Locus 4441

Sequence ID X_DroMel_CAF1
Location 11,759,304 – 11,759,461
Length 157
Max. P 0.972346
window7293 window7294 window7295 window7296

overview

Window 3

Location 11,759,304 – 11,759,401
Length 97
Sequences 3
Columns 97
Reading direction reverse
Mean pairwise identity 87.41
Mean single sequence MFE -21.07
Consensus MFE -16.72
Energy contribution -16.73
Covariance contribution 0.01
Combinations/Pair 1.19
Mean z-score -2.62
Structure conservation index 0.79
SVM decision value 0.89
SVM RNA-class probability 0.876196
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11759304 97 - 22224390
ACAAAUUGGGAUAGCCGUUCUAAAUGAAUUGCAUAUAUUGAAUAUAUAUGUAUAUGCAUACAUUUGUCUUAGAUCAUAUGUAAUUUAAGGUUGGUUA
...........((((((..((...(((((((((((((((.((.(((.((((((....)))))).))).)).))).))))))))))))))..)))))) ( -21.80)
>DroSec_CAF1 12709 92 - 1
ACAAAUUG-GACAGACGUUCCAAAUGAACUACAUAUAUUGAAUGUAUAUGCAUAU----ACAUAUGUCUCAGAUCUUAUAUAACUUAAGGUUUGUUA
.......(-((((...((((.....))))..(((((((.....))))))).....----.....)))))(((((((((.......)))))))))... ( -18.30)
>DroSim_CAF1 7620 92 - 1
ACAAAUUG-GACAGACGUUCCAAAUGAACUGCAUAUAUUGAAUGUAUAUGCAUAU----ACAUAUGUCUCAGAUCUUAUAUAACUUAAGGUUUGUUA
.......(-((((...((((.....))))(((((((((.....)))))))))...----.....)))))(((((((((.......)))))))))... ( -23.10)
>consensus
ACAAAUUG_GACAGACGUUCCAAAUGAACUGCAUAUAUUGAAUGUAUAUGCAUAU____ACAUAUGUCUCAGAUCUUAUAUAACUUAAGGUUUGUUA
.........((((...((((.....))))(((((((((.....)))))))))............)))).(((((((((.......)))))))))... (-16.72 = -16.73 +   0.01)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,759,321 – 11,759,441
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.94
Mean single sequence MFE -24.06
Consensus MFE -9.75
Energy contribution -12.65
Covariance contribution 2.90
Combinations/Pair 1.18
Mean z-score -2.06
Structure conservation index 0.41
SVM decision value 1.02
SVM RNA-class probability 0.902020
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11759321 120 + 22224390
CAUAUGAUCUAAGACAAAUGUAUGCAUAUACAUAUAUAUUCAAUAUAUGCAAUUCAUUUAGAACGGCUAUCCCAAUUUGUUAGCCAGUGUAAAUUGGCCAAAAUACUUAUAGAAUCGACU
....(((((((.(((((((...((((((((.............)))))))).............((.....)).))))))).((((((....))))))...........))).))))... ( -22.72)
>DroSec_CAF1 12726 115 + 1
UAUAAGAUCUGAGACAUAUGU----AUAUGCAUAUACAUUCAAUAUAUGUAGUUCAUUUGGAACGUCUGUC-CAAUUUGUUAGCCAGUGUAAAUUGGCCAACAUACUUAUAGAAUCGACU
((((((.....((((......----...((((((((.......))))))))((((.....))))))))...-.....((((.((((((....)))))).))))..))))))......... ( -28.10)
>DroSim_CAF1 7637 115 + 1
UAUAAGAUCUGAGACAUAUGU----AUAUGCAUAUACAUUCAAUAUAUGCAGUUCAUUUGGAACGUCUGUC-CAAUUUGUUAGCCAGUGUAAAUUGGCCAACAUACUUAUAGAAUCGACU
((((((.....((((......----...((((((((.......))))))))((((.....))))))))...-.....((((.((((((....)))))).))))..))))))......... ( -30.10)
>DroEre_CAF1 41881 99 + 1
CAUAAGAUCUAGGACCAUUGC----A---GCCGCC---CUU-----------UUCAUUCAAAACGUUUUUCGUAACUUGUUGGCCAUUGUAAAUUGGCCAACAUACUUAUAGAAUCGACU
.....((...(((......((----.---...)))---)).-----------.))........((.((((.((((..(((((((((........)))))))))...)))))))).))... ( -20.80)
>DroYak_CAF1 13913 108 + 1
CAAAAGCUCCAAGAUUA--GC----A---GCAGAU---UUUCAUACAUGCAAUUAAUUUAGAACGACUUUCAUAACUUGUUGACCAGUGUAAAUUGGCCAACAUGCCUAUAGAAUCGACU
.....(((........)--))----(---(..(((---(((.(((...(((.........(((.....)))......(((((.(((((....))))).)))))))).)))))))))..)) ( -18.60)
>consensus
CAUAAGAUCUAAGACAAAUGU____AUAUGCAUAUA_AUUCAAUAUAUGCAAUUCAUUUAGAACGUCUGUC_CAAUUUGUUAGCCAGUGUAAAUUGGCCAACAUACUUAUAGAAUCGACU
.....((((((((((.............((((((((.......)))))))).............)))).........((((.((((((....)))))).))))......))).))).... ( -9.75 = -12.65 +   2.90)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,759,321 – 11,759,441
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.94
Mean single sequence MFE -26.70
Consensus MFE -15.41
Energy contribution -17.52
Covariance contribution 2.11
