Locus 5885

Sequence ID 2L_DroMel_CAF1
Location 16,635,479 – 16,635,697
Length 218
Max. P 0.993647
window9337 window9338 window9339 window9340

overview

Window 7

Location 16,635,479 – 16,635,575
Length 96
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 90.47
Mean single sequence MFE -29.57
Consensus MFE -22.88
Energy contribution -23.16
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -3.21
Structure conservation index 0.77
SVM decision value 2.41
SVM RNA-class probability 0.993647
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16635479 96 + 22407834
GCGAAUGUAUCUGUGACGCGUAUCUACAAUAUAUCUACAUGU--GUAUGUACACACAUAUCUUUUGUUGAGCGCGUAUCUCACGGAUGCAGUUCAAAU
..(((((((((((((((((((.((.((((.........((((--((......)))))).....)))).)))))))....))))))))))).))).... ( -30.84)
>DroSec_CAF1 90253 93 + 1
GCGAAUGUAUCUGUGUCGCGUAUCU-----AUAUCUACAUGUGUGUAUGUACACACAUAUCUUUUGUCGAGCGCGUAUCUCACGGAUGCAGUUCAAAU
..(((((((((((((.(((((.((.-----(((.....((((((((....))))))))......))).))))))).....)))))))))).))).... ( -33.20)
>DroSim_CAF1 92455 93 + 1
GCGAAUGUAUCUGUGUCGCGUAUCU-----AUAUCUACAUGUGUGUAUGUACACACAUAUCUUUUGUCGAGCGCGUAUCUCACGGAUGCAGUUCAAAU
..(((((((((((((.(((((.((.-----(((.....((((((((....))))))))......))).))))))).....)))))))))).))).... ( -33.20)
>DroEre_CAF1 91447 91 + 1
GUGUAUGUAUCUGUGUCGCGUAUCU-----GCAUCUACAUGU--GUAUGUGCAUACAAAUCUUUUGUCGAGCGCGUAUCUCGCGGAUGCAGUUCAAAU
.((..((((((((((.(((((.(((-----((((.(((....--))).))))).((((.....)))).))))))).....))))))))))...))... ( -29.00)
>DroYak_CAF1 89331 91 + 1
GCGAAUGUAUCUGUGUCGCGUAUCU-----AUAUCUACACGU--GUCUGUACAUACAUCUCUUUUGUCGAGCGCGUAUCUCAGGGAUGCAGUUCAAAU
..((((((((((.((....(((...-----.....)))((((--(..((.(((...........)))))..)))))....)).))))))).))).... ( -21.60)
>consensus
GCGAAUGUAUCUGUGUCGCGUAUCU_____AUAUCUACAUGU__GUAUGUACACACAUAUCUUUUGUCGAGCGCGUAUCUCACGGAUGCAGUUCAAAU
..(((((((((((((.(((((.((...........((((((....))))))...(((.......))).))))))).....)))))))))).))).... (-22.88 = -23.16 +   0.28)

