Locus 1575

Sequence ID 3R_DroMel_CAF1
Location 4,506,554 – 4,506,767
Length 213
Max. P 0.981893
window2601 window2602 window2603 window2604 window2605

overview

Window 1

Location 4,506,554 – 4,506,647
Length 93
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 87.34
Mean single sequence MFE -20.60
Consensus MFE -13.62
Energy contribution -14.88
Covariance contribution 1.25
Combinations/Pair 1.08
Mean z-score -1.98
Structure conservation index 0.66
SVM decision value 0.25
SVM RNA-class probability 0.654934
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4506554 93 - 27905053
GAUCGAUGGCCAUCGCCCAAGUGGAUGUUGUUCUUUCUUUGGCCACUCAAAAAGUGAGUAAAAGAGAGUGCUACUCAAAACUAAGAAAAUCUA
....((((((....)))..(((.((.((.((.((((((((.((((((.....)))).)).)))))))).)).))))...)))......))).. ( -22.10)
>DroSec_CAF1 6533 85 - 1
GAUCGAUGGCCAUCGCCCAAGUGGAUU-------UU-UUUUACCACUCAAAAAGUGAGUAAAAGAGAGUGCUACUCAAAAUUGAGAAAAUCUU
..((((((((....)))..(((((.((-------((-((((((((((.....)))).))))))))))...)))))....)))))......... ( -22.10)
>DroSim_CAF1 6534 86 - 1
GAUCGAUGGCCAUCGCCCAAGUGGAUU-------UUUUUUUGCCACUCAAAAAGUGAGUAAAAGAGAGUGCAACUCAAAAUUGAGAAAAUCUA
....((((((....)))....((.(((-------(((((((((((((.....)))).)))))))))))).)).((((....))))...))).. ( -22.30)
>DroYak_CAF1 6586 84 - 1
GAUCGAUGGCCAUCGCCCAAGUGGAUU-------UCCUUUGCCCACUCAAAAAGUGAGUAAAAGAGAGUUAUACUCAAAAC--AAAAAAUCUA
....((((((....)))..((((..((-------((.(((((.((((.....)))).))))).))))....))))......--.....))).. ( -15.90)
>consensus
GAUCGAUGGCCAUCGCCCAAGUGGAUU_______UUCUUUGGCCACUCAAAAAGUGAGUAAAAGAGAGUGCUACUCAAAACUGAGAAAAUCUA
((((.(((((....)))...)).))))........((((((((((((.....)))).))))))))(((.....)))................. (-13.62 = -14.88 +   1.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,506,612 – 4,506,706
Length 94
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 76.75
Mean single sequence MFE -22.08
Consensus MFE -14.06
Energy contribution -13.57
Covariance contribution -0.50
Combinations/Pair 1.19
Mean z-score -1.24
Structure conservation index 0.64
SVM decision value 0.04
SVM RNA-class probability 0.552924
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4506612 94 + 27905053
AAGAACAACAUCCACUUGGGCGAUGGCC-----AUCGAUCCUUGUCCAC-GC-----AGGACAUUUCCGGAUUGCAUUCAAUUGUCAUCCUGCAACAAUUGCGCU
................(((((((.((..-----......)))))))))(-((-----((((....)))((((.(((......))).)))).........)))).. ( -22.60)
>DroVir_CAF1 8587 85 + 1
C-------UACCCACUUGGGCGAU-----------CUAUCU-UGUCCGC-GCAGCACAGGACAUUUCCGGAUUGCAUUCAAUUGUCAUGCUGCAACAAUUGCGCU
.-------.........((((((.-----------.....)-)))))..-((((((...((((......((......))...)))).))))))............ ( -21.40)
>DroPse_CAF1 6636 92 + 1
A-------AAACCGCUUGGGCGAUGGCCAUCCCAUCGAUCCUUGUCCAC-GC-----AGGACACUUCCGGAUUGCAUUCAAUUGUAGUUCUGCAACAAUUGCGCU
.-------.....((..(((((((((.....)))))).))).(((((..-..-----.))))).....((((((((......)))))))).(((.....))))). ( -27.70)
>DroGri_CAF1 6383 86 + 1
A-------UUUCCACUUGGGCGAU-----------CCAUCU-UGUCCAUAGCGGUACAGGACAUUUCCGGAUUGCAUUCAAUUGUCAUGCUGUAACAAUUGCGCA
.-------...((....))(((((-----------((....-(((((.....)).)))(((....))))))))))...(((((((.........))))))).... ( -21.30)
>DroMoj_CAF1 5822 86 + 1
A-------UUUCCACUUGGGCGAU-----------CUAUCUAUGUCCAU-GCAGCAUAGGACAUUUCCGGAUUCCAUUCAAUUGUCAUAUUGCAACAAUUGUGCU
