Locus 2221

Sequence ID 3R_DroMel_CAF1
Location 6,333,834 – 6,333,956
Length 122
Max. P 0.996849
window3605 window3606 window3607 window3608

overview

Window 5

Location 6,333,834 – 6,333,938
Length 104
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 90.88
Mean single sequence MFE -19.48
Consensus MFE -17.81
Energy contribution -18.38
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.51
Structure conservation index 0.91
SVM decision value 0.50
SVM RNA-class probability 0.758656
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6333834 104 + 27905053
CAAGUCCUUUGUUAAUUU----UUUUCUGGUGCAUUUUAGUCUAUGCUCAGGGUUGCAUUUCUGCUCCCUAUCCGUCUCUUACCAUUUAUCGCUAGGAUCUAGCUUUA
..................----.....((((((((........))))..((((..(((....))).))))...........))))......(((((...))))).... ( -19.50)
>DroSim_CAF1 112184 104 + 1
CAUUUCCAUUGUUAAUUUUCUUUUUUCUGGUGCAUUUUAGUCUAUGCUCGGGGUUGCAUUUCUGCUCCCUAUCC----CUUACCAUUUAUCGCUAGGAUCUAGCUUUA
...........................((((((((........))))..((((..(((....))).))))....----...))))......(((((...))))).... ( -19.50)
>DroEre_CAF1 109773 102 + 1
CAUGUCCUUUGUUAAUUU-----UUUCUGGUGCACUUUAGUCUAUGCUCAGGGUUGCAUUUCUGCGCCCUAUC-GUCCCUUACCAUUUAUCGCUAGGAUCUAGCUUUA
..................-----....(((((((..........)))..(((((.(((....))))))))...-.......))))......(((((...))))).... ( -18.10)
>DroYak_CAF1 99068 103 + 1
CAUGUCCUUUGUUAAUUUA----CUUCUGGUGCAUUUUAGUCUAUGCUCAGGGUUGCAUUUCUGCGCCCUAUC-GUCCCUUACCAUUUAUCGCUAGGAUCUAGCUUUA
...................----....((((((((........))))..(((((.(((....))))))))...-.......))))......(((((...))))).... ( -20.80)
>consensus
CAUGUCCUUUGUUAAUUU_____UUUCUGGUGCAUUUUAGUCUAUGCUCAGGGUUGCAUUUCUGCGCCCUAUC_GUCCCUUACCAUUUAUCGCUAGGAUCUAGCUUUA
...........................((((((((........))))..(((((.(((....))))))))...........))))......(((((...))))).... (-17.81 = -18.38 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,333,834 – 6,333,938
Length 104
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 90.88
Mean single sequence MFE -23.07
Consensus MFE -22.74
Energy contribution -22.80
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -2.51
Structure conservation index 0.99
SVM decision value 2.76
SVM RNA-class probability 0.996849
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6333834 104 - 27905053
UAAAGCUAGAUCCUAGCGAUAAAUGGUAAGAGACGGAUAGGGAGCAGAAAUGCAACCCUGAGCAUAGACUAAAAUGCACCAGAAAA----AAAUUAACAAAGGACUUG
....(((((...)))))......((((..........(((((.(((....)))..))))).((((........)))))))).....----.................. ( -23.40)
>DroSim_CAF1 112184 104 - 1
UAAAGCUAGAUCCUAGCGAUAAAUGGUAAG----GGAUAGGGAGCAGAAAUGCAACCCCGAGCAUAGACUAAAAUGCACCAGAAAAAAGAAAAUUAACAAUGGAAAUG
....(((((...)))))......((((...----.....(((.(((....)))...)))..((((........))))))))........................... ( -21.40)
>DroEre_CAF1 109773 102 - 1
UAAAGCUAGAUCCUAGCGAUAAAUGGUAAGGGAC-GAUAGGGCGCAGAAAUGCAACCCUGAGCAUAGACUAAAGUGCACCAGAAA-----AAAUUAACAAAGGACAUG
....(((((...)))))......((((.......-..(((((.(((....)))..))))).((((........))))))))....-----.................. ( -23.90)
>DroYak_CAF1 99068 103 - 1
UAAAGCUAGAUCCUAGCGAUAAAUGGUAAGGGAC-GAUAGGGCGCAGAAAUGCAACCCUGAGCAUAGACUAAAAUGCACCAGAAG----UAAAUUAACAAAGGACAUG
....(((((...)))))......((((.......-..(((((.(((....)))..))))).((((........))))))))....----................... ( -23.60)
>consensus
UAAAGCUAGAUCCUAGCGAUAAAUGGUAAGGGAC_GAUAGGGAGCAGAAAUGCAACCCUGAGCAUAGACUAAAAUGCACCAGAAA_____AAAUUAACAAAGGACAUG
....(((((...)))))......((((..........(((((.(((....)))..))))).((((........))))))))........................... (-22.74 = -22.80 +   0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,333,866 – 6,333,956
Length 90
Sequences 6
Columns 92
Reading direction forward
Mean pairwise identity 82.75
Mean single sequence MFE -17.33
Consensus MFE -14.61
Energy contribution -14.75
Covariance contribution 0.14
Combinations/Pair 1.16
