Locus 6586

Sequence ID 3L_DroMel_CAF1
Location 17,475,671 – 17,475,808
Length 137
Max. P 0.651671
window10725 window10726 window10727

overview

Window 5

Location 17,475,671 – 17,475,791
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.89
Mean single sequence MFE -29.24
Consensus MFE -25.10
Energy contribution -25.80
Covariance contribution 0.70
Combinations/Pair 1.03
Mean z-score -1.56
Structure conservation index 0.86
SVM decision value 0.25
SVM RNA-class probability 0.651671
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17475671 120 + 23771897
CUGUGAUAAUAACUGCAAGAACUUCAUCUACUUUAUACUGAUCUUUGCCAUUUGCGUAUUUAUGCAUUCCACCUCCGAGGUGGGCAGCAUGCUGCUCGUCAUGCGCUGCACACACCCCAA
.((((.........(((((....(((............)))..))))).....((((((.........(((((.....)))))((((....)))).....))))))....))))...... ( -26.60)
>DroVir_CAF1 40320 120 + 1
CUGUGAUAAUAACUGCAAGAACUUCAUCUACUUUAUACUGAUUUUUGCCAUUUGCGUAUUUAUGCAUUCCACCUCCGAGGUGGGCAGCAUGCUGCUCGUUAUGCGCUGCACACAUCCUAA
.((((.........(((((((..(((............)))))))))).....((((((....((...(((((.....)))))((((....))))..)).))))))....))))...... ( -30.10)
>DroGri_CAF1 39695 120 + 1
CUGUGAUAAUAACUGCAAGAACUUUAUCUACUUUAUAUUGAUUUUUGCCAUUUGCGUAUUUAUGCAUUCCACCUCCGAGGUGGGCAGCAUGCUGCUCGUCAUGCGCUGCACACAUCCUAA
.((((.........((((((((..(((.......)))..).))))))).....((((((.........(((((.....)))))((((....)))).....))))))....))))...... ( -29.30)
>DroWil_CAF1 43935 120 + 1
CUGUGAUAAUAACUGCAAGAACUUCAUCUACUUUAUACUGAUUUUUGCCAUUUGCGUAUUUAUGCAUUCCACCUCCGAGGUGGGCAGCAUGCUGCUUGUCAUGCGCUGUACACAUCCAAA
.((((.........(((((((..(((............)))))))))).....((((((....(((..(((((.....)))))((((....)))).))).))))))....))))...... ( -29.10)
>DroMoj_CAF1 39017 120 + 1
CUGUGAUAAUAACUGCAAGAACUUCAUCUACUUUAUAGCGAUUUUUGCCAUUUGCGUAUUUAUGCAUUCCACCUCUGAGGUGGGCAGCAUGCUGCUCGUCAUGCGCUGUACACAUCCUAA
.((((............(((......)))....((((((......((((...(((((....)))))...((((.....))))))))((((((.....).)))))))))))))))...... ( -31.50)
>DroAna_CAF1 35271 120 + 1
CUGUGAUAAUAACUGCAAGAACUUCAUAUACUUUAUACUGAUCUUUGCCAUUUGCGUAUUCAUGCAUUCCACCUCCGAGGUGGGCAGUAUGCUUCUCGUCAUGCGGUGUACACAUCCCAA
.((((.((...((((((.((.............(((((((............(((((....))))).((((((.....))))))))))))).......)).)))))).))))))...... ( -28.85)
>consensus
CUGUGAUAAUAACUGCAAGAACUUCAUCUACUUUAUACUGAUUUUUGCCAUUUGCGUAUUUAUGCAUUCCACCUCCGAGGUGGGCAGCAUGCUGCUCGUCAUGCGCUGCACACAUCCUAA
.((((.........((((((...(((............))).)))))).....((((((....((...(((((.....)))))((((....))))..)).))))))....))))...... (-25.10 = -25.80 +   0.70)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,475,711 – 17,475,808
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.31
Mean single sequence MFE -26.40
Consensus MFE -23.92
Energy contribution -23.42
Covariance contribution -0.50
Combinations/Pair 1.18
Mean z-score -1.17
Structure conservation index 0.91
SVM decision value 0.16
SVM RNA-class probability 0.611493
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17475711 97 + 23771897
AUCUUUGCCAUUUGCGUAUUUAUGCAUUCCACCUCCGAGGUGGGCAGCAUGCUGCUCGUCAUGCGCUGCACACACCCCAAAGGUAAUAA-------C-----CA-------GGAUU----
....(((((...(((((....)))))..(((((.....)))))(((((..((..........)))))))............)))))...-------.-----..-------.....---- ( -25.60)
>DroVir_CAF1 40360 91 + 1
AUUUUUGCCAUUUGCGUAUUUAUGCAUUCCACCUCCGAGGUGGGCAGCAUGCUGCUCGUUAUGCGCUGCACACAUCCUAAAGGUGAGU--------C-----AA----------------
...((..((...(((((....)))))..(((((.....)))))(((((..((..........)))))))............))..)).--------.-----..---------------- ( -25.70)
>DroGri_CAF1 39735 104 + 1
AUUUUUGCCAUUUGCGUAUUUAUGCAUUCCACCUCCGAGGUGGGCAGCAUGCUGCUCGUCAUGCGCUGCACACAUCCUAAAGGUAACCAGACAUCCC-----CA-------UAUCU----