.-------..........((.(((-----------((....((((((((-(...))).))))))....)))))))...(((((((.........))))))).... ( -17.30)
>DroAna_CAF1 4877 87 + 1
A-------AUGUCACUUGGAUGAUGGCC-----AUCGAUCCUUGUCCAC-GC-----AGGACAUUUCCGGAUUGCAUUCAAUUGUGAUUCUGCAACAAUUGCGCU
.-------..((((((((((((......-----..((((((.(((((..-..-----.))))).....)))))))))))))..)))))...(((.....)))... ( -22.20)
>consensus
A_______UAUCCACUUGGGCGAU___________CGAUCCUUGUCCAC_GC_____AGGACAUUUCCGGAUUGCAUUCAAUUGUCAUGCUGCAACAAUUGCGCU
...........((....))(((...............((((.(((((...........))))).....))))......(((((((.........)))))))))). (-14.06 = -13.57 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,506,647 – 4,506,744
Length 97
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 74.75
Mean single sequence MFE -17.96
Consensus MFE -11.13
Energy contribution -11.05
Covariance contribution -0.08
Combinations/Pair 1.06
Mean z-score -1.37
Structure conservation index 0.62
SVM decision value 0.35
SVM RNA-class probability 0.698929
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4506647 97 + 27905053
CUUGUCCAC-GC-----AGGACAUUUCCGGAUUGCAUUCAAUUGUCAUCCUGCAACAAUUGCGCUUUUCUCUGGAUUCUCCAUUUGUUUGUCU--UCUUCCGAUU
..(((((..-..-----.)))))....((((..(((..(((.((..((((((((.....)))).........))))....)).)))..)))..--...))))... ( -19.20)
>DroVir_CAF1 8609 82 + 1
U-UGUCCGC-GCAGCACAGGACAUUUCCGGAUUGCAUUCAAUUGUCAUGCUGCAACAAUUGCGCUUUUUAUU-------CAUGCUGUUUGU--------------
.-....((.-((((((..(((....)))((((.((...(((((((.........))))))).)).....)))-------).)))))).)).-------------- ( -17.10)
>DroGri_CAF1 6405 91 + 1
U-UGUCCAUAGCGGUACAGGACAUUUCCGGAUUGCAUUCAAUUGUCAUGCUGUAACAAUUGCGCAUUUUUCU-------A---AUGCUUGUUU---CUUCCGAUU
.-(((((...........)))))....((((..(((..(((((((.........))))))).(((((.....-------)---)))).)))..---..))))... ( -19.80)
>DroSim_CAF1 6620 97 + 1
CUUGUCCAC-GC-----AGGACAUUUCCGGAUUGCAUUCAAUUGUCAUCCUGCAACAAUUGCGCUUUUCUUUUGAUUCUCCAUUUGUUUGUCU--UCUUCCGAUU
..(((((..-..-----.)))))....((((..(((..(((.((.......(((.....))).....((....)).....)).)))..)))..--...))))... ( -17.10)
>DroMoj_CAF1 5844 97 + 1
UAUGUCCAU-GCAGCAUAGGACAUUUCCGGAUUCCAUUCAAUUGUCAUAUUGCAACAAUUGUGCUUUUUAUU-------CCAAAUGUUUGUUUUUUUUUCGGAUU
.((((((((-(...))).)))))).((((((...((..((.(((..(((..(((.(....))))....))).-------.))).))..)).......)))))).. ( -18.20)
>DroAna_CAF1 4905 96 + 1
CUUGUCCAC-GC-----AGGACAUUUCCGGAUUGCAUUCAAUUGUGAUUCUGCAACAAUUGCGCUUUUCUUCACAUUUUCCAUUUGUCUGUCU---CUUCCUAUU
..(((((..-..-----.)))))....(((((..........(((((...((((.....)))).......)))))..........)))))...---......... ( -16.35)
>consensus
CUUGUCCAC_GC_____AGGACAUUUCCGGAUUGCAUUCAAUUGUCAUCCUGCAACAAUUGCGCUUUUCUUU_______CCAUUUGUUUGUCU___CUUCCGAUU
..(((((...........))))).....(((..((...(((((((.........))))))).))..))).................................... (-11.13 = -11.05 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,506,647 – 4,506,744
Length 97
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 74.75
Mean single sequence MFE -21.02
Consensus MFE -12.95
Energy contribution -13.15
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -2.18
Structure conservation index 0.62
SVM decision value 1.90
SVM RNA-class probability 0.981893
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4506647 97 - 27905053
AAUCGGAAGA--AGACAAACAAAUGGAGAAUCCAGAGAAAAGCGCAAUUGUUGCAGGAUGACAAUUGAAUGCAAUCCGGAAAUGUCCU-----GC-GUGGACAAG
