Locus 717

Sequence ID 2R_DroMel_CAF1
Location 3,530,227 – 3,530,437
Length 210
Max. P 0.993959
window1254 window1255 window1256 window1257 window1258 window1259

overview

Window 4

Location 3,530,227 – 3,530,341
Length 114
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 96.35
Mean single sequence MFE -32.85
Consensus MFE -33.12
Energy contribution -32.75
Covariance contribution -0.38
Combinations/Pair 1.07
Mean z-score -1.76
Structure conservation index 1.01
SVM decision value 0.87
SVM RNA-class probability 0.870365
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3530227 114 + 20766785
UUCUGAGUAGGAGCCUAAUUGGGUUAGAUACUCGAAGUAUCUCUAUUCUGCAAACUUUCAGCUGCCUUCCUGCAGAUUUAACAGCAGCUAACAAACCGAAUUCGUCGGCUGCUG
....((((((((((((....))))).(((((.....)))))))))))).............((((......))))......(((((((..((...........))..))))))) ( -33.00)
>DroSim_CAF1 24109 114 + 1
UUCUGAGUAGGAGCCUAAUUGGGUUAGAUGCUCGAAGUAUCUCUAUUCUGCAAACUUUCAGCUGCCUUCCUGCAGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUG
....((((((((((((....))))).(((((.....)))))))))))).............((((......))))......(((((((..((...........))..))))))) ( -33.00)
>DroEre_CAF1 22751 114 + 1
UUCUGGGUAGGAGCCUAAUUGGGUUAGAUGCUCAAAGUAUCUCUAUUCUGCAAACUUUCCGCUGCCUUCCUGCAGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUG
....((((((((((((....))))).(((((.....)))))))))))).............((((......))))......(((((((..((...........))..))))))) ( -32.00)
>DroYak_CAF1 21862 114 + 1
UUUUGAGUAGGAGCCUAAUUGGGUUAGAUGCUCAGAGUAUCUCUAUUCUGUAAACUUUCAGCUGCCUUCCUGCAGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUG
(((((((((..(((((....)))))...)))))))))..........(((........)))((((......))))......(((((((..((...........))..))))))) ( -33.40)
>consensus
UUCUGAGUAGGAGCCUAAUUGGGUUAGAUGCUCAAAGUAUCUCUAUUCUGCAAACUUUCAGCUGCCUUCCUGCAGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUG
....((((((((((((....))))).(((((.....)))))))))))).............((((......))))......(((((((..((...........))..))))))) (-33.12 = -32.75 +  -0.38) 

alignment

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secondary structure

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Window 5

Location 3,530,263 – 3,530,372
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.46
Mean single sequence MFE -25.28
Consensus MFE -16.62
Energy contribution -18.02
Covariance contribution 1.39
Combinations/Pair 1.22
Mean z-score -1.92
Structure conservation index 0.66
SVM decision value 1.57
SVM RNA-class probability 0.964758
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3530263 109 + 20766785
GUAUCUCUAUUCUGCAAACUUUCAG--CUGCCUUCCUGCAGAUUUAACAGCAGCUAACAAACCGAAUUCGUCGGCUGCUGUAAUUAAA-----ACAAAGAGUGCGUUCAGCACACA----
.....(((..((((((.........--.........))))))....((((((((..((...........))..)))))))).......-----....)))((((.....))))...---- ( -28.87)
>DroSim_CAF1 24145 109 + 1
GUAUCUCUAUUCUGCAAACUUUCAG--CUGCCUUCCUGCAGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAA-----ACAAAGAGUGCGUUCAGCACACA----
.....(((..((((((.........--.........))))))....((((((((..((...........))..)))))))).......-----....)))((((.....))))...---- ( -28.87)
>DroEre_CAF1 22787 113 + 1
GUAUCUCUAUUCUGCAAACUUUCCG--CUGCCUUCCUGCAGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAA-----ACAAAGAGUGCGUUCCGCACAUCCUGU
.....(((..((((((.........--.........))))))....((((((((..((...........))..)))))))).......-----....)))(((((...)))))....... ( -28.97)
>DroYak_CAF1 21898 109 + 1
GUAUCUCUAUUCUGUAAACUUUCAG--CUGCCUUCCUGCAGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAA-----ACAAAGAGUGCGUUCAGCACACA----
.....(((...(((........)))--((((......)))).....((((((((..((...........))..)))))))).......-----....)))((((.....))))...---- ( -27.60)
>DroAna_CAF1 17651 100 + 1
UUAUAUCUAUUCGGAAAACUUUGGGAUCUGCC-UCCUACGGAUUUAACAGCAGUUAACAAACCAAGCCCGUCGGUGGCUGUAAUUAAA-----ACAAAAAAAACA---------G-----
(((((.((((.(((....((.(((((......-))))).))..(((((....)))))..........)))...)))).))))).....-----............---------.----- ( -15.00)
>DroPer_CAF1 6455 103 + 1
-----UCGCCACAGCGGAACUUCAG--CCAUUUUCCUAGAGACCUAACAGCAGCUAACCAAACCAAGAAACUGGCUGCUGUAAUUAAACAGAUGCUAAGAGU------AGCACACA----
-----((((....))))..((..((--........))..)).....((((((((((...............))))))))))...........(((((....)------))))....---- ( -22.36)
>consensus
GUAUCUCUAUUCUGCAAACUUUCAG__CUGCCUUCCUGCAGAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAA_____ACAAAGAGUGCGUUCAGCACACA____
...........................((((......)))).....((((((((..((...........))..))))))))...................((((.....))))....... (-16.62 = -18.02 +   1.39) 

