Locus 4263

Sequence ID 3L_DroMel_CAF1
Location 12,484,061 – 12,484,214
Length 153
Max. P 0.965714
window6590 window6591 window6592

overview

Window 0

Location 12,484,061 – 12,484,181
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.92
Mean single sequence MFE -28.76
Consensus MFE -21.64
Energy contribution -21.12
Covariance contribution -0.52
Combinations/Pair 1.41
Mean z-score -1.22
Structure conservation index 0.75
SVM decision value 0.40
SVM RNA-class probability 0.722076
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12484061 120 - 23771897
UAUAUUUUAGCUCAAAGUUGAGGACCUAUCCGCCAAGAAGAAAAAGACAUUGGCGGACAAACUUUUCGGUUCUAGCCACACAAACAAGGAGAACGUGUCACCCAAUGACGUGGAAUCUUC
....(((((((.....))))))).....((((((((.............))))))))..........(((....)))..........(((((.(((((((.....)))))))...))))) ( -26.32)
>DroVir_CAF1 21215 119 - 1
-UUUUUUCAGCUUAAAGUCGAGGAUUUGUCAGCCAAGAAGAAGAAAACUUUGGCCGACAAAAUCUUUGGAUCCAACAGCAAUACUAAGGAGAACAUAUCGCCCAACGAUGUAGAAUCAUC
-........(((.....(((((((((((((.((((((...........)))))).))).)))))))))).......))).........((....((((((.....))))))....))... ( -27.60)
>DroEre_CAF1 10475 118 - 1
--UAUUUUAGCUUAAGGUAGAGGACCUGUCUUCCAAGAAGAAAAAGACAUUGGCGGACAAGCUCUUCGGUUCCAGCCAUACAAACAAGGAGAACAUGUCACCCAAUGACGUGGAAUCUUC
--..............(((((((((.(((((.((((.............)))).))))).).)))))(((....))).)))......(((((.(((((((.....)))))))...))))) ( -30.32)
>DroYak_CAF1 9542 118 - 1
--UCUAUUAGCUUAAAGUAGAGGACUUGUCUUCCAAGAAGAAAAAGACUUUGGCGGACAAGCUCUUCGGUUCCAGCCACACAAACAAGGAGAACGUGUCACCCAAUGACGUGGAAUCUUC
--.................((((((((((((.(((((...........))))).))))))).)))))(((((((.((..........)).......((((.....)))).)))))))... ( -30.80)
>DroMoj_CAF1 11579 119 - 1
-AAAUUGUAGCUUAAGGUGGAGGAUUUGUCUGCGAAGAAGAAGAAAACACUUGCAGACAAAAUCUUUGGAUCCAACAGCAAUACCAAGGAGAACAUAUCGCCUAAUGAUGUGGAGUCAUC
-.............((((((....(((((((((((...............))))))))))).(((((((..............))))))).......)))))).(((((.....))))). ( -28.60)
>DroAna_CAF1 8509 120 - 1
UGAAUUUCAGCUCAAAGUAGAAGACUUGUCUUCAAAGAAAAAGAAGACCCUAGCGGACAAGCUCUUCGGCUCCAGUCACACCAAUAAGGAGAACGUGUCACCCAAUGACGUGGAGUCCUC
...................((((((((((((((.........))))))((....))..))).)))))(((((((((((..((.....)).((.....))......)))).)))))))... ( -28.90)
>consensus
__UAUUUUAGCUUAAAGUAGAGGACUUGUCUGCCAAGAAGAAAAAGACAUUGGCGGACAAACUCUUCGGUUCCAGCCACACAAACAAGGAGAACAUGUCACCCAAUGACGUGGAAUCUUC
...................((((((((((((.((((.............)))).))))))).)))))(((((((.............(.....).(((((.....))))))))))))... (-21.64 = -21.12 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,484,101 – 12,484,214
Length 113
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 72.37
Mean single sequence MFE -23.06
Consensus MFE -17.75
Energy contribution -18.03
Covariance contribution 0.28
Combinations/Pair 1.45
Mean z-score -1.37
Structure conservation index 0.77
SVM decision value 1.58
SVM RNA-class probability 0.965714
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12484101 113 + 23771897
UGUGGCUAGAACCGAAAAGUUUGUCCGCCAAUGUCUUUUUCUUCUUGGCGGAUAGGUCCUCAACUUUGAGCUAAAAUAUAAAUACAAAAAUGUUUUUAAUCUCAUUAACUAUU
..(((((...........(..((((((((((.............))))))))))..)...........))))).....((((.(((....))).))))............... ( -21.47)
>DroVir_CAF1 21255 100 + 1
UGCUGUUGGAUCCAAAGAUUUUGUCGGCCAAAGUUUUCUUCUUCUUGGCUGACAAAUCCUCGACUUUAAGCUGAAAAAA--------AUAUGCAUUGGAG---AACAAGCA--
.((((((...(((((((..((((((((((((((.......))..))))))))))))..)).........((........--------....)).))))).---))).))).-- ( -27.80)
>DroSec_CAF1 9576 113 + 1
UGUGGCUAGAACCGAAAAGCUUGUCCGCCAAUGUCUUUUUCUUCUUGGCGGACAGGUCCUCAACUUUGAGCUAAAAUAUAAAUUUAAAAAUGUAUGUAAUCUCAUUAAAUAUU
