Locus 4566

Sequence ID 2L_DroMel_CAF1
Location 13,096,714 – 13,096,820
Length 106
Max. P 0.937333
window7192 window7193 window7194 window7195

overview

Window 2

Location 13,096,714 – 13,096,804
Length 90
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 63.58
Mean single sequence MFE -18.43
Consensus MFE -5.78
Energy contribution -6.67
Covariance contribution 0.89
Combinations/Pair 1.12
Mean z-score -2.39
Structure conservation index 0.31
SVM decision value 1.26
SVM RNA-class probability 0.937333
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13096714 90 + 22407834
UUUCGAUUA------AA-UAUUG-----------GCUUGUUUUGCUCUUGUAAUCACUACAAAUGAUGAUCAUGCGAUCAUCAUUUUACUGACUGAUCUAUCUCACCA
....(((((------.(-((..(-----------((.......)))..)))..(((.((.(((((((((((....))))))))))))).))).))))).......... ( -20.10)
>DroSec_CAF1 77831 90 + 1
UUUAGAUUG------AA-UAUUG-----------GCUUGUUUUGCUCUUGCAAUCACUAAAAAUGAUGAUCAUGAGAUCAUCAUUUUACAGCCUGAUCUAUCUCACCA
...((((.(------(.-....(-----------(((.((.((((....))))......((((((((((((....))))))))))))))))))...)).))))..... ( -24.80)
>DroSim_CAF1 75690 90 + 1
UUUAGAUUG------AA-UAUUG-----------GCUUGUCUUGCUUUUGCAAUCACUAAAAAUGAUGAUCAUGCGAUCAUCAAAUUACUGCCUGAUCUAUCUCACCA
...((((.(------(.-....(-----------((.....((((....))))..........((((((((....)))))))).......)))...)).))))..... ( -19.80)
>DroEre_CAF1 78955 87 + 1
UUUGCUUUG------AA-UAUUACGUUACAACAAGCUUGUUGUGAUUUUACA--------------UGAUCACGCGAUCAUCAUUUCGGUGCCUGAUCUAUCUCACCA
........(------((-......(((((((((....))))))))).....(--------------(((((....))))))...)))((((...((....)).)))). ( -18.10)
>DroYak_CAF1 78670 103 + 1
UUUAGUUUGUAUACGAG-UAUUACAUUACAA----CUUGUUGUGCGUUUACAAUCACUAAAAAUGAUGAUCAUGCGAUCACCAAUUCGCUGCCUGAUCUAUCUCACCA
(((((((((((.((..(-(((.(((......----..))).)))))).)))))..))))))...((((((((.((((........))))....))))).)))...... ( -22.70)
>DroAna_CAF1 63668 72 + 1
UUUCCAUGA------AAACCUUU-----------CCUUAUCGUU----------CCUUAGAAAU-AUCAACUUGUGUUUAUUUUUUCA--GA------AAUCUGAUCG
.......((------........-----------..........----------....((((((-(..(((....))))))))))(((--(.------...)))))). (  -5.10)
>consensus
UUUAGAUUG______AA_UAUUG___________GCUUGUUGUGCUUUUGCAAUCACUAAAAAUGAUGAUCAUGCGAUCAUCAUUUCACUGCCUGAUCUAUCUCACCA
...............................................................((((((((....))))))))......................... ( -5.78 =  -6.67 +   0.89)