alignment

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secondary structure

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Window 8

Location 16,635,575 – 16,635,666
Length 91
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 77.87
Mean single sequence MFE -29.62
Consensus MFE -18.95
Energy contribution -20.87
Covariance contribution 1.92
Combinations/Pair 1.10
Mean z-score -3.00
Structure conservation index 0.64
SVM decision value 2.13
SVM RNA-class probability 0.988566
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16635575 91 - 22407834
-------UUGUGUGGGCGUAAUCUCGAGGCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAAC-GGCCAAAUGCUCAC----------UAAACACG----------AGCAUAACGAA
-------....((((((((......(((((((((.....))))))))).......(((.......-.)))..))))))))----------........----------........... ( -31.00)
>DroPse_CAF1 102623 103 - 1
GCCUCUCCCGUGUGGGCGUAAUCUCGAGGCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAAC------AAAGCGCAU----------UCAACACGACCAGAGCUGAGCAGAGCAAC
(((((((..((.(((.(((......(((((((((.....)))))))))........((.(((...------.))).))..----------.....))).)))..)).))).)).))... ( -32.00)
>DroSim_CAF1 92548 89 - 1
-------UUG--UGGGCGUAAUCUCGAGGCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAAC-GGCCAAAUGCUCAC----------UAAACACG----------AGCAUAACGAA
-------..(--(((((((......(((((((((.....))))))))).......(((.......-.)))..))))))))----------........----------........... ( -31.00)
>DroYak_CAF1 89422 90 - 1
-------UUGUGUGGGCGUAAUCUCGAGGCAUUGUCACUCAAUGUC-CACUUAACGGCACUUAAC-GGCCAAAUGCUCAC----------UAAACACG----------AGCAUAACGAA
-------....((((((((......(.(((((((.....)))))))-).......(((.......-.)))..))))))))----------........----------........... ( -23.30)
>DroAna_CAF1 31684 102 - 1
-------AUGUGUGGGCGUAAUCUCGAGGCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAACAGGCCAAAUGCUCAAAAAAAAAAAUAAAACAUG----------AGCAUAACGAA
-------.........(((......(((((((((.....))))))))).......(((.((....)))))..(((((((.................))----------))))).))).. ( -28.43)
>DroPer_CAF1 103195 103 - 1
GCCUCUCCCGUGUGGGCGUAAUCUCGAGGCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAAC------AAAGCGCAU----------UCAACACGACCAGAGCUGAGCAGAGCAAC
(((((((..((.(((.(((......(((((((((.....)))))))))........((.(((...------.))).))..----------.....))).)))..)).))).)).))... ( -32.00)
>consensus
_______UUGUGUGGGCGUAAUCUCGAGGCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAAC_GGCCAAAUGCUCAC__________UAAACACG__________AGCAUAACGAA
...........((((((((......(((((((((.....))))))))).......(((.........)))..))))))))....................................... (-18.95 = -20.87 +   1.92)

