Locus 8250

Sequence ID 3R_DroMel_CAF1
Location 22,075,724 – 22,075,933
Length 209
Max. P 0.932614
window13300 window13301 window13302 window13303 window13304

overview

Window 0

Location 22,075,724 – 22,075,833
Length 109
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 89.20
Mean single sequence MFE -32.16
Consensus MFE -29.28
Energy contribution -29.36
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.43
Structure conservation index 0.91
SVM decision value 0.65
SVM RNA-class probability 0.812708
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22075724 109 + 27905053
UUACUCUGCGAAGUGCCAGGGGAAUCCCUGCCAGCUGCUAAAAGGCUUUGCAUGUUCCAUUUUCCAGCUGAAUGGAACGGCAAGGGGAUG----AAUAAGAAUAU--AUUCUA----AG
...(((((.(.....))))))..(((((((((.((.(((....)))...))..(((((((((.......))))))))))))..))))))(----((((......)--))))..----.. ( -35.30)
>DroSec_CAF1 67773 115 + 1
UUACUCUGCCAAGUGCCAGGGGAAUCCCUGCCAGCUGCUAAAAGGCUUUGCAUGUUCCAUUUUCCAGCUGAAUGGAACGACAAGGGGAUG----AAUAAGAAUAUAUAUUCUAAGUAAG
...(((((.(....).)))))..((((((((.((((.......))))..)).((((((((((.......))))))))))....)))))).----....(((((....)))))....... ( -31.60)
>DroSim_CAF1 61213 115 + 1
UUACUCUGCCAAGUGCCAGGGGAAUCCCUGCCAGCUGCUAAAAGGCUUUGCAUGUUCCAUUUUCCAGCUGAAUGGAACGACAAGGGGAUG----AAUAAGAAUAUAUAUUCUAAGUAAG
...(((((.(....).)))))..((((((((.((((.......))))..)).((((((((((.......))))))))))....)))))).----....(((((....)))))....... ( -31.60)
>DroEre_CAF1 62403 105 + 1
UUACUCUGCGAAGUGCCAGGGGAAUCCCUGCCAGCUGCUAAAAGGCUUUGCGUGUUCCAUUUUCCGGCUAAAUGGAAUGGCAAGGGGAUG----CAUAAGAAUAUA----------AAG
...(((((.(.....))))))(.(((((((((.((.(((....)))...))..(((((((((.......))))))))))))..)))))).----)...........----------... ( -30.80)
>DroYak_CAF1 70253 109 + 1
UUACUCUGCGAAGUGCCAGGGGAAUCCCUGCCAGCUGCUAAAAGGCUUUGCAUGUUCCAUUUUCCAGCUGAAUGGAACGCCAAGGGGAUGGAUCCGUAAGAAUAUA----------AAG
...((((((((((((.(((((....))))).)..((......)))))))))..(((((((((.......)))))))))....)))).(((....))).........----------... ( -31.50)
>consensus
UUACUCUGCGAAGUGCCAGGGGAAUCCCUGCCAGCUGCUAAAAGGCUUUGCAUGUUCCAUUUUCCAGCUGAAUGGAACGACAAGGGGAUG____AAUAAGAAUAUA_AUUCUA___AAG
...((((((((((((.(((((....))))).)..((......))))))))).((((((((((.......))))))))))...))))................................. (-29.28 = -29.36 +   0.08)