....(((((...(((((....)))))..(((((.....)))))(((((..((..........)))))))............)))))...........-----..-------.....---- ( -25.50)
>DroWil_CAF1 43975 101 + 1
AUUUUUGCCAUUUGCGUAUUUAUGCAUUCCACCUCCGAGGUGGGCAGCAUGCUGCUUGUCAUGCGCUGUACACAUCCAAAGGGUAAUUA-------U-----UA-------UAUUCAUAC
....(((((...((.((((...(((((.(((((.....)))))((((....)))).....)))))..)))).)).......)))))...-------.-----..-------......... ( -26.30)
>DroMoj_CAF1 39057 96 + 1
AUUUUUGCCAUUUGCGUAUUUAUGCAUUCCACCUCUGAGGUGGGCAGCAUGCUGCUCGUCAUGCGCUGUACACAUCCUAAAGGUAAGU--------C-----CA-------AGCUC----
...((((((...((.((((...(((((.(((((.....)))))((((....)))).....)))))..)))).)).......)))))).--------.-----..-------.....---- ( -25.80)
>DroAna_CAF1 35311 109 + 1
AUCUUUGCCAUUUGCGUAUUCAUGCAUUCCACCUCCGAGGUGGGCAGUAUGCUUCUCGUCAUGCGGUGUACACAUCCCAAAGGUAGGAU-------ACUUUUCAGAGGAAGGGAAU----
(((((.(((....(((....(((((..((((((.....))))))..))))).....)))..((.((((....)))).))..))))))))-------.((((((....))))))...---- ( -29.50)
>consensus
AUUUUUGCCAUUUGCGUAUUUAUGCAUUCCACCUCCGAGGUGGGCAGCAUGCUGCUCGUCAUGCGCUGCACACAUCCUAAAGGUAAGUA_______C_____CA_______GGAUU____
....(((((...(((((....)))))..(((((.....)))))(((((..((..........)))))))............))))).................................. (-23.92 = -23.42 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,475,711 – 17,475,808
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.31
Mean single sequence MFE -27.57
Consensus MFE -22.50
Energy contribution -22.42
Covariance contribution -0.08
Combinations/Pair 1.05
Mean z-score -1.13
Structure conservation index 0.82
SVM decision value 0.10
SVM RNA-class probability 0.585557
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17475711 97 - 23771897
----AAUCC-------UG-----G-------UUAUUACCUUUGGGGUGUGUGCAGCGCAUGACGAGCAGCAUGCUGCCCACCUCGGAGGUGGAAUGCAUAAAUACGCAAAUGGCAAAGAU
----.(((.-------..-----(-------(((((((((((((((((.(.(((((((.((.....))))..))))))))))))))))))....(((........)))))))))...))) ( -35.40)
>DroVir_CAF1 40360 91 - 1
----------------UU-----G--------ACUCACCUUUAGGAUGUGUGCAGCGCAUAACGAGCAGCAUGCUGCCCACCUCGGAGGUGGAAUGCAUAAAUACGCAAAUGGCAAAAAU
----------------..-----.--------..((((((((((((((((.....)))))...(.((((....)))).).))).))))))))..(((........)))............ ( -25.40)
>DroGri_CAF1 39735 104 - 1
----AGAUA-------UG-----GGGAUGUCUGGUUACCUUUAGGAUGUGUGCAGCGCAUGACGAGCAGCAUGCUGCCCACCUCGGAGGUGGAAUGCAUAAAUACGCAAAUGGCAAAAAU
----(((((-------(.-----...)))))).((((((....))...(((((((((((((.(.....)))))).))(((((.....)))))..))))))..........))))...... ( -28.50)
>DroWil_CAF1 43975 101 - 1
GUAUGAAUA-------UA-----A-------UAAUUACCCUUUGGAUGUGUACAGCGCAUGACAAGCAGCAUGCUGCCCACCUCGGAGGUGGAAUGCAUAAAUACGCAAAUGGCAAAAAU
((((.....-------..-----.-------......((....)).((((((..(((((((........))))).))(((((.....)))))..)))))).))))((.....))...... ( -23.60)
>DroMoj_CAF1 39057 96 - 1
----GAGCU-------UG-----G--------ACUUACCUUUAGGAUGUGUACAGCGCAUGACGAGCAGCAUGCUGCCCACCUCAGAGGUGGAAUGCAUAAAUACGCAAAUGGCAAAAAU
----..(((-------((-----.--------.....((....))(((((.....)))))..)))))....((((..(((((.....)))))..(((........)))...))))..... ( -27.00)
>DroAna_CAF1 35311 109 - 1
----AUUCCCUUCCUCUGAAAAGU-------AUCCUACCUUUGGGAUGUGUACACCGCAUGACGAGAAGCAUACUGCCCACCUCGGAGGUGGAAUGCAUGAAUACGCAAAUGGCAAAGAU
----(((((...(((((((..(((-------((.((...((((..(((((.....)))))..)))).)).))))).......))))))).)))))..........((.....))...... ( -25.50)
>consensus
____AAACA_______UG_____G_______UACUUACCUUUAGGAUGUGUACAGCGCAUGACGAGCAGCAUGCUGCCCACCUCGGAGGUGGAAUGCAUAAAUACGCAAAUGGCAAAAAU
.....................................((....)).((((((....((((.....((((....))))(((((.....))))).)))).....))))))............ (-22.50 = -22.42 +  -0.08)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:06 2006