Locus 6396

Sequence ID X_DroMel_CAF1
Location 16,040,843 – 16,041,070
Length 227
Max. P 0.992380
window10439 window10440 window10441 window10442 window10443

overview

Window 9

Location 16,040,843 – 16,040,962
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.59
Mean single sequence MFE -31.70
Consensus MFE -24.37
Energy contribution -23.60
Covariance contribution -0.77
Combinations/Pair 1.19
Mean z-score -1.67
Structure conservation index 0.77
SVM decision value 0.86
SVM RNA-class probability 0.869155
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16040843 119 + 22224390
UUAAAUGGGUAAUUAACAGGGCUA-AAUAAGUGGUCCUAGAACCCAAGUUUCCCGGAGGUCCCAAGUACCCCAGUGGCUUGGCCAAUGUGACAACAUGGAAUAGUUGUUCCCAGUUGAUU
((((.((((....(((((((((((-......))))))).....((((((..(..((.(((.......))))).)..))))))(((.(((....))))))....))))..)))).)))).. ( -33.20)
>DroEre_CAF1 107785 98 + 1
UUAAUUGGGUAAUUGGGAGCGCUA-AGUAAGUGGUCCUAGAAC-CAGGUUUCCCGGAGGUCCC--------------------CAAUGUGACAACAUGGAACAGUUGUUCCCGGUUGAUU
...((((((...((((((.((((.-....)))).)))))).((-(.((....))...))).))--------------------))))....((((..(((((....)))))..))))... ( -32.40)
>DroYak_CAF1 90783 102 + 1
UUAACUGGGUAAUUAAGAGGACUGGAGUAAGUGGUCCUAGAACUCAAGUUUCCCGGAGGUCCUAG------------------CAAUGUGACAACAUGGAAUAGUUGUUCCCAGUUAAUU
(((((((((((((((.(((..(((((.(....).))).))..)))....((((..(..(((.((.------------------...)).)))..)..))))))))))..))))))))).. ( -29.50)
>consensus
UUAAAUGGGUAAUUAAGAGGGCUA_AGUAAGUGGUCCUAGAAC_CAAGUUUCCCGGAGGUCCCA___________________CAAUGUGACAACAUGGAAUAGUUGUUCCCAGUUGAUU
(((((((((((((((..(((((((.......)))))))...........((((.((....)).......................((((....))))))))))))))..))))))))).. (-24.37 = -23.60 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,040,843 – 16,040,962
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.59
Mean single sequence MFE -32.03
Consensus MFE -18.26
Energy contribution -18.60
Covariance contribution 0.34
Combinations/Pair 1.21
Mean z-score -3.32
Structure conservation index 0.57
SVM decision value 2.32
SVM RNA-class probability 0.992380
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16040843 119 - 22224390
AAUCAACUGGGAACAACUAUUCCAUGUUGUCACAUUGGCCAAGCCACUGGGGUACUUGGGACCUCCGGGAAACUUGGGUUCUAGGACCACUUAUU-UAGCCCUGUUAAUUACCCAUUUAA
...(((((((((.......))))).))))...((.((((...)))).))(((((((((((((((..((....)).)))))))))).........(-((((...))))).)))))...... ( -35.40)
>DroEre_CAF1 107785 98 - 1
AAUCAACCGGGAACAACUGUUCCAUGUUGUCACAUUG--------------------GGGACCUCCGGGAAACCUG-GUUCUAGGACCACUUACU-UAGCGCUCCCAAUUACCCAAUUAA
...((((..(((((....)))))..))))....((((--------------------((((((...((....)).)-)))...(((.(.((....-.)).).)))......))))))... ( -28.60)
>DroYak_CAF1 90783 102 - 1
AAUUAACUGGGAACAACUAUUCCAUGUUGUCACAUUG------------------CUAGGACCUCCGGGAAACUUGAGUUCUAGGACCACUUACUCCAGUCCUCUUAAUUACCCAGUUAA
..(((((((((.(((((........)))))...((((------------------..((((((((.((....)).))).....(((........))).)))))..))))..))))))))) ( -32.10)
>consensus
AAUCAACUGGGAACAACUAUUCCAUGUUGUCACAUUG___________________UGGGACCUCCGGGAAACUUG_GUUCUAGGACCACUUACU_UAGCCCUCUUAAUUACCCAAUUAA
........(((.(((((........))))).........................(((((((.((.((....)).)))))))))...........................)))...... (-18.26 = -18.60 +   0.34)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,040,882 – 16,041,002
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 76.90
Mean single sequence MFE -35.97
Consensus MFE -24.23
Energy contribution -24.47
Covariance contribution 0.24
Combinations/Pair 1.22
Mean z-score -1.75
Structure conservation index 0.67
SVM decision value 0.92
SVM RNA-class probability 0.881605
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16040882 120 + 22224390
AACCCAAGUUUCCCGGAGGUCCCAAGUACCCCAGUGGCUUGGCCAAUGUGACAACAUGGAAUAGUUGUUCCCAGUUGAUUGGGUUACUGCCUCCGGCGGCAACUUCAUGUUCUUAUGUGA
.....(((((((((((((((....((((.(((((((((...))).......((((..(((((....)))))..)))))))))).)))))))))))).)).)))))(((((....))))). ( -41.90)
>DroEre_CAF1 107824 97 + 1