alignment

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secondary structure

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Window 1

Location 22,075,724 – 22,075,833
Length 109
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 89.20
Mean single sequence MFE -29.42
Consensus MFE -25.92
Energy contribution -26.12
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.88
SVM decision value 0.70
SVM RNA-class probability 0.827626
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22075724 109 - 27905053
CU----UAGAAU--AUAUUCUUAUU----CAUCCCCUUGCCGUUCCAUUCAGCUGGAAAAUGGAACAUGCAAAGCCUUUUAGCAGCUGGCAGGGAUUCCCCUGGCACUUCGCAGAGUAA
..----..((((--(......))))----).......((((((((((((.........)))))))).(((...((......))((.((.(((((....))))).))))..)))).))). ( -28.50)
>DroSec_CAF1 67773 115 - 1
CUUACUUAGAAUAUAUAUUCUUAUU----CAUCCCCUUGUCGUUCCAUUCAGCUGGAAAAUGGAACAUGCAAAGCCUUUUAGCAGCUGGCAGGGAUUCCCCUGGCACUUGGCAGAGUAA
..(((((.(((((........))))----).......((((((((((((.........)))))))).(((...((......))......(((((....))))))))...))))))))). ( -30.80)
>DroSim_CAF1 61213 115 - 1
CUUACUUAGAAUAUAUAUUCUUAUU----CAUCCCCUUGUCGUUCCAUUCAGCUGGAAAAUGGAACAUGCAAAGCCUUUUAGCAGCUGGCAGGGAUUCCCCUGGCACUUGGCAGAGUAA
..(((((.(((((........))))----).......((((((((((((.........)))))))).(((...((......))......(((((....))))))))...))))))))). ( -30.80)
>DroEre_CAF1 62403 105 - 1
CUU----------UAUAUUCUUAUG----CAUCCCCUUGCCAUUCCAUUUAGCCGGAAAAUGGAACACGCAAAGCCUUUUAGCAGCUGGCAGGGAUUCCCCUGGCACUUCGCAGAGUAA
...----------..((((((...(----(......((((..((((((((.......))))))))...)))).........(.((.((.(((((....))))).)))).))))))))). ( -27.70)
>DroYak_CAF1 70253 109 - 1
CUU----------UAUAUUCUUACGGAUCCAUCCCCUUGGCGUUCCAUUCAGCUGGAAAAUGGAACAUGCAAAGCCUUUUAGCAGCUGGCAGGGAUUCCCCUGGCACUUCGCAGAGUAA
...----------..((((((..((((...........(((((((((((.........)))))))).(((...........))))))(.(((((....))))).)..)))).)))))). ( -29.30)
>consensus
CUU___UAGAAU_UAUAUUCUUAUU____CAUCCCCUUGCCGUUCCAUUCAGCUGGAAAAUGGAACAUGCAAAGCCUUUUAGCAGCUGGCAGGGAUUCCCCUGGCACUUCGCAGAGUAA
...............((((((....................((((((((.........))))))))..((...((......))((.((.(((((....))))).))))..)))))))). (-25.92 = -26.12 +   0.20)

