Locus 8235

Sequence ID 3R_DroMel_CAF1
Location 22,065,714 – 22,065,907
Length 193
Max. P 0.986143
window13272 window13273 window13274 window13275

overview

Window 2

Location 22,065,714 – 22,065,834
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.25
Mean single sequence MFE -38.78
Consensus MFE -32.12
Energy contribution -32.24
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -2.26
Structure conservation index 0.83
SVM decision value 2.03
SVM RNA-class probability 0.986143
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22065714 120 + 27905053
AGUUGCGCCGGAUGAACUUGCAUUUACAUGUAACUCCAAGUCUAUUGGGGAAACAGUGAGUCGAAUUGUGCAUUAAAGUUGCACACGAGUGUCGGUUGAAUCGAACUCGAUUUGCGGCAC
.((((((((((....(((((.((((((.(((..((((((.....))))))..))))))))).....((((((.......))))))))))).))))).((((((....))))))))))).. ( -41.80)
>DroSec_CAF1 57703 120 + 1
AGUUGCGCCGGAUGAACUUGCAUUUACAUGUAACUCCAAGUCUAUUGGGAAAACAGCGAGUCGAAUUGUGUAUUAAAGUUGCACAAGAGUGUCGGUUGAAUCGAACUCGAUUUGCGGCAC
.(((...((.((((.(((((...(((....)))...))))).)))).))..))).(((((((...(((((((.......)))))))((((.(((((...))))))))))))))))..... ( -36.50)
>DroSim_CAF1 50712 120 + 1
UGUUGCGCCGGAUGAACUUGCAUUUACAUGUAACUCCAAGUCUAUUGGGGAAACAGCGAGUCGAAUUGUGUAUUAAAGUUGCACAAGAGUGUCGGUUGAAUCGAACUCGAUUUGCGGCAC
......((((((((......)))))...(((..((((((.....))))))..)))(((((((...(((((((.......)))))))((((.(((((...))))))))))))))))))).. ( -38.90)
>DroEre_CAF1 52251 120 + 1
AGUUGCGCCGGAUGCACUUGCAUUUGCAUGUAACUUCAAGUCCAUUGGGGAAACAGCGAGUUGAAUUGUGUAUUAAAGUUGCACAAGAGUGGCGGUUGAAUCGAACUCGAUUUGCGGCAC
.((((((((.(((((((...(((((((.(((..((((((.....))))))..)))))))).))....)))))))...((..(......)..))))).((((((....))))))))))).. ( -38.70)
>DroYak_CAF1 60123 120 + 1
AGUUGCGCCGGAUGAACUUGCAUUUACAUGCAACUCCAAGUCUAGUGGGGAAACAUCGAGUGGAAUUGUGUAUUAAAGUUGCACAAGAAUGGCGGUUGAAUCGAAAUCGAUUUGCGGCAC
.(((((((((((((...((((((....))))))(((((.......)))))...))))........(((((((.......)))))))...))))....((((((....))))))))))).. ( -38.00)
>consensus
AGUUGCGCCGGAUGAACUUGCAUUUACAUGUAACUCCAAGUCUAUUGGGGAAACAGCGAGUCGAAUUGUGUAUUAAAGUUGCACAAGAGUGUCGGUUGAAUCGAACUCGAUUUGCGGCAC
.(((((((((.....((((((..............((((.....))))(....).))))))....(((((((.......)))))))......)))).((((((....))))))))))).. (-32.12 = -32.24 +   0.12)

