Locus 4731

Sequence ID X_DroMel_CAF1
Location 12,301,074 – 12,301,201
Length 127
Max. P 0.968218
window7756 window7757 window7758 window7759

overview

Window 6

Location 12,301,074 – 12,301,180
Length 106
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 79.87
Mean single sequence MFE -29.15
Consensus MFE -18.24
Energy contribution -18.77
Covariance contribution 0.53
Combinations/Pair 1.05
Mean z-score -2.96
Structure conservation index 0.63
SVM decision value 1.58
SVM RNA-class probability 0.965642
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12301074 106 + 22224390
AUGUACG----UGUGUCUGUGUGUGUGUGCAUUUUAAAGCAAUAUAUAUAUGUAUAUAAGUGGGUCAACUUCAUUCGGUGGUUGUUGACCCACAUCUUUUUCGGC-UGCAU
(((((((----((((..(((((((((.(((........))))))))))))..)))))..((((((((((.((((...))))..))))))))))..........).-))))) ( -33.50)
>DroVir_CAF1 1955 89 + 1
--GUG------UAUGUGUGUGUGUGUGUGCAUUUUAAGGCAUGAU--------------GUAGGUCAACUUCAUUUGGUGGUUGUUGACCCACAUCUUUUUGGGCCUGCUU
--(((------((((..(....)..)))))))....((((..(((--------------((.(((((((.((((...))))..))))))).))))).......)))).... ( -27.70)
>DroEre_CAF1 3229 102 + 1
ACGUAAG----UGUGUUUGUG--UGUGUGCAUUUUAAAGCAAUAU--AUAUAUAUAUAAGUGGGUCAACUUCAUUCGGUGGUUGUUGACCCACAUCUUUUUCGGC-UGCAU
.((.(((----(((((.((((--(((((((........)).))))--))))).))))).((((((((((.((((...))))..))))))))))..)))...))..-..... ( -31.70)
>DroWil_CAF1 6626 100 + 1
AUCUCCCUCUCUCUUUGUGUGUGUGUGUGCAUUUUAAACCAUAAU--GUUU--------GUAGGUCAACUUCAUUUGGUGGUUGUUGACCCACAUCUUUUUCGGU-UGCAU
................((((((((....))))....((((..((.--...(--------((.(((((((.((((...))))..))))))).)))....))..)))-))))) ( -19.50)
>DroYak_CAF1 2747 100 + 1
AUGUAAG----UGUGUUUGUA--UGUGUGCAUUUUAAAGCAAUAU--AUA--UAUAUAAGUGGGUCAACUUCAUUCGGUGGUUGUUGACCCACAUCUUUUUCGGC-UGCAU
(((((.(----(.(((.((((--(((((((........)).))))--)))--)).))).((((((((((.((((...))))..))))))))))..........))-))))) ( -31.00)
>DroAna_CAF1 1549 102 + 1
AUGUACA----UAUGUAUGUGUAUGUGUGCAUUUUAAAGCAUUAU----GUGUAUAUAAGUGGGUCAACUUCAUUCGGUGGUUGAUGACCCACAUCUUUUUCGGG-UGCAC
.(((((.----..((((((..((((.((((........)))))))----)..)))))).((((((((.(.((((...))))..).))))))))...........)-)))). ( -31.50)
>consensus
AUGUACG____UGUGUGUGUGUGUGUGUGCAUUUUAAAGCAAUAU__AUAU_UAUAUAAGUGGGUCAACUUCAUUCGGUGGUUGUUGACCCACAUCUUUUUCGGC_UGCAU
..........................(((((............................((((((((((.((((...))))..)))))))))).((......))..))))) (-18.24 = -18.77 +   0.53)