alignment

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secondary structure

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Window 6

Location 3,530,263 – 3,530,372
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.46
Mean single sequence MFE -33.48
Consensus MFE -20.63
Energy contribution -23.42
Covariance contribution 2.79
Combinations/Pair 1.33
Mean z-score -2.26
Structure conservation index 0.62
SVM decision value 1.91
SVM RNA-class probability 0.982118
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3530263 109 - 20766785
----UGUGUGCUGAACGCACUCUUUGU-----UUUAAUUACAGCAGCCGACGAAUUCGGUUUGUUAGCUGCUGUUAAAUCUGCAGGAAGGCAG--CUGAAAGUUUGCAGAAUAGAGAUAC
----.(((((.....)))))(((((((-----.......((((((((..((((((...))))))..))))))))....((((((((....(..--..)....)))))))))))))))... ( -37.50)
>DroSim_CAF1 24145 109 - 1
----UGUGUGCUGAACGCACUCUUUGU-----UUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUCUGCAGGAAGGCAG--CUGAAAGUUUGCAGAAUAGAGAUAC
----.(((((.....)))))(((((((-----.......((((((((..((((((...))))))..))))))))....((((((((....(..--..)....)))))))))))))))... ( -37.10)
>DroEre_CAF1 22787 113 - 1
ACAGGAUGUGCGGAACGCACUCUUUGU-----UUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUCUGCAGGAAGGCAG--CGGAAAGUUUGCAGAAUAGAGAUAC
.......(((((...)))))(((((((-----.......((((((((..((((((...))))))..))))))))....((((((((....(..--..)....)))))))))))))))... ( -37.40)
>DroYak_CAF1 21898 109 - 1
----UGUGUGCUGAACGCACUCUUUGU-----UUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUCUGCAGGAAGGCAG--CUGAAAGUUUACAGAAUAGAGAUAC
----.(((((.....)))))(((((((-----(((....((((((((..((((((...))))))..)))))))).....((((......))))--............))))))))))... ( -35.40)
>DroAna_CAF1 17651 100 - 1
-----C---------UGUUUUUUUUGU-----UUUAAUUACAGCCACCGACGGGCUUGGUUUGUUAACUGCUGUUAAAUCCGUAGGA-GGCAGAUCCCAAAGUUUUCCGAAUAGAUAUAA
-----(---------(((((....(((-----.......)))(((.((.((((..((((...((.....))..))))..)))).)).-))).................))))))...... ( -19.70)
>DroPer_CAF1 6455 103 - 1
----UGUGUGCU------ACUCUUAGCAUCUGUUUAAUUACAGCAGCCAGUUUCUUGGUUUGGUUAGCUGCUGUUAGGUCUCUAGGAAAAUGG--CUGAAGUUCCGCUGUGGCGA-----
----....((((------((....(((..((((......))))((((((.((((((((...(.(((((....))))).)..)))))))).)))--))).......))))))))).----- ( -33.80)
>consensus
____UGUGUGCUGAACGCACUCUUUGU_____UUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUCUGCAGGAAGGCAG__CUGAAAGUUUGCAGAAUAGAGAUAC
.......((((.....))))(((((((............((((((((.(((((((...))))))).))))))))....((((((((....((....))....)))))))))))))))... (-20.63 = -23.42 +   2.79) 