alignment

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secondary structure

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Window 2

Location 22,075,763 – 22,075,873
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.43
Mean single sequence MFE -27.78
Consensus MFE -22.90
Energy contribution -22.58
Covariance contribution -0.32
Combinations/Pair 1.09
Mean z-score -1.74
Structure conservation index 0.82
SVM decision value 0.73
SVM RNA-class probability 0.835997
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22075763 110 + 27905053
AAAAGGCUUUGCAUGUUCCAUUUUCCAGCUGAAUGGAACGGCAAGGGGAUG----AAUAAGAAUAU--AUUCUA----AGUAUAAUAUGUUCCCUCUCAUUACACACACUAGCGGCAGCA
......((((((.((((((((((.......)))))))))))))))).((((----(....((((((--(((...----.....)))))))))....)))))..........((....)). ( -30.30)
>DroSec_CAF1 67812 114 + 1
AAAAGGCUUUGCAUGUUCCAUUUUCCAGCUGAAUGGAACGACAAGGGGAUG----AAUAAGAAUAUAUAUUCUAAGUAAGUAUAAUAAGUUCCCUCUCAUUACAC--ACUCGCGGCAGCA
.....(((((((..(((((((((.......)))))))))((..(((((((.----.......((((.(((.....))).)))).....))))))).)).......--....)))).))). ( -27.02)
>DroSim_CAF1 61252 114 + 1
AAAAGGCUUUGCAUGUUCCAUUUUCCAGCUGAAUGGAACGACAAGGGGAUG----AAUAAGAAUAUAUAUUCUAAGUAAGUAUAAUAAGUUCCCUCUCAUUACAC--ACUCGCGGCAGCA
.....(((((((..(((((((((.......)))))))))((..(((((((.----.......((((.(((.....))).)))).....))))))).)).......--....)))).))). ( -27.02)
>DroEre_CAF1 62442 104 + 1
AAAAGGCUUUGCGUGUUCCAUUUUCCGGCUAAAUGGAAUGGCAAGGGGAUG----CAUAAGAAUAUA----------AAGUAUAAUAAGUUCCCCCUCAUUACAC--ACUCGCGGCAGCC
....(((((((((.(((((((((.......)))))))))....(((((..(----(...........----------...........))..)))))........--...))))).)))) ( -26.15)
>DroYak_CAF1 70292 108 + 1
AAAAGGCUUUGCAUGUUCCAUUUUCCAGCUGAAUGGAACGCCAAGGGGAUGGAUCCGUAAGAAUAUA----------AAGUAUAAUAUGUUCCCUCUCAUUACAC--ACUCGCGGCAGCA
.....(((((((..(((((((((.......)))))))))....((((((((....)))..(((((((----------........))))))))))))........--....)))).))). ( -28.40)
>consensus
AAAAGGCUUUGCAUGUUCCAUUUUCCAGCUGAAUGGAACGACAAGGGGAUG____AAUAAGAAUAUA_AUUCUA___AAGUAUAAUAAGUUCCCUCUCAUUACAC__ACUCGCGGCAGCA
.....(((((((.((((((((((.......))))))))))....((((((......................................)))))).................)))).))). (-22.90 = -22.58 +  -0.32)

alignment

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secondary structure

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Window 3

Location 22,075,803 – 22,075,913
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.61
Mean single sequence MFE -30.88
Consensus MFE -26.86
Energy contribution -27.42
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -1.69
Structure conservation index 0.87
SVM decision value 0.92
SVM RNA-class probability 0.881515
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22075803 110 - 27905053
ACCAUUUAAUUCAAAUGGGUGGGCCGCAGAGCAAACGUUUUGCUGCCGCUAGUGUGUGUAAUGAGAGGGAACAUAUUAUACU----UAGAAU--AUAUUCUUAUU----CAUCCCCUUGC
.((((((.....))))))...(((.(((((((....))))))).)))((.((.(..((.((((((((....)(((((.....----...)))--))..)))))))----))..).)).)) ( -29.40)
>DroSec_CAF1 67852 114 - 1
ACCAUUUAAUUCAAAUGGGUGGGCCGCAGAGCAAACGUUUUGCUGCCGCGAGU--GUGUAAUGAGAGGGAACUUAUUAUACUUACUUAGAAUAUAUAUUCUUAUU----CAUCCCCUUGU
.((((((.....))))))...(((.(((((((....))))))).)))(((((.--((((((((((......)))))))))).......(((((........))))----).....))))) ( -34.90)
>DroSim_CAF1 61292 114 - 1
ACCAUUUAAUUCAAAUGGGUGGGCCGCAGAGCAAACGUUUUGCUGCCGCGAGU--GUGUAAUGAGAGGGAACUUAUUAUACUUACUUAGAAUAUAUAUUCUUAUU----CAUCCCCUUGU
.((((((.....))))))...(((.(((((((....))))))).)))(((((.--((((((((((......)))))))))).......(((((........))))----).....))))) ( -34.90)
>DroEre_CAF1 62482 104 - 1
AGCAUUUAAUUCGAAUGGGUGGACCGCAGAGCAAACGUUUGGCUGCCGCGAGU--GUGUAAUGAGGGGGAACUUAUUAUACUU----------UAUAUUCUUAUG----CAUCCCCUUGC
.((((...(((((....((..(.((...((((....)))))))..)).)))))--((((((((((......))))))))))..----------.........)))----).......... ( -26.50)
>DroYak_CAF1 70332 108 - 1
ACCAUUUAAUUCGAAUGGGUGGGCCGCAGAGCAAACGUUUUGCUGCCGCGAGU--GUGUAAUGAGAGGGAACAUAUUAUACUU----------UAUAUUCUUACGGAUCCAUCCCCUUGG
.((((((.....))))))...(((.(((((((....))))))).))).((((.--((((((((...(....).))))))))..----------...........(((....))).)))). ( -28.70)
>consensus
ACCAUUUAAUUCAAAUGGGUGGGCCGCAGAGCAAACGUUUUGCUGCCGCGAGU__GUGUAAUGAGAGGGAACUUAUUAUACUU___UAGAAU_UAUAUUCUUAUU____CAUCCCCUUGC
...........(((..((((((((.(((((((....))))))).)))........((((((((((......))))))))))............................)))))..))). (-26.86 = -27.42 +   0.56)