Combinations/Pair 1.37
Mean z-score -2.16
Structure conservation index 0.58
SVM decision value 1.69
SVM RNA-class probability 0.972346
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11759321 120 - 22224390
AGUCGAUUCUAUAAGUAUUUUGGCCAAUUUACACUGGCUAACAAAUUGGGAUAGCCGUUCUAAAUGAAUUGCAUAUAUUGAAUAUAUAUGUAUAUGCAUACAUUUGUCUUAGAUCAUAUG
....(((.(((.........((((((........))))))((((((((((((....)))))))(((...(((((((((.....)))))))))....)))...)))))..))))))..... ( -24.60)
>DroSec_CAF1 12726 115 - 1
AGUCGAUUCUAUAAGUAUGUUGGCCAAUUUACACUGGCUAACAAAUUG-GACAGACGUUCCAAAUGAACUACAUAUAUUGAAUGUAUAUGCAUAU----ACAUAUGUCUCAGAUCUUAUA
.........((((((..(((((((((........)))))))))..(((-((((...((((.....))))..(((((((.....))))))).....----.....)))).)))..)))))) ( -27.10)
>DroSim_CAF1 7637 115 - 1
AGUCGAUUCUAUAAGUAUGUUGGCCAAUUUACACUGGCUAACAAAUUG-GACAGACGUUCCAAAUGAACUGCAUAUAUUGAAUGUAUAUGCAUAU----ACAUAUGUCUCAGAUCUUAUA
.........((((((..(((((((((........)))))))))..(((-((((...((((.....))))(((((((((.....)))))))))...----.....)))).)))..)))))) ( -31.90)
>DroEre_CAF1 41881 99 - 1
AGUCGAUUCUAUAAGUAUGUUGGCCAAUUUACAAUGGCCAACAAGUUACGAAAAACGUUUUGAAUGAA-----------AAG---GGCGGC---U----GCAAUGGUCCUAGAUCUUAUG
(((((.((((.......(((((((((........))))))))).....(((((....)))))......-----------.))---))))))---)----.....((((...))))..... ( -23.70)
>DroYak_CAF1 13913 108 - 1
AGUCGAUUCUAUAGGCAUGUUGGCCAAUUUACACUGGUCAACAAGUUAUGAAAGUCGUUCUAAAUUAAUUGCAUGUAUGAAA---AUCUGC---U----GC--UAAUCUUGGAGCUUUUG
....((((.....(((.(((((((((........))))))))).))).....))))(((((((((((...(((.(.((....---))))))---.----..--)))).)))))))..... ( -26.20)
>consensus
AGUCGAUUCUAUAAGUAUGUUGGCCAAUUUACACUGGCUAACAAAUUG_GAAAGACGUUCUAAAUGAACUGCAUAUAUUGAAU_UAUAUGCAUAU____ACAUUUGUCUUAGAUCUUAUG
.........((((((..(((((((((........)))))))))..(((.((((...((((.....))))(((((((((.....)))))))))............)))).)))..)))))) (-15.41 = -17.52 +   2.11)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,759,361 – 11,759,461
Length 100
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 84.30
Mean single sequence MFE -24.70
Consensus MFE -19.48
Energy contribution -18.56
Covariance contribution -0.92
Combinations/Pair 1.32
Mean z-score -1.62
Structure conservation index 0.79
SVM decision value 0.20
SVM RNA-class probability 0.632791
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11759361 100 - 22224390
GCGAACG--GCUGAUGCGUAAAAGUCGAUUCUAUAAGUAUUUUGGCCAAUUUACACUGGCUAACAAAUUGGGAUAGCCGUUCUAAAUGAAUUGCAUAUAUUG
..(((((--((((((........))).((((((........(((((((........))))))).....)))))))))))))).................... ( -25.02)
>DroSec_CAF1 12762 101 - 1
GCGAACGGGGCUGAUGCGUAAAAGUCGAUUCUAUAAGUAUGUUGGCCAAUUUACACUGGCUAACAAAUUG-GACAGACGUUCCAAAUGAACUACAUAUAUUG
(.((((...((....))......(((...((((...((.(((((((((........))))))))).))))-))..))))))))................... ( -23.20)
>DroSim_CAF1 7673 101 - 1
GCGAACGGGGCUGAUGCGUAAAAGUCGAUUCUAUAAGUAUGUUGGCCAAUUUACACUGGCUAACAAAUUG-GACAGACGUUCCAAAUGAACUGCAUAUAUUG
((.......))..((((......(((...((((...((.(((((((((........))))))))).))))-))..)))((((.....)))).))))...... ( -24.40)
>DroEre_CAF1 41911 89 - 1
GCGAACG--GCUGAUGCGUAAAAGUCGAUUCUAUAAGUAUGUUGGCCAAUUUACAAUGGCCAACAAGUUACGAAAAACGUUUUGAAUGAA-----------A
..(((((--(((..........))))).)))........(((((((((........))))))))).....(((((....)))))......-----------. ( -22.10)
>DroYak_CAF1 13941 100 - 1
GCGAACG--GCUGAUGCGUAAAAGUCGAUUCUAUAGGCAUGUUGGCCAAUUUACACUGGUCAACAAGUUAUGAAAGUCGUUCUAAAUUAAUUGCAUGUAUGA
..(((((--(((....(((((..(((.........))).(((((((((........)))))))))..)))))..)))))))).................... ( -28.80)
>consensus
GCGAACG__GCUGAUGCGUAAAAGUCGAUUCUAUAAGUAUGUUGGCCAAUUUACACUGGCUAACAAAUUG_GAAAGACGUUCUAAAUGAACUGCAUAUAUUG
..(((((..((....))..................(((.(((((((((........))))))))).)))........))))).................... (-19.48 = -18.56 +  -0.92)

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 11:25:06 2006