alignment

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secondary structure

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Window 3

Location 22,065,754 – 22,065,874
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.32
Mean single sequence MFE -34.70
Consensus MFE -24.90
Energy contribution -26.86
Covariance contribution 1.96
Combinations/Pair 1.09
Mean z-score -2.62
Structure conservation index 0.72
SVM decision value 1.34
SVM RNA-class probability 0.943772
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22065754 120 + 27905053
UCUAUUGGGGAAACAGUGAGUCGAAUUGUGCAUUAAAGUUGCACACGAGUGUCGGUUGAAUCGAACUCGAUUUGCGGCACCCCGAAGUGCAGAGAGAAGUCCCUGGAAGAAAGAAGCUAA
(((.(..((((....(..((((....((((((.......)))))).((((.(((((...)))))))))))))..).((((......)))).........))))..).))).......... ( -38.70)
>DroSec_CAF1 57743 110 + 1
UCUAUUGGGAAAACAGCGAGUCGAAUUGUGUAUUAAAGUUGCACAAGAGUGUCGGUUGAAUCGAACUCGAUUUGCGGCACCCCAAAGUGCAGAGAUAA----------GGAAGAAGCUAC
....(((((......(((((((...(((((((.......)))))))((((.(((((...)))))))))))))))).....))))).............----------............ ( -29.90)
>DroSim_CAF1 50752 120 + 1
UCUAUUGGGGAAACAGCGAGUCGAAUUGUGUAUUAAAGUUGCACAAGAGUGUCGGUUGAAUCGAACUCGAUUUGCGGCACCCCAAAGUGCAGAGAUAAGUCCCUGAAAGGAAUAAACUAA
(((.(..((((....(((((((...(((((((.......)))))))((((.(((((...)))))))))))))))).((((......)))).........))))..).))).......... ( -39.20)
>DroEre_CAF1 52291 120 + 1
UCCAUUGGGGAAACAGCGAGUUGAAUUGUGUAUUAAAGUUGCACAAGAGUGGCGGUUGAAUCGAACUCGAUUUGCGGCACACAGAAGUGCAAAAAGAAGUCCCUGGAAGAAAAAAGCUAA
((((...((((....(((((((...(((((((.......)))))))((((..((((...)))).))))))))))).((((......)))).........))))))))............. ( -35.10)
>DroYak_CAF1 60163 119 + 1
UCUAGUGGGGAAACAUCGAGUGGAAUUGUGUAUUAAAGUUGCACAAGAAUGGCGGUUGAAUCGAAAUCGAUUUGCGGCACCCAGGAGUGCAAAAAUAAAUC-CUGGAUAAAAAAAGCUAA
((((.((((....).)))..)))).(((((((.......)))))))...((((.((((.((((....))))...))))..((((((.............))-)))).........)))). ( -30.62)
>consensus
UCUAUUGGGGAAACAGCGAGUCGAAUUGUGUAUUAAAGUUGCACAAGAGUGUCGGUUGAAUCGAACUCGAUUUGCGGCACCCCGAAGUGCAGAGAUAAGUCCCUGGAAGAAAAAAGCUAA
......(((((....(((((((...(((((((.......)))))))((((.(((((...)))))))))))))))).((((......)))).........)))))................ (-24.90 = -26.86 +   1.96)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,065,794 – 22,065,907
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.57
Mean single sequence MFE -26.33
Consensus MFE -15.18
Energy contribution -15.78
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.58
SVM decision value 0.12
SVM RNA-class probability 0.591868
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22065794 113 + 27905053
GCACACGAGUGUCGGUUGAAUCGAACUCGAUUUGCGGCACCCCGAAGUGCAGAGAGAAGUCCCUGGAAGAAAGAAGCUAAAUUCUAUCCAAAG------AUAGAUAGUAAUG-UAUUGAC
((((.((.((((((...((((((....)))))).))))))..))..)))).........((....))........((((...((((((....)------)))))))))....-....... ( -26.80)
>DroSec_CAF1 57783 109 + 1
GCACAAGAGUGUCGGUUGAAUCGAACUCGAUUUGCGGCACCCCAAAGUGCAGAGAUAA----------GGAAGAAGCUACAUUCUAUCUAAAGAGUUAGAUGGAGAAUAAAA-UAUUGCC
((((..(.((((((...((((((....)))))).)))))).)....))))........----------.............((((((((((....)))))))))).......-....... ( -27.20)
>DroSim_CAF1 50792 119 + 1