..(((((...--...........(((.....))).......((.((((((((.......))))))))...))..)))))...(((((.-----..-..))))).. ( -24.80)
>DroVir_CAF1 8609 82 - 1
--------------ACAAACAGCAUG-------AAUAAAAAGCGCAAUUGUUGCAGCAUGACAAUUGAAUGCAAUCCGGAAAUGUCCUGUGCUGC-GCGGACA-A
--------------.....((((((.-------........((.((((((((.......))))))))...)).....(((....))).)))))).-.......-. ( -18.80)
>DroGri_CAF1 6405 91 - 1
AAUCGGAAG---AAACAAGCAU---U-------AGAAAAAUGCGCAAUUGUUACAGCAUGACAAUUGAAUGCAAUCCGGAAAUGUCCUGUACCGCUAUGGACA-A
..(((((..---......((((---(-------.....))))).(((((((((.....))))))))).......)))))...(((((...........)))))-. ( -23.90)
>DroSim_CAF1 6620 97 - 1
AAUCGGAAGA--AGACAAACAAAUGGAGAAUCAAAAGAAAAGCGCAAUUGUUGCAGGAUGACAAUUGAAUGCAAUCCGGAAAUGUCCU-----GC-GUGGACAAG
..((....))--...........((((...((....))...((.((((((((.......))))))))...))..))))....(((((.-----..-..))))).. ( -21.30)
>DroMoj_CAF1 5844 97 - 1
AAUCCGAAAAAAAAACAAACAUUUGG-------AAUAAAAAGCACAAUUGUUGCAAUAUGACAAUUGAAUGGAAUCCGGAAAUGUCCUAUGCUGC-AUGGACAUA
..((((.........(((....))).-------...........((((((((.......)))))))).........)))).((((((.(((...)-)))))))). ( -19.40)
>DroAna_CAF1 4905 96 - 1
AAUAGGAAG---AGACAGACAAAUGGAAAAUGUGAAGAAAAGCGCAAUUGUUGCAGAAUCACAAUUGAAUGCAAUCCGGAAAUGUCCU-----GC-GUGGACAAG
.........---...........((((...((((........))))....(((((...(((....))).)))))))))....(((((.-----..-..))))).. ( -17.90)
>consensus
AAUCGGAAG___AGACAAACAAAUGG_______AAAAAAAAGCGCAAUUGUUGCAGCAUGACAAUUGAAUGCAAUCCGGAAAUGUCCU_____GC_GUGGACAAA
.........................................(((((((((((.......))))))))..)))..........(((((...........))))).. (-12.95 = -13.15 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,506,675 – 4,506,767
Length 92
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 68.10
Mean single sequence MFE -15.66
Consensus MFE -6.19
Energy contribution -6.25
Covariance contribution 0.06
Combinations/Pair 1.11
Mean z-score -2.24
Structure conservation index 0.40
SVM decision value 0.25
SVM RNA-class probability 0.653134
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4506675 92 - 27905053
AGAAG-------UAAGAAAAUGUGACAGGCAAUCGGAAGA--AGACAAACAAAUGGAGAAUCCAGAGAAAAGCGCAAUUGUUGCAGGAUGACAAUUGAAUG
....(-------(.......((..(((.((..((....))--...........(((.....))).........))...)))..)).....))......... ( -15.10)
>DroGri_CAF1 6438 88 - 1
AACCAUUUGUAUGAAGAAAAGGUGACAAACAAUCGGAAG---AAACAAGCAU---U-------AGAAAAAUGCGCAAUUGUUACAGCAUGACAAUUGAAUG
......((((..........(....)......((....)---).))))((((---(-------.....))))).(((((((((.....))))))))).... ( -17.60)
>DroMoj_CAF1 5877 93 - 1
AACCAUUGCCC-UAAGAAAAGGUGACAAGCAAUCCGAAAAAAAAACAAACAUUUGG-------AAUAAAAAGCACAAUUGUUGCAAUAUGACAAUUGAAUG
......(((..-........(....)......((((((.............)))))-------).......)))((((((((.......)))))))).... ( -14.22)
>DroAna_CAF1 4933 89 - 1
ACAAG-------AAAC--AAUGUGACAGGCAAUAGGAAG---AGACAGACAAAUGGAAAAUGUGAAGAAAAGCGCAAUUGUUGCAGAAUCACAAUUGAAUG
.....-------...(--(((((((...(((((((....---...((......)).....((((........)))).)))))))....)))).)))).... ( -15.70)
>consensus
AAAAA_______UAAGAAAAGGUGACAAGCAAUCGGAAG___AAACAAACAAAUGG_______AAAAAAAAGCGCAAUUGUUGCAGAAUGACAAUUGAAUG
..........................................................................(((((((((.....))))))))).... ( -6.19 =  -6.25 +   0.06)

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 10:14:00 2006