alignment

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secondary structure

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Window 7

Location 3,530,301 – 3,530,404
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 69.82
Mean single sequence MFE -23.80
Consensus MFE -16.43
Energy contribution -17.77
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.43
Structure conservation index 0.69
SVM decision value 2.44
SVM RNA-class probability 0.993959
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3530301 103 + 20766785
GAUUUAACAGCAGCUAACAAACCGAAUUCGUCGGCUGCUGUAAUUAAA-----ACAAAGAGUGCGUUCAGCACACA------G-GACCCCAUC-----CCACGCACUUCCUUCCUCCCCU
......((((((((..((...........))..)))))))).......-----.....((((((((..........------(-((.....))-----).))))))))............ ( -25.60)
>DroPse_CAF1 11562 100 + 1
GACCUAACAGCAGCUAACCAAACCAAGAAACUGGCUGCUGUAAUUAAACAGAUGCUAAGAGU------AGCACACA------G-ACUCCCGCCUCAGCCCCAGCCA------CAGCCAC-
......((((((((((...............)))))))))).........((.((...((((------........------.-))))..)).))...........------.......- ( -19.76)
>DroSim_CAF1 24183 103 + 1
GAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAA-----ACAAAGAGUGCGUUCAGCACACA------G-GACCCCAUC-----CCUCGCACUUCCUUCCUCCCCU
......((((((((..((...........))..)))))))).......-----.....(((((((..........(------(-(........-----))))))))))............ ( -25.40)
>DroEre_CAF1 22825 103 + 1
GAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAA-----ACAAAGAGUGCGUUCCGCACAUCCUGUGUGCAUCCCCAGC-----UUCCUC-G------GAACCCCA
......((((((((..((...........))..)))))))).......-----...........(((((((((((...))))))......((.-----...)).-)------)))).... ( -27.50)
>DroYak_CAF1 21936 97 + 1
GAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAA-----ACAAAGAGUGCGUUCAGCACACA------G-GACCUCAUC-----CUUCUCAA------CAACCCCU
......((((((((..((...........))..)))))))).......-----....(((((((.....))))..(------(-((.....))-----)))))...------........ ( -24.80)
>DroPer_CAF1 6488 100 + 1
GACCUAACAGCAGCUAACCAAACCAAGAAACUGGCUGCUGUAAUUAAACAGAUGCUAAGAGU------AGCACACA------G-ACUCCCGCCUCAGCCCCAGCCA------CAGCCAC-
......((((((((((...............)))))))))).........((.((...((((------........------.-))))..)).))...........------.......- ( -19.76)
>consensus
GAUUUAACAGCAGCUAACAAACCGAAUCCGUCGGCUGCUGUAAUUAAA_____ACAAAGAGUGCGUUCAGCACACA______G_AACCCCAUC_____CCCCGCAA______CAACCCCU
......(((((((((.((...........)).)))))))))...................((((.....))))............................................... (-16.43 = -17.77 +   1.33) 