alignment

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secondary structure

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Window 3

Location 13,096,714 – 13,096,804
Length 90
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 63.58
Mean single sequence MFE -19.11
Consensus MFE -6.17
Energy contribution -6.78
Covariance contribution 0.61
Combinations/Pair 1.25
Mean z-score -1.89
Structure conservation index 0.32
SVM decision value 0.33
SVM RNA-class probability 0.691393
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13096714 90 - 22407834
UGGUGAGAUAGAUCAGUCAGUAAAAUGAUGAUCGCAUGAUCAUCAUUUGUAGUGAUUACAAGAGCAAAACAAGC-----------CAAUA-UU------UAAUCGAAA
((((((......))(((((.(((((((((((((....))))))))))).)).)))))...............))-----------))...-..------......... ( -21.70)
>DroSec_CAF1 77831 90 - 1
UGGUGAGAUAGAUCAGGCUGUAAAAUGAUGAUCUCAUGAUCAUCAUUUUUAGUGAUUGCAAGAGCAAAACAAGC-----------CAAUA-UU------CAAUCUAAA
.....((((.((...((((..((((((((((((....))))))))))))..((..((((....)))).)).)))-----------)....-.)------).))))... ( -26.40)
>DroSim_CAF1 75690 90 - 1
UGGUGAGAUAGAUCAGGCAGUAAUUUGAUGAUCGCAUGAUCAUCAUUUUUAGUGAUUGCAAAAGCAAGACAAGC-----------CAAUA-UU------CAAUCUAAA
.....((((.((...(((..(((..((((((((....))))))))...)))((..((((....)))).))..))-----------)....-.)------).))))... ( -21.80)
>DroEre_CAF1 78955 87 - 1
UGGUGAGAUAGAUCAGGCACCGAAAUGAUGAUCGCGUGAUCA--------------UGUAAAAUCACAACAAGCUUGUUGUAACGUAAUA-UU------CAAAGCAAA
..((((.((((((((.((...............)).))))).--------------)))....)))).....((((...(((......))-).------..))))... ( -17.86)
>DroYak_CAF1 78670 103 - 1
UGGUGAGAUAGAUCAGGCAGCGAAUUGGUGAUCGCAUGAUCAUCAUUUUUAGUGAUUGUAAACGCACAACAAG----UUGUAAUGUAAUA-CUCGUAUACAAACUAAA
....(((.((...((.((((((((.((((((((....)))))))).)))..(((........))).......)----))))..))...))-))).............. ( -19.60)
>DroAna_CAF1 63668 72 - 1
CGAUCAGAUU------UC--UGAAAAAAUAAACACAAGUUGAU-AUUUCUAAGG----------AACGAUAAGG-----------AAAGGUUU------UCAUGGAAA
...((((...------.)--)))...........((.(..(((-.(((((....----------........))-----------))).))).------.).)).... (  -7.30)
>consensus
UGGUGAGAUAGAUCAGGCAGUAAAAUGAUGAUCGCAUGAUCAUCAUUUUUAGUGAUUGCAAAAGCAAAACAAGC___________CAAUA_UU______CAAUCUAAA
.........................((((((((....))))))))............................................................... ( -6.17 =  -6.78 +   0.61)