alignment

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secondary structure

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Window 4

Location 22,075,833 – 22,075,933
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 95.95
Mean single sequence MFE -28.40
Consensus MFE -23.04
Energy contribution -23.60
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.15
Structure conservation index 0.81
SVM decision value 1.22
SVM RNA-class probability 0.932614
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22075833 100 - 27905053
AAUGAGCAAGUGCAAUGAGUACCAUUUAAUUCAAAUGGGUGGGCCGCAGAGCAAACGUUUUGCUGCCGCUAGUGUGUGUAAUGAGAGGGAACAUAUUAUA
....(((..............((((((.....))))))...(((.(((((((....))))))).))))))(((((((....(....)...)))))))... ( -27.60)
>DroSec_CAF1 67888 98 - 1
AAUGAGCAAGUGCAAUGAGUACCAUUUAAUUCAAAUGGGUGGGCCGCAGAGCAAACGUUUUGCUGCCGCGAGU--GUGUAAUGAGAGGGAACUUAUUAUA
.....(((..(((........((((((.....))))))...(((.(((((((....))))))).))))))..)--))((((((((......)))))))). ( -31.40)
>DroSim_CAF1 61328 98 - 1
AAUGAGCAAGUGCAAUGAGUACCAUUUAAUUCAAAUGGGUGGGCCGCAGAGCAAACGUUUUGCUGCCGCGAGU--GUGUAAUGAGAGGGAACUUAUUAUA
.....(((..(((........((((((.....))))))...(((.(((((((....))))))).))))))..)--))((((((((......)))))))). ( -31.40)
>DroEre_CAF1 62508 98 - 1
AAUGAGCAAGUGCAAUGAGUAGCAUUUAAUUCGAAUGGGUGGACCGCAGAGCAAACGUUUGGCUGCCGCGAGU--GUGUAAUGAGGGGGAACUUAUUAUA
.....(((..(((.........(((((.....)))))((..(.((...((((....)))))))..)))))..)--))((((((((......)))))))). ( -24.00)
>DroYak_CAF1 70362 98 - 1
AAUGAGCAAGUGCAAUGAGUACCAUUUAAUUCGAAUGGGUGGGCCGCAGAGCAAACGUUUUGCUGCCGCGAGU--GUGUAAUGAGAGGGAACAUAUUAUA
.....(((..(((........((((((.....))))))...(((.(((((((....))))))).))))))..)--))((((((...(....).)))))). ( -27.60)
>consensus
AAUGAGCAAGUGCAAUGAGUACCAUUUAAUUCAAAUGGGUGGGCCGCAGAGCAAACGUUUUGCUGCCGCGAGU__GUGUAAUGAGAGGGAACUUAUUAUA
.....((....))........((((((.....))))))((((.(.(((((((....))))))).))))).......(((((((((......))))))))) (-23.04 = -23.60 +   0.56)

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 13:06:50 2006