alignment

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secondary structure

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Window 7

Location 12,301,074 – 12,301,180
Length 106
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 79.87
Mean single sequence MFE -21.21
Consensus MFE -15.85
Energy contribution -15.97
Covariance contribution 0.11
Combinations/Pair 1.07
Mean z-score -3.09
Structure conservation index 0.75
SVM decision value 1.62
SVM RNA-class probability 0.968218
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12301074 106 - 22224390
AUGCA-GCCGAAAAAGAUGUGGGUCAACAACCACCGAAUGAAGUUGACCCACUUAUAUACAUAUAUAUAUUGCUUUAAAAUGCACACACACACAGACACA----CGUACAU
.((((-......((((..((((((((((..(........)..)))))))))).((((((....))))))...))))....))))................----....... ( -22.20)
>DroVir_CAF1 1955 89 - 1
AAGCAGGCCCAAAAAGAUGUGGGUCAACAACCACCAAAUGAAGUUGACCUAC--------------AUCAUGCCUUAAAAUGCACACACACACACACAUA------CAC--
..((((((.......(((((((((((((..(........)..))))))))))--------------)))..)))......))).................------...-- ( -23.00)
>DroEre_CAF1 3229 102 - 1
AUGCA-GCCGAAAAAGAUGUGGGUCAACAACCACCGAAUGAAGUUGACCCACUUAUAUAUAUAU--AUAUUGCUUUAAAAUGCACACA--CACAAACACA----CUUACGU
.((((-......((((..((((((((((..(........)..)))))))))).(((((....))--)))...))))....))))....--..........----....... ( -21.30)
>DroWil_CAF1 6626 100 - 1
AUGCA-ACCGAAAAAGAUGUGGGUCAACAACCACCAAAUGAAGUUGACCUAC--------AAAC--AUUAUGGUUUAAAAUGCACACACACACACAAAGAGAGAGGGAGAU
.((((-((((.......(((((((((((..(........)..))))))))))--------)...--....))))......))))........................... ( -20.34)
>DroYak_CAF1 2747 100 - 1
AUGCA-GCCGAAAAAGAUGUGGGUCAACAACCACCGAAUGAAGUUGACCCACUUAUAUA--UAU--AUAUUGCUUUAAAAUGCACACA--UACAAACACA----CUUACAU
.((((-......((((..((((((((((..(........)..)))))))))).((((..--..)--)))...))))....))))....--..........----....... ( -20.00)
>DroAna_CAF1 1549 102 - 1
GUGCA-CCCGAAAAAGAUGUGGGUCAUCAACCACCGAAUGAAGUUGACCCACUUAUAUACAC----AUAAUGCUUUAAAAUGCACACAUACACAUACAUA----UGUACAU
(((((-............(((((((((((.........)))...))))))))..........----....(((........)))................----))))).. ( -20.40)
>consensus
AUGCA_GCCGAAAAAGAUGUGGGUCAACAACCACCGAAUGAAGUUGACCCACUUAUAUA_AUAU__AUAAUGCUUUAAAAUGCACACACACACAAACACA____CGUACAU
..................((((((((((..(........)..))))))))))..................(((........)))........................... (-15.85 = -15.97 +   0.11)

