))))...... (-25.16 = -25.68 +   0.52)

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 11:57:09 2006