Locus 4210

Sequence ID X_DroMel_CAF1
Location 11,037,203 – 11,037,362
Length 159
Max. P 0.999994
window6920 window6921 window6922 window6923

overview

Window 0

Location 11,037,203 – 11,037,323
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 75.83
Mean single sequence MFE -23.80
Consensus MFE -15.74
Energy contribution -16.18
Covariance contribution 0.44
Combinations/Pair 1.32
Mean z-score -2.51
Structure conservation index 0.66
SVM decision value 2.86
SVM RNA-class probability 0.997436
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11037203 120 + 22224390
UUUAAAUCUAUUUAAAAAUUAAUUCAAUUCAUUUAUGAUUUAUUUUGCCAAAGCAACAUGGCGUAUGAGCAAUAAUUUGGUAAUGAUCACUUAUACGCCACGUUGUCAUUGCAAAUUUUA
..((((((............................)))))).(((((....(((((.(((((((((((..((.(((....))).))..))))))))))).)))))....)))))..... ( -27.89)
>DroSec_CAF1 24454 113 + 1
UUUUAAUCUAUUUCAAAAUUAAUUCAAUUCUAUUAUGAUUUCUCUUGCCAAAGCAACAUGGCGUAUGCGCAAUAAUUUGGUAUUGAUCACCUAUACGUCACGUUGCCAUUAUA-------
....................................................(((((.(((((((((..(((((......)))))......))))))))).))))).......------- ( -19.00)
>DroEre_CAF1 18699 120 + 1
UUCAAGCCUAUUUAAAAACUGAUUCAAUUCUAUAACGAUUUAUUUUGCAAAUACAACUUGGCGUAUGAGUAAUAAAUUCGCGCUGAUCACGUAUACGCCAUGUUGCUAUUACAAAUAUUA
...........................................((((..((((((((.((((((((((((.....))))(((.......))))))))))).)))).)))).))))..... ( -20.30)
>DroYak_CAF1 19630 120 + 1
UGCAAACAUAUAUAAAUAUUAAUUCAAUUGUAUUACGAUUUACUUGGCAAAUACAACAUGGCGUAUGCGUAAUACAUUUUCAUUAAUCACUCAUACGCCAUGUUGCGGUCACAAAUAUUA
..............((((((.....(((((.....)))))....((((.....((((((((((((((.((.((............)).)).))))))))))))))..))))..)))))). ( -28.00)
>consensus
UUCAAACCUAUUUAAAAAUUAAUUCAAUUCUAUUACGAUUUAUUUUGCAAAAACAACAUGGCGUAUGAGCAAUAAAUUGGCAUUGAUCACUUAUACGCCACGUUGCCAUUACAAAUAUUA
....................................................(((((.(((((((((..(((((......)))))......))))))))).))))).............. (-15.74 = -16.18 +   0.44)

alignment

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secondary structure

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Window 1

Location 11,037,203 – 11,037,323
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 75.83
Mean single sequence MFE -31.11
Consensus MFE -23.91
Energy contribution -25.35
Covariance contribution 1.44
Combinations/Pair 1.29
Mean z-score -3.79
Structure conservation index 0.77
SVM decision value 5.16
SVM RNA-class probability 0.999977
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11037203 120 - 22224390
UAAAAUUUGCAAUGACAACGUGGCGUAUAAGUGAUCAUUACCAAAUUAUUGCUCAUACGCCAUGUUGCUUUGGCAAAAUAAAUCAUAAAUGAAUUGAAUUAAUUUUUAAAUAGAUUUAAA
.....(((((...(.(((((((((((((.((..((.(((....))).))..)).))))))))))))))....))))).((((((......((((((...)))))).......)))))).. ( -33.92)
>DroSec_CAF1 24454 113 - 1
-------UAUAAUGGCAACGUGACGUAUAGGUGAUCAAUACCAAAUUAUUGCGCAUACGCCAUGUUGCUUUGGCAAGAGAAAUCAUAAUAGAAUUGAAUUAAUUUUGAAAUAGAUUAAAA
-------......(((((((((.(((((..(((..(((((......))))))))))))).))))))))).......((....))..............(((((((......))))))).. ( -23.90)
>DroEre_CAF1 18699 120 - 1
UAAUAUUUGUAAUAGCAACAUGGCGUAUACGUGAUCAGCGCGAAUUUAUUACUCAUACGCCAAGUUGUAUUUGCAAAAUAAAUCGUUAUAGAAUUGAAUCAGUUUUUAAAUAGGCUUGAA
.....(((((((..(((((.((((((((..(((((.((......)).)))))..)))))))).)))))..))))))).(((..(.(((.(((((((...))))))))))...)..))).. ( -28.30)
>DroYak_CAF1 19630 120 - 1
UAAUAUUUGUGACCGCAACAUGGCGUAUGAGUGAUUAAUGAAAAUGUAUUACGCAUACGCCAUGUUGUAUUUGCCAAGUAAAUCGUAAUACAAUUGAAUUAAUAUUUAUAUAUGUUUGCA
...((((((..(..(((((((((((((((.(((((..((....))..))))).)))))))))))))))..)..).)))))....((((.(((..(((((....)))))....))))))). ( -38.30)
>consensus
UAAUAUUUGUAAUGGCAACAUGGCGUAUAAGUGAUCAAUACCAAAUUAUUACGCAUACGCCAUGUUGCAUUGGCAAAAUAAAUCAUAAUAGAAUUGAAUUAAUUUUUAAAUAGAUUUAAA
.....(((((((.(((((((((((((((..(((((.(((....))).)))))..))))))))))))))).))))))).......................(((((......))))).... (-23.91 = -25.35 +   1.44)