alignment

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secondary structure

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Window 4

Location 13,096,730 – 13,096,820
Length 90
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 81.03
Mean single sequence MFE -16.56
Consensus MFE -7.56
Energy contribution -9.00
Covariance contribution 1.44
Combinations/Pair 1.05
Mean z-score -2.30
Structure conservation index 0.46
SVM decision value 0.39
SVM RNA-class probability 0.718211
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13096730 90 + 22407834
------GCUUGUUUUGCUCUUGUAAUCACUACAAAUGAUGAUCAUGCGAUCAUCAUUUUACUGACUGAUCUAUCUCACCAAUUAGUUAAAUAAUCA
------(.((((((.(((.(((...(((.((.(((((((((((....))))))))))))).))).(((......))).)))..))).)))))).). ( -17.60)
>DroSec_CAF1 77847 90 + 1
------GCUUGUUUUGCUCUUGCAAUCACUAAAAAUGAUGAUCAUGAGAUCAUCAUUUUACAGCCUGAUCUAUCUCACCAAUUAGUUAAAUAAUCA
------(((.((.((((....))))......((((((((((((....)))))))))))))))))................................ ( -18.90)
>DroSim_CAF1 75706 90 + 1
------GCUUGUCUUGCUUUUGCAAUCACUAAAAAUGAUGAUCAUGCGAUCAUCAAAUUACUGCCUGAUCUAUCUCACCAAUUAGUUAAAUAAUCA
------.......((((....))))..(((((...((((((((....))))))))..........(((......)))....))))).......... ( -15.00)
>DroEre_CAF1 78976 82 + 1
CAACAAGCUUGUUGUGAUUUUACA--------------UGAUCACGCGAUCAUCAUUUCGGUGCCUGAUCUAUCUCACCAAUUAGCUAAAUAAUCA
.....((((.(((((((..(....--------------.(((((.((.(((........))))).))))).)..))).)))).))))......... ( -16.40)
>DroYak_CAF1 78697 92 + 1
CAA----CUUGUUGUGCGUUUACAAUCACUAAAAAUGAUGAUCAUGCGAUCACCAAUUCGCUGCCUGAUCUAUCUCACCAAUUAGUUAAAUAAUCA
.((----((.((((((.(......((((.......))))(((((.((((........))))....)))))...).)).)))).))))......... ( -14.90)
>consensus
______GCUUGUUUUGCUUUUGCAAUCACUAAAAAUGAUGAUCAUGCGAUCAUCAUUUUACUGCCUGAUCUAUCUCACCAAUUAGUUAAAUAAUCA
........((((((.((..................((((((((....))))))))..........(((......))).......)).))))))... ( -7.56 =  -9.00 +   1.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,096,730 – 13,096,820
Length 90
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 81.03
Mean single sequence MFE -20.69
Consensus MFE -12.86
Energy contribution -13.18
Covariance contribution 0.32
Combinations/Pair 1.10
Mean z-score -1.97
Structure conservation index 0.62
SVM decision value 0.51
SVM RNA-class probability 0.763464
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13096730 90 - 22407834
UGAUUAUUUAACUAAUUGGUGAGAUAGAUCAGUCAGUAAAAUGAUGAUCGCAUGAUCAUCAUUUGUAGUGAUUACAAGAGCAAAACAAGC------
.((((((((.(((....))).)))).))))(((((.(((((((((((((....))))))))))).)).))))).................------ ( -22.00)
>DroSec_CAF1 77847 90 - 1
UGAUUAUUUAACUAAUUGGUGAGAUAGAUCAGGCUGUAAAAUGAUGAUCUCAUGAUCAUCAUUUUUAGUGAUUGCAAGAGCAAAACAAGC------
(((((((((.(((....))).)))).))))).((((.((((((((((((....))))))))))))))))..((((....)))).......------ ( -25.30)
>DroSim_CAF1 75706 90 - 1
UGAUUAUUUAACUAAUUGGUGAGAUAGAUCAGGCAGUAAUUUGAUGAUCGCAUGAUCAUCAUUUUUAGUGAUUGCAAAAGCAAGACAAGC------
(((((((((.(((....))).)))).)))))..((.(((..((((((((....))))))))...))).)).((((....)))).......------ ( -20.60)
>DroEre_CAF1 78976 82 - 1
UGAUUAUUUAGCUAAUUGGUGAGAUAGAUCAGGCACCGAAAUGAUGAUCGCGUGAUCA--------------UGUAAAAUCACAACAAGCUUGUUG
.........((((.....((((.((((((((.((...............)).))))).--------------)))....))))....))))..... ( -16.76)
>DroYak_CAF1 78697 92 - 1
UGAUUAUUUAACUAAUUGGUGAGAUAGAUCAGGCAGCGAAUUGGUGAUCGCAUGAUCAUCAUUUUUAGUGAUUGUAAACGCACAACAAG----UUG
........(((((..((((((.....(((((......(((.((((((((....)))))))).)))...))))).....))).)))..))----))) ( -18.80)
>consensus
UGAUUAUUUAACUAAUUGGUGAGAUAGAUCAGGCAGUAAAAUGAUGAUCGCAUGAUCAUCAUUUUUAGUGAUUGCAAAAGCAAAACAAGC______
(((((((((.(((....))).)))).)))))..........((((((((....))))))))................................... (-12.86 = -13.18 +   0.32)

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 11:21:11 2006