GCACAAGAGUGUCGGUUGAAUCGAACUCGAUUUGCGGCACCCCAAAGUGCAGAGAUAAGUCCCUGAAAGGAAUAAACUAAAUUCUAUACAAAGAGUUAGAUAGAGAAUAAAA-UAUUGAC
((((..(.((((((...((((((....)))))).)))))).)....))))...((((..(((......))).....((((.((((......)))))))).............-))))... ( -23.70)
>DroEre_CAF1 52331 117 + 1
GCACAAGAGUGGCGGUUGAAUCGAACUCGAUUUGCGGCACACAGAAGUGCAAAAAGAAGUCCCUGGAAGAAAAAAGCUAAAUUCCAAUCAAAGGGAUAAAUA-GUGAUUAAAAU--GGAG
((((....(((((.((.((((((....)))))))).)).)))....))))........((((((((((.............))))......)))))).....-...........--.... ( -27.72)
>DroYak_CAF1 60203 112 + 1
GCACAAGAAUGGCGGUUGAAUCGAAAUCGAUUUGCGGCACCCAGGAGUGCAAAAAUAAAUC-CUGGAUAAAAAAAGCUAAAUUCCAUCCAAAGGAAUAAAUAAGUGAUAAAA-U------
.(((.....((((.((((.((((....))))...))))..((((((.............))-)))).........)))).(((((.......)))))......)))......-.------ ( -26.22)
>consensus
GCACAAGAGUGUCGGUUGAAUCGAACUCGAUUUGCGGCACCCCGAAGUGCAGAGAUAAGUCCCUGGAAGAAAAAAGCUAAAUUCUAUCCAAAGAGAUAAAUAGAUAAUAAAA_UAUUGAC
((((..(.((((((...((((((....)))))).)))))).)....))))...................................................................... (-15.18 = -15.78 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 22,065,794 – 22,065,907
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.57
Mean single sequence MFE -24.30
Consensus MFE -14.50
Energy contribution -15.78
Covariance contribution 1.28
Combinations/Pair 1.25
Mean z-score -1.59
Structure conservation index 0.60
SVM decision value -0.05
SVM RNA-class probability 0.506149
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22065794 113 - 27905053
GUCAAUA-CAUUACUAUCUAU------CUUUGGAUAGAAUUUAGCUUCUUUCUUCCAGGGACUUCUCUCUGCACUUCGGGGUGCCGCAAAUCGAGUUCGAUUCAACCGACACUCGUGUGC
.......-............(------(((((((.((((..........)))))))))))).........(((((....))))).(((...((((((((.......))).)))))..))) ( -27.60)
>DroSec_CAF1 57783 109 - 1
GGCAAUA-UUUUAUUCUCCAUCUAACUCUUUAGAUAGAAUGUAGCUUCUUCC----------UUAUCUCUGCACUUUGGGGUGCCGCAAAUCGAGUUCGAUUCAACCGACACUCUUGUGC
(((.(((-(((((.......(((((....))))))))))))).)))......----------........((((...((((((.((..(((((....)))))....)).)))))).)))) ( -24.61)
>DroSim_CAF1 50792 119 - 1
GUCAAUA-UUUUAUUCUCUAUCUAACUCUUUGUAUAGAAUUUAGUUUAUUCCUUUCAGGGACUUAUCUCUGCACUUUGGGGUGCCGCAAAUCGAGUUCGAUUCAACCGACACUCUUGUGC
(((((((-..(((...(((((.(((....))).)))))...)))..))))((.....)))))........((((...((((((.((..(((((....)))))....)).)))))).)))) ( -24.50)
>DroEre_CAF1 52331 117 - 1
CUCC--AUUUUAAUCAC-UAUUUAUCCCUUUGAUUGGAAUUUAGCUUUUUUCUUCCAGGGACUUCUUUUUGCACUUCUGUGUGCCGCAAAUCGAGUUCGAUUCAACCGCCACUCUUGUGC
....--...........-......(((((..((..((((........))))..)).))))).........((((....(((.((.(..(((((....)))))...).)))))....)))) ( -21.50)
>DroYak_CAF1 60203 112 - 1
------A-UUUUAUCACUUAUUUAUUCCUUUGGAUGGAAUUUAGCUUUUUUUAUCCAG-GAUUUAUUUUUGCACUCCUGGGUGCCGCAAAUCGAUUUCGAUUCAACCGCCAUUCUUGUGC
------.-.................((((..((((((((.........))))))))))-)).........((((.....((((.....(((((....)))))....))))......)))) ( -23.30)
>consensus
GUCAAUA_UUUUAUUAUCUAUCUAACCCUUUGGAUAGAAUUUAGCUUCUUUCUUCCAGGGACUUAUCUCUGCACUUCGGGGUGCCGCAAAUCGAGUUCGAUUCAACCGACACUCUUGUGC
................((((((((......))))))))................................((((....(((((.((..(((((....)))))....)).)))))..)))) (-14.50 = -15.78 +   1.28)

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 13:06:22 2006