alignment

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secondary structure

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dotplot

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Window 8

Location 3,530,301 – 3,530,404
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 69.82
Mean single sequence MFE -34.92
Consensus MFE -17.73
Energy contribution -17.87
Covariance contribution 0.14
Combinations/Pair 1.28
Mean z-score -2.09
Structure conservation index 0.51
SVM decision value 1.75
SVM RNA-class probability 0.975366
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3530301 103 - 20766785
AGGGGAGGAAGGAAGUGCGUGG-----GAUGGGGUC-C------UGUGUGCUGAACGCACUCUUUGU-----UUUAAUUACAGCAGCCGACGAAUUCGGUUUGUUAGCUGCUGUUAAAUC
.((((((...(..((..((..(-----(((...)))-)------..))..))...)...))))))..-----.......((((((((..((((((...))))))..))))))))...... ( -39.00)
>DroPse_CAF1 11562 100 - 1
-GUGGCUG------UGGCUGGGGCUGAGGCGGGAGU-C------UGUGUGCU------ACUCUUAGCAUCUGUUUAAUUACAGCAGCCAGUUUCUUGGUUUGGUUAGCUGCUGUUAGGUC
-.((((.(------..((((..((..((.((((((.-(------((.(((((------(....))))..((((......))))..))))).)))))).))..))))))..).)))).... ( -32.20)
>DroSim_CAF1 24183 103 - 1
AGGGGAGGAAGGAAGUGCGAGG-----GAUGGGGUC-C------UGUGUGCUGAACGCACUCUUUGU-----UUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUC
.((((((...(..((..((.((-----(((...)))-)------).))..))...)...))))))..-----.......((((((((..((((((...))))))..))))))))...... ( -35.90)
>DroEre_CAF1 22825 103 - 1
UGGGGUUC------C-GAGGAA-----GCUGGGGAUGCACACAGGAUGUGCGGAACGCACUCUUUGU-----UUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUC
..(.((((------(-.((...-----.)).))))).)(((.((((.(((((...))))))))))))-----.......((((((((..((((((...))))))..))))))))...... ( -38.40)
>DroYak_CAF1 21936 97 - 1
AGGGGUUG------UUGAGAAG-----GAUGAGGUC-C------UGUGUGCUGAACGCACUCUUUGU-----UUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUC
((((((((------((.((.((-----(((...)))-)------).....)).)))).))))))...-----.......((((((((..((((((...))))))..))))))))...... ( -31.80)
>DroPer_CAF1 6488 100 - 1
-GUGGCUG------UGGCUGGGGCUGAGGCGGGAGU-C------UGUGUGCU------ACUCUUAGCAUCUGUUUAAUUACAGCAGCCAGUUUCUUGGUUUGGUUAGCUGCUGUUAGGUC
-.((((.(------..((((..((..((.((((((.-(------((.(((((------(....))))..((((......))))..))))).)))))).))..))))))..).)))).... ( -32.20)
>consensus
AGGGGAUG______UUGCGGGG_____GAUGGGGUC_C______UGUGUGCUGAACGCACUCUUUGU_____UUUAAUUACAGCAGCCGACGGAUUCGGUUUGUUAGCUGCUGUUAAAUC
...............................................((((.....))))...................((((((((.((((((.....)))))).))))))))...... (-17.73 = -17.87 +   0.14) 

alignment

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secondary structure

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Window 9

Location 3,530,341 – 3,530,437
Length 96
Sequences 3
Columns 101
Reading direction forward
Mean pairwise identity 75.25
Mean single sequence MFE -19.33
Consensus MFE -10.13
Energy contribution -11.13
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.52
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3530341 96 + 20766785
UAAUUAAAACAAAGAGUGCGUUCAGCACACAGGACCCCAUCCCACGCACUUCCUUCCUCCCCUCCUCUUUGUCCCCACAAAA-----GCAACGCAUAUGCA
........(((((((((((.....))))...(((.....))).......................)))))))..........-----(((.......))). ( -15.50)
>DroSim_CAF1 24223 101 + 1
UAAUUAAAACAAAGAGUGCGUUCAGCACACAGGACCCCAUCCCUCGCACUUCCUUCCUCCCCUCCUCUUCGUCCCCACGUAGUCCGUGCAACGCAUAUGCA
...............(((((((..((((...(((.....)))........................((.(((....))).))...)))))))))))..... ( -16.70)
>DroYak_CAF1 21976 87 + 1
UAAUUAAAACAAAGAGUGCGUUCAGCACACAGGACCUCAUCCUUCUCAA------CAACCCCUCACCGUUG---CG-----GGGGGUUGCACGCAUAUGCA
............(((((((.....))))..((((.....)))))))...------(((((((((.......---.)-----))))))))...((....)). ( -25.80)
>consensus
UAAUUAAAACAAAGAGUGCGUUCAGCACACAGGACCCCAUCCCUCGCACUUCCUUCCUCCCCUCCUCUUUGUCCCCAC__AG___GUGCAACGCAUAUGCA
.........((((((((((.....))))...(((.....))).......................)))))).....................((....)). (-10.13 = -11.13 +   1.00) 

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 09:45:25 2006