..(((((...........(((((((((((((.............)))))))))))))...........)))))..(((((.(((....))).)))))................ ( -26.57)
>DroEre_CAF1 10515 105 + 1
UAUGGCUGGAACCGAAGAGCUUGUCCGCCAAUGUCUUUUUCUUCUUGGAAGACAGGUCCUCUACCUUAAGCUAAAAUA--------GACAUGUAUUCAGGUUCAUUAAAUAUU
........((((((((..((.((((......((((((((.......))))))))(((.....))).............--------)))).)).))).))))).......... ( -22.70)
>DroYak_CAF1 9582 105 + 1
UGUGGCUGGAACCGAAGAGCUUGUCCGCCAAAGUCUUUUUCUUCUUGGAAGACAAGUCCUCUACUUUAAGCUAAUAGA--------AAAAUGUAUUUAGUUUCAUAAAAUAUU
..(((((.(((....((..((((((..((((((.......))..))))..))))))..))....))).))))).....--------..(((((.((((......))))))))) ( -19.30)
>DroMoj_CAF1 11619 101 + 1
UGCUGUUGGAUCCAAAGAUUUUGUCUGCAAGUGUUUUCUUCUUCUUCGCAGACAAAUCCUCCACCUUAAGCUACAAUUU--------UGGUGUAUUAGUU---AUCAAUUAU-
.(((...((......((..((((((((((((............))).)))))))))..))...))...))).......(--------(((((.......)---)))))....- ( -20.50)
>consensus
UGUGGCUGGAACCGAAGAGCUUGUCCGCCAAUGUCUUUUUCUUCUUGGCAGACAAGUCCUCAACUUUAAGCUAAAAUAU_______AAAAUGUAUUUAAU_UCAUUAAAUAUU
..(((((........((.(((((((((((((.............))))))))))))).))........)))))........................................ (-17.75 = -18.03 +   0.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,484,101 – 12,484,214
Length 113
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 72.37
Mean single sequence MFE -23.14
Consensus MFE -15.17
Energy contribution -14.84
Covariance contribution -0.33
Combinations/Pair 1.38
Mean z-score -1.53
Structure conservation index 0.66
SVM decision value 1.21
SVM RNA-class probability 0.930731
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12484101 113 - 23771897
AAUAGUUAAUGAGAUUAAAAACAUUUUUGUAUUUAUAUUUUAGCUCAAAGUUGAGGACCUAUCCGCCAAGAAGAAAAAGACAUUGGCGGACAAACUUUUCGGUUCUAGCCACA
....(((..((((((((((.(((....))).)))).)))))).((((....)))))))...((((((((.............))))))))..........(((....)))... ( -22.72)
>DroVir_CAF1 21255 100 - 1
--UGCUUGUU---CUCCAAUGCAUAU--------UUUUUUCAGCUUAAAGUCGAGGAUUUGUCAGCCAAGAAGAAGAAAACUUUGGCCGACAAAAUCUUUGGAUCCAACAGCA
--((((((..---...))).)))...--------........(((.....(((((((((((((.((((((...........)))))).))).)))))))))).......))). ( -24.60)
>DroSec_CAF1 9576 113 - 1
AAUAUUUAAUGAGAUUACAUACAUUUUUAAAUUUAUAUUUUAGCUCAAAGUUGAGGACCUGUCCGCCAAGAAGAAAAAGACAUUGGCGGACAAGCUUUUCGGUUCUAGCCACA
.........((((.....(((.(((....))).))).......))))..(((.((((((((((((((((.............))))))))))........))))))))).... ( -24.52)
>DroEre_CAF1 10515 105 - 1
AAUAUUUAAUGAACCUGAAUACAUGUC--------UAUUUUAGCUUAAGGUAGAGGACCUGUCUUCCAAGAAGAAAAAGACAUUGGCGGACAAGCUCUUCGGUUCCAGCCAUA
..........(((((.(((...(((((--------(.((((..((((((..((.....))..)))..)))..)))).)))))).(((......))).))))))))........ ( -22.10)
>DroYak_CAF1 9582 105 - 1
AAUAUUUUAUGAAACUAAAUACAUUUU--------UCUAUUAGCUUAAAGUAGAGGACUUGUCUUCCAAGAAGAAAAAGACUUUGGCGGACAAGCUCUUCGGUUCCAGCCACA
..(((((((.....((((.........--------....))))..)))))))((((((((((((.(((((...........))))).))))))).)))))(((....)))... ( -23.22)
>DroMoj_CAF1 11619 101 - 1
-AUAAUUGAU---AACUAAUACACCA--------AAAUUGUAGCUUAAGGUGGAGGAUUUGUCUGCGAAGAAGAAGAAAACACUUGCAGACAAAAUCUUUGGAUCCAACAGCA
-.........---......((((...--------....))))(((...(((.((((((((((((((((...............)))))))).)))))))).)..))...))). ( -21.66)
>consensus
AAUAUUUAAUGA_AUUAAAUACAUUUU_______AUAUUUUAGCUUAAAGUAGAGGACCUGUCUGCCAAGAAGAAAAAGACAUUGGCGGACAAACUCUUCGGUUCCAGCCACA
....................................................((((((.((((((((((.............)))))))))).).)))))............. (-15.17 = -14.84 +  -0.33)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:01 2006