AAC-CAGGUUUCCCGGAGGUCCC--------------------CAAUGUGACAACAUGGAACAGUUGUUCCCGGUUGAUUGGCACACUGCCUCC--GGGCAGCUCCGUGUUCCUAUGUGA
.((-..((((.(((((((((..(--------------------((((....((((..(((((....)))))..)))))))))......))))))--))).))))..))............ ( -34.80)
>DroYak_CAF1 90823 102 + 1
AACUCAAGUUUCCCGGAGGUCCUAG------------------CAAUGUGACAACAUGGAAUAGUUGUUCCCAGUUAAUUGGGAUACUGCCUCCAGGGGCAACUUCGUGUGCUCAUGUGA
.....(((((((((((((((((...------------------..((((....))))))).((((...((((((....)))))).))))))))).)))).)))))((((....))))... ( -31.20)
>consensus
AAC_CAAGUUUCCCGGAGGUCCCA___________________CAAUGUGACAACAUGGAAUAGUUGUUCCCAGUUGAUUGGGAUACUGCCUCC_GGGGCAACUUCGUGUUCUUAUGUGA
.....(((((.((((((((((((((....................((((....))))(((((....))))).......))))).....))))))..))).)))))((((....))))... (-24.23 = -24.47 +   0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,040,882 – 16,041,002
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 76.90
Mean single sequence MFE -35.33
Consensus MFE -20.50
Energy contribution -19.73
Covariance contribution -0.77
Combinations/Pair 1.17
Mean z-score -1.88
Structure conservation index 0.58
SVM decision value 0.28
SVM RNA-class probability 0.665356
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16040882 120 - 22224390
UCACAUAAGAACAUGAAGUUGCCGCCGGAGGCAGUAACCCAAUCAACUGGGAACAACUAUUCCAUGUUGUCACAUUGGCCAAGCCACUGGGGUACUUGGGACCUCCGGGAAACUUGGGUU
.........(((.(.(((((..(.((((((((((((.(((...(((((((((.......))))).))))...((.((((...)))).)))))))))...).)))))))).))))).)))) ( -38.40)
>DroEre_CAF1 107824 97 - 1
UCACAUAGGAACACGGAGCUGCCC--GGAGGCAGUGUGCCAAUCAACCGGGAACAACUGUUCCAUGUUGUCACAUUG--------------------GGGACCUCCGGGAAACCUG-GUU
.........(((.(((.(...(((--((((((((((((.....((((..(((((....)))))..)))).)))))))--------------------....))))))))...))))-))) ( -37.20)
>DroYak_CAF1 90823 102 - 1
UCACAUGAGCACACGAAGUUGCCCCUGGAGGCAGUAUCCCAAUUAACUGGGAACAACUAUUCCAUGUUGUCACAUUG------------------CUAGGACCUCCGGGAAACUUGAGUU
...............(((((...((((((((((((((((((......)))))(((((........))))).....))------------------))..).)))))))).)))))..... ( -30.40)
>consensus
UCACAUAAGAACACGAAGUUGCCCC_GGAGGCAGUAUCCCAAUCAACUGGGAACAACUAUUCCAUGUUGUCACAUUG___________________UGGGACCUCCGGGAAACUUG_GUU
..((.((((.........(((((......)))))...(((...((((..((((......))))..)))).............................((....)))))...)))).)). (-20.50 = -19.73 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,040,962 – 16,041,070
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.46
Mean single sequence MFE -25.07
Consensus MFE -17.81
Energy contribution -17.23
Covariance contribution -0.58
Combinations/Pair 1.14
Mean z-score -1.59
Structure conservation index 0.71
SVM decision value 0.16
SVM RNA-class probability 0.613943
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16040962 108 - 22224390
CAUUUUAAUUUACAAUUCAUGGAAACAUGAUGGGUUGUCUUCGCACACAACCACAUUUGCAUUC------------ACAUUCACAUAAGAACAUGAAGUUGCCGCCGGAGGCAGUAACCC
................(((((....)))))((((((((........)))))).))......(((------------(..(((......)))..))))(((((.(((...))).))))).. ( -26.30)
>DroEre_CAF1 107883 105 - 1
CAUUUUAAUUUACGUUUCAUGGAAAAAUGAUGGCUUGUCUUC-CACACAGCCACAUUAACAUUC------------ACAUUCACAUAGGAACACGGAGCUGCCC--GGAGGCAGUGUGCC
.............(((((((((((.((((.((((((((....-.))).))))))))).......------------...))).))).)))))..((.((((((.--...))))))...)) ( -25.70)
>DroYak_CAF1 90885 120 - 1
CAUUUUAAUUUACAUUUCAUGGAAACAUGAUGGGUUGUCUUCGCACACAACCACACUCACAUUCACUAUAACCAUCACAUUCACAUGAGCACACGAAGUUGCCCCUGGAGGCAGUAUCCC
...............(((((((((...(((((((((((........))))))........((.....))...)))))..))).)))))).....((..(((((......)))))..)).. ( -23.20)
>consensus
CAUUUUAAUUUACAUUUCAUGGAAACAUGAUGGGUUGUCUUCGCACACAACCACAUUAACAUUC____________ACAUUCACAUAAGAACACGAAGUUGCCCC_GGAGGCAGUAUCCC
................(((((....))))).((((((((((((....((((..(........................................)..))))....)))))))))...))) (-17.81 = -17.23 +  -0.58)

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 12:12:40 2006