Mean z-score -1.58
Structure conservation index 0.84
SVM decision value 0.36
SVM RNA-class probability 0.705253
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6333866 90 + 27905053
UUAGUCUAUGCUCAGGGUUGCAUUUCUGCUCCCUAUCCGUCUCUUACCAUUUAUCGCUAGGAUCUAGCUUUAGAUUAGAUU--UAAACUUAA
((((((((.....((((..(((....))).)))).....................(((((...)))))..))))))))...--......... ( -18.60)
>DroSec_CAF1 98661 86 + 1
UUAGUCUAUGCUCAGGGUUGCAUUUCUGCUCCCUAUCC----CUUACCAUUUAUCGCUAGGAUCUAGCUUUAGAUUAGAUU--UUAACUUAG
((((((((.....((((..(((....))).))))....----.............(((((...)))))..))))))))...--......... ( -18.60)
>DroSim_CAF1 112220 86 + 1
UUAGUCUAUGCUCGGGGUUGCAUUUCUGCUCCCUAUCC----CUUACCAUUUAUCGCUAGGAUCUAGCUUUAGAUUAGAUU--UAAACUUAG
((((((((.....((((..(((....))).))))....----.............(((((...)))))..))))))))...--......... ( -18.60)
>DroEre_CAF1 109804 89 + 1
UUAGUCUAUGCUCAGGGUUGCAUUUCUGCGCCCUAUC-GUCCCUUACCAUUUAUCGCUAGGAUCUAGCUUUAGAUUAGGUU--UAAACUUAG
((((((((.....(((((.(((....))))))))...-.................(((((...)))))..))))))))...--......... ( -19.90)
>DroWil_CAF1 187956 74 + 1
UUAGUCUAUGCUCAGGGUUGCU--UUUGCUCC---------------GCUUUUUCAUUAUCAACUAACAUUAGAUUAAAUUAUUAUAUUUC-
((((((((.......(((((.(--..((....---------------.......))..).))))).....)))))))).............- (  -8.40)
>DroYak_CAF1 99100 89 + 1
UUAGUCUAUGCUCAGGGUUGCAUUUCUGCGCCCUAUC-GUCCCUUACCAUUUAUCGCUAGGAUCUAGCUUUAGAUUAGGUU--UAAACUUAG
((((((((.....(((((.(((....))))))))...-.................(((((...)))))..))))))))...--......... ( -19.90)
>consensus
UUAGUCUAUGCUCAGGGUUGCAUUUCUGCUCCCUAUC_____CUUACCAUUUAUCGCUAGGAUCUAGCUUUAGAUUAGAUU__UAAACUUAG
((((((((.....((((..((......)).)))).....................(((((...)))))..)))))))).............. (-14.61 = -14.75 +   0.14)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,333,866 – 6,333,956
Length 90
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 82.75
Mean single sequence MFE -19.60
Consensus MFE -13.63
Energy contribution -14.22
Covariance contribution 0.58
Combinations/Pair 1.12
Mean z-score -2.22
Structure conservation index 0.70
SVM decision value 0.46
SVM RNA-class probability 0.745287
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6333866 90 - 27905053
UUAAGUUUA--AAUCUAAUCUAAAGCUAGAUCCUAGCGAUAAAUGGUAAGAGACGGAUAGGGAGCAGAAAUGCAACCCUGAGCAUAGACUAA
...((((((--..(((.(((....(((((...))))).......))).)))......(((((.(((....)))..)))))....)))))).. ( -22.00)
>DroSec_CAF1 98661 86 - 1
CUAAGUUAA--AAUCUAAUCUAAAGCUAGAUCCUAGCGAUAAAUGGUAAG----GGAUAGGGAGCAGAAAUGCAACCCUGAGCAUAGACUAA
(((.(((..--..(((.(((....(((((...))))).......))).))----)..(((((.(((....)))..)))))))).)))..... ( -19.60)
>DroSim_CAF1 112220 86 - 1
CUAAGUUUA--AAUCUAAUCUAAAGCUAGAUCCUAGCGAUAAAUGGUAAG----GGAUAGGGAGCAGAAAUGCAACCCCGAGCAUAGACUAA
...((((((--..((..((((...((((.(((.....)))...))))...----)))).(((.(((....)))...)))))...)))))).. ( -19.80)
>DroEre_CAF1 109804 89 - 1
CUAAGUUUA--AACCUAAUCUAAAGCUAGAUCCUAGCGAUAAAUGGUAAGGGAC-GAUAGGGCGCAGAAAUGCAACCCUGAGCAUAGACUAA
...((((((--..(((.(((....(((((...))))).......))).)))...-..(((((.(((....)))..)))))....)))))).. ( -24.30)
>DroWil_CAF1 187956 74 - 1
-GAAAUAUAAUAAUUUAAUCUAAUGUUAGUUGAUAAUGAAAAAGC---------------GGAGCAAA--AGCAACCCUGAGCAUAGACUAA
-........................((((((....(((....((.---------------((.((...--.))..))))...))).)))))) (  -7.60)
>DroYak_CAF1 99100 89 - 1
CUAAGUUUA--AACCUAAUCUAAAGCUAGAUCCUAGCGAUAAAUGGUAAGGGAC-GAUAGGGCGCAGAAAUGCAACCCUGAGCAUAGACUAA
...((((((--..(((.(((....(((((...))))).......))).)))...-..(((((.(((....)))..)))))....)))))).. ( -24.30)
>consensus
CUAAGUUUA__AAUCUAAUCUAAAGCUAGAUCCUAGCGAUAAAUGGUAAG_____GAUAGGGAGCAGAAAUGCAACCCUGAGCAUAGACUAA
..................((((..(((((...)))))....................(((((.(((....)))..)))))....)))).... (-13.63 = -14.22 +   0.58)

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 10:30:13 2006