alignment

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secondary structure

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Window 9

Location 16,635,595 – 16,635,697
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.58
Mean single sequence MFE -30.73
Consensus MFE -14.70
Energy contribution -14.90
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -1.88
Structure conservation index 0.48
SVM decision value 0.09
SVM RNA-class probability 0.578657
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16635595 102 + 22407834
UGAGCAUUUGGCC-GUUAAGUGCCGUUAAGUGAGGCAUUGAGUGACAAUGC-CUCGAGAUUACGCCCACACAA------------CGCCACUCGACUAAAUGCAAAACAAAAGAC----C
...((((((((.(-(...((((.((((..(((((((((((.....))))))-)))..(........)))..))------------)).)))))).))))))))............----. ( -31.70)
>DroPse_CAF1 102653 107 + 1
UGCGCUUU------GUUAAGUGCCGUUAAGUGAGGCAUUGAGUGACAAUGC-CUCGAGAUUACGCCCACACGGGAGAGGCUCUGGGGCUAUCCG--UAAAUGCAAAACAAAAGCC----C
...(((((------(((..(((.(((....((((((((((.....))))))-)))).....)))..)))(((((...((((....)))).))))--)........))).))))).----. ( -35.30)
>DroSim_CAF1 92568 100 + 1
UGAGCAUUUGGCC-GUUAAGUGCCGUUAAGUGAGGCAUUGAGUGACAAUGC-CUCGAGAUUACGCCCA--CAA------------CGCCACUCGACUAAAUGCAAAACAAAAGAC----C
...((((((((.(-(...((((.((((...((((((((((.....))))))-)))).(........).--.))------------)).)))))).))))))))............----. ( -31.70)
>DroWil_CAF1 183387 92 + 1
-----UUGUUUCG-GCUAAGUGCCGUUAAGUGAGGCAUUGAGUGACAAUGCUCUAAAGAUUACGCCCACACGA------------UAA------AACGAAUGCAAAACAAUAGCC----C
-----((((((((-((.....))))....(((.(((...((((......))))....(....)))))))....------------...------..........)))))).....----. ( -19.30)
>DroAna_CAF1 31714 107 + 1
UGAGCAUUUGGCCUGUUAAGUGCCGUUAAGUGAGGCAUUGAGUGACAAUGC-CUCGAGAUUACGCCCACACAU------------CAGCACUCGACUAAAUGCAAAACAAAAGAGCUAUC
...(((((((....((..((((((((....((((((((((.....))))))-)))).....))).........------------..)))))..)))))))))................. ( -31.10)
>DroPer_CAF1 103225 107 + 1
UGCGCUUU------GUUAAGUGCCGUUAAGUGAGGCAUUGAGUGACAAUGC-CUCGAGAUUACGCCCACACGGGAGAGGCUCUGGGGCUAUCCG--UAAAUGCAAAACAAAAGCC----C
...(((((------(((..(((.(((....((((((((((.....))))))-)))).....)))..)))(((((...((((....)))).))))--)........))).))))).----. ( -35.30)
>consensus
UGAGCAUUUGGCC_GUUAAGUGCCGUUAAGUGAGGCAUUGAGUGACAAUGC_CUCGAGAUUACGCCCACACAA____________CGCCACUCGACUAAAUGCAAAACAAAAGAC____C
...................(((.(((....((((((((((.....)))))).)))).....)))..)))................................................... (-14.70 = -14.90 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,635,595 – 16,635,697
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.58
Mean single sequence MFE -34.35
Consensus MFE -13.95
Energy contribution -14.45
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.58
Structure conservation index 0.41
SVM decision value 1.14
SVM RNA-class probability 0.921004
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16635595 102 - 22407834
G----GUCUUUUGUUUUGCAUUUAGUCGAGUGGCG------------UUGUGUGGGCGUAAUCUCGAG-GCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAAC-GGCCAAAUGCUCA
.----............((((((.((((((((.((------------(((.(((((......)))(((-((((((.....))))))))))).))))).))))...)-))).))))))... ( -38.90)
>DroPse_CAF1 102653 107 - 1
G----GGCUUUUGUUUUGCAUUUA--CGGAUAGCCCCAGAGCCUCUCCCGUGUGGGCGUAAUCUCGAG-GCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAAC------AAAGCGCA
(----.(((((.(((.(((.....--.((((.(((((((((...)))...)).))))...)))).(((-((((((.....)))))))))........)))...)))------))))).). ( -36.50)
>DroSim_CAF1 92568 100 - 1
G----GUCUUUUGUUUUGCAUUUAGUCGAGUGGCG------------UUG--UGGGCGUAAUCUCGAG-GCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAAC-GGCCAAAUGCUCA
.----............((((((.((((((((.((------------(((--.(((......)))(((-((((((.....)))))))))...))))).))))...)-))).))))))... ( -37.60)
>DroWil_CAF1 183387 92 - 1
G----GGCUAUUGUUUUGCAUUCGUU------UUA------------UCGUGUGGGCGUAAUCUUUAGAGCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAGC-CGAAACAA-----
.----(((((........(((.((..------...------------.)).)))(.(((.......((.((((((.....))))))))......))).)...))))-).......----- ( -20.72)
>DroAna_CAF1 31714 107 - 1
GAUAGCUCUUUUGUUUUGCAUUUAGUCGAGUGCUG------------AUGUGUGGGCGUAAUCUCGAG-GCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAACAGGCCAAAUGCUCA
.................((((((.(((((((((((------------((((....))))......(((-((((((.....)))))))))......))))))))....))).))))))... ( -35.90)
>DroPer_CAF1 103225 107 - 1
G----GGCUUUUGUUUUGCAUUUA--CGGAUAGCCCCAGAGCCUCUCCCGUGUGGGCGUAAUCUCGAG-GCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAAC------AAAGCGCA
(----.(((((.(((.(((.....--.((((.(((((((((...)))...)).))))...)))).(((-((((((.....)))))))))........)))...)))------))))).). ( -36.50)
>consensus
G____GGCUUUUGUUUUGCAUUUAGUCGAGUGGCG____________UCGUGUGGGCGUAAUCUCGAG_GCAUUGUCACUCAAUGCCUCACUUAACGGCACUUAAC_GGCCAAAAGCUCA
.................................................((((.(...(((....(((.((((((.....)))))))))..))).).))))................... (-13.95 = -14.45 +   0.50)

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 11:55:28 2006