alignment

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secondary structure

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Window 2

Location 11,037,243 – 11,037,362
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 69.16
Mean single sequence MFE -29.37
Consensus MFE -17.67
Energy contribution -17.57
Covariance contribution -0.11
Combinations/Pair 1.10
Mean z-score -3.02
Structure conservation index 0.60
SVM decision value 5.84
SVM RNA-class probability 0.999994
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11037243 119 + 22224390
UAUUUUGCCAAAGCAACAUGGCGUAUGAGCAAUAAUUUGGUAAUGAUCACUUAUACGCCACGUUGUCAUUGCAAAUUUUAUGC-GACUCUAUUAUGGGGUAAUAUUUUUGCAUUUUUGCU
......((.((((((((.(((((((((((..((.(((....))).))..))))))))))).)))))...((((((...(((..-.(((((.....))))).)))..)))))).))).)). ( -33.80)
>DroEre_CAF1 18739 108 + 1
UAUUUUGCAAAUACAACUUGGCGUAUGAGUAAUAAAUUCGCGCUGAUCACGUAUACGCCAUGUUGCUAUUACAAAUAUUAUAUUUGCUCCAUUAUUGGGUCAUAUAUU------------
...((((..((((((((.((((((((((((.....))))(((.......))))))))))).)))).)))).))))....((((.((..(((....)))..)).)))).------------ ( -25.60)
>DroYak_CAF1 19670 107 + 1
UACUUGGCAAAUACAACAUGGCGUAUGCGUAAUACAUUUUCAUUAAUCACUCAUACGCCAUGUUGCGGUCACAAAUAUUAUAC-GGCUCCAUUUUAGGGUUAAGCAGU------------
..((((((.....((((((((((((((.((.((............)).)).)))))))))))))).((((.............-))))((......))))))))....------------ ( -28.72)
>consensus
UAUUUUGCAAAUACAACAUGGCGUAUGAGUAAUAAAUUCGCAAUGAUCACUUAUACGCCAUGUUGCCAUUACAAAUAUUAUAC_GGCUCCAUUAUAGGGUAAUAUAUU____________
.............((((.(((((((((.((.((............)).)).))))))))).))))....................((((.......)))).................... (-17.67 = -17.57 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,037,243 – 11,037,362
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 69.16
Mean single sequence MFE -34.23
Consensus MFE -26.58
Energy contribution -27.37
Covariance contribution 0.79
Combinations/Pair 1.21
Mean z-score -4.97
Structure conservation index 0.78
SVM decision value 5.86
SVM RNA-class probability 0.999994
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11037243 119 - 22224390
AGCAAAAAUGCAAAAAUAUUACCCCAUAAUAGAGUC-GCAUAAAAUUUGCAAUGACAACGUGGCGUAUAAGUGAUCAUUACCAAAUUAUUGCUCAUACGCCAUGUUGCUUUGGCAAAAUA
.......((((.....(((((.....))))).....-))))....(((((...(.(((((((((((((.((..((.(((....))).))..)).))))))))))))))....)))))... ( -35.10)
>DroEre_CAF1 18739 108 - 1
------------AAUAUAUGACCCAAUAAUGGAGCAAAUAUAAUAUUUGUAAUAGCAACAUGGCGUAUACGUGAUCAGCGCGAAUUUAUUACUCAUACGCCAAGUUGUAUUUGCAAAAUA
------------.((((.((..(((....)))..)).))))....(((((((..(((((.((((((((..(((((.((......)).)))))..)))))))).)))))..)))))))... ( -30.40)
>DroYak_CAF1 19670 107 - 1
------------ACUGCUUAACCCUAAAAUGGAGCC-GUAUAAUAUUUGUGACCGCAACAUGGCGUAUGAGUGAUUAAUGAAAAUGUAUUACGCAUACGCCAUGUUGUAUUUGCCAAGUA
------------((.(((....((......))))).-))....((((((..(..(((((((((((((((.(((((..((....))..))))).)))))))))))))))..)..).))))) ( -37.20)
>consensus
____________AAUAUAUAACCCAAUAAUGGAGCC_GUAUAAUAUUUGUAAUAGCAACAUGGCGUAUAAGUGAUCAAUGCAAAUUUAUUACUCAUACGCCAUGUUGUAUUUGCAAAAUA
.............................................(((((((..((((((((((((((..(((((.(((....))).)))))..))))))))))))))..)))))))... (-26.58 = -27.37 +   0.79)

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 11:19:19 2006