alignment

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secondary structure

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Window 8

Location 12,301,107 – 12,301,201
Length 94
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 80.56
Mean single sequence MFE -22.54
Consensus MFE -15.24
Energy contribution -14.85
Covariance contribution -0.39
Combinations/Pair 1.28
Mean z-score -2.07
Structure conservation index 0.68
SVM decision value 0.83
SVM RNA-class probability 0.862641
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12301107 94 + 22224390
AGCAAUAUAUAUAUGUAUAUAAGUGGGUCA-ACUUCAUUCGGUGGUUGUUGACCCACAUCUUUUUCGGCUGCAUUUUG-UGUAUCCC--CGUAUCUGA----
.....((((((....)))))).((((((((-((.((((...))))..)))))))))).((.....(((.(((((...)-))))...)--)).....))---- ( -25.30)
>DroPse_CAF1 2502 82 + 1
AGCAAUAU--AAAU--------GUGGGUCAAACUUCGUUUGGUGGUUGUUGACCCACAUCUUUUUUGGCUGCAUU-UG-UGUAUC----UGUCUUCGG----
(((.....--..((--------(((((((((...(((.....)))...)))))))))))........))).....-..-......----.........---- ( -20.46)
>DroSim_CAF1 3956 90 + 1
AGCAAUAU--AUAUGUAUAUAAGUGGGUCA-ACUUCAUUUGGUGGUUGUUGACCCACAUCUUUUUCGGCUGCAUUUUG-UGUAUC----CGUAUCUGA----
....((((--(....)))))..((((((((-((.((((...))))..)))))))))).((.....(((.(((((...)-)))).)----)).....))---- ( -26.20)
>DroWil_CAF1 6663 91 + 1
ACCAUAAU--GUUU--------GUAGGUCA-ACUUCAUUUGGUGGUUGUUGACCCACAUCUUUUUCGGUUGCAUUUCGUUGUAUCACUUCGUAUCUAAUAUA
(((..((.--...(--------((.(((((-((.((((...))))..))))))).)))....))..)))((((......))))................... ( -16.90)
>DroYak_CAF1 2778 88 + 1
AGCAAUAU--AUA--UAUAUAAGUGGGUCA-ACUUCAUUCGGUGGUUGUUGACCCACAUCUUUUUCGGCUGCAUUUUG-UGUAUC----CGUAUCUGA----
........--...--.......((((((((-((.((((...))))..)))))))))).((.....(((.(((((...)-)))).)----)).....))---- ( -25.90)
>DroPer_CAF1 2444 82 + 1
AGCAAUAU--AAAU--------GUGGGUCAAACUUCGUUUGGUGGUUGUUGACCCACAUCUUUUUUGGCUGCAUU-UG-UGUAUC----UGUCUUCGG----
(((.....--..((--------(((((((((...(((.....)))...)))))))))))........))).....-..-......----.........---- ( -20.46)
>consensus
AGCAAUAU__AUAU________GUGGGUCA_ACUUCAUUUGGUGGUUGUUGACCCACAUCUUUUUCGGCUGCAUUUUG_UGUAUC____CGUAUCUGA____
......................((((((((....(((.....)))....)))))))).......((((.(((..................))).)))).... (-15.24 = -14.85 +  -0.39)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,301,107 – 12,301,201
Length 94
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 80.56
Mean single sequence MFE -19.01
Consensus MFE -11.99
Energy contribution -11.85
Covariance contribution -0.14
Combinations/Pair 1.09
Mean z-score -2.40
Structure conservation index 0.63
SVM decision value 0.97
SVM RNA-class probability 0.892352
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12301107 94 - 22224390
----UCAGAUACG--GGGAUACA-CAAAAUGCAGCCGAAAAAGAUGUGGGUCAACAACCACCGAAUGAAGU-UGACCCACUUAUAUACAUAUAUAUAUUGCU
----.........--........-......((((...........((((((((((..(........)..))-)))))))).((((((....)))))))))). ( -20.50)
>DroPse_CAF1 2502 82 - 1
----CCGAAGACA----GAUACA-CA-AAUGCAGCCAAAAAAGAUGUGGGUCAACAACCACCAAACGAAGUUUGACCCAC--------AUUU--AUAUUGCU
----.........----......-..-.....(((......((((((((((((((..(........)..).)))))))))--------))))--.....))) ( -18.30)
>DroSim_CAF1 3956 90 - 1
----UCAGAUACG----GAUACA-CAAAAUGCAGCCGAAAAAGAUGUGGGUCAACAACCACCAAAUGAAGU-UGACCCACUUAUAUACAUAU--AUAUUGCU
----.......((----(...((-.....))...)))........((((((((((..(........)..))-))))))))............--........ ( -19.60)
>DroWil_CAF1 6663 91 - 1
UAUAUUAGAUACGAAGUGAUACAACGAAAUGCAACCGAAAAAGAUGUGGGUCAACAACCACCAAAUGAAGU-UGACCUAC--------AAAC--AUUAUGGU
...............((......))........((((.......(((((((((((..(........)..))-))))))))--------)...--....)))) ( -17.74)
>DroYak_CAF1 2778 88 - 1
----UCAGAUACG----GAUACA-CAAAAUGCAGCCGAAAAAGAUGUGGGUCAACAACCACCGAAUGAAGU-UGACCCACUUAUAUA--UAU--AUAUUGCU
----.......((----(...((-.....))...)))........((((((((((..(........)..))-)))))))).......--...--........ ( -19.60)
>DroPer_CAF1 2444 82 - 1
----CCGAAGACA----GAUACA-CA-AAUGCAGCCAAAAAAGAUGUGGGUCAACAACCACCAAACGAAGUUUGACCCAC--------AUUU--AUAUUGCU
----.........----......-..-.....(((......((((((((((((((..(........)..).)))))))))--------))))--.....))) ( -18.30)
>consensus
____UCAGAUACG____GAUACA_CAAAAUGCAGCCGAAAAAGAUGUGGGUCAACAACCACCAAAUGAAGU_UGACCCAC________AUAU__AUAUUGCU
.............................................((((((((((..(........)..)).))))))))...................... (-11.99 = -11.85 +  -0.14)

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 11:32:00 2006