Locus 4610

Sequence ID 3R_DroMel_CAF1
Location 12,118,430 – 12,118,574
Length 144
Max. P 0.999735
window7575 window7576 window7577 window7578

overview

Window 5

Location 12,118,430 – 12,118,538
Length 108
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 89.82
Mean single sequence MFE -23.25
Consensus MFE -22.63
Energy contribution -22.38
Covariance contribution -0.25
Combinations/Pair 1.13
Mean z-score -1.96
Structure conservation index 0.97
SVM decision value 2.85
SVM RNA-class probability 0.997407
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12118430 108 + 27905053
UUUCUU-----------UUAUUUCAGGCAAAAACCUUUACAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCUAUGAAGUCAAAGGCUCCGCAACUACACUUAGAGUAUAGGUUUUAUA
......-----------............(((((((.(((..........................(((((((.((....)).)))))))....(((....))).))).)))))))... ( -24.90)
>DroVir_CAF1 30023 108 + 1
UCUUUU-----------CUUUUGCAGGAAAAAAUCUUUACAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCUAUGAAGUCAAAGGCUCCGCAACUACACUUAGAGUAUAGGUUUUAUA
....((-----------((......))))(((((((.(((..........................(((((((.((....)).)))))))....(((....))).))).)))))))... ( -23.40)
>DroGri_CAF1 32513 108 + 1
UUCUCU-----------CUUUUGCAGGAAAAAAUCUUUACAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCGAUGAAGUCAAAGGCUCCGCAACUACACUUAGAGUAUAGGUUUUAUA
((((..-----------(....)..))))(((((((.(((..........................((((((..((....))..))))))....(((....))).))).)))))))... ( -21.50)
>DroWil_CAF1 28978 112 + 1
UUUC---AAUUUC----UUUUUACAGGCAAAAAUCUUUACAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCUAUGAAGUCAAAGGCUCCGCAACUACACUUAGAGUAUAGGUUUUAUA
....---......----............(((((((.(((..........................(((((((.((....)).)))))))....(((....))).))).)))))))... ( -22.30)
>DroMoj_CAF1 30010 108 + 1
CUCUUU-----------CUUUUGCAGGAAAAAAUCUUUACAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCUAUGAAGUCGAAGGCUCCACAACUACACUUAGAGUAUAGGUUUUAUA
....((-----------((......))))(((((((.(((.........................((((((((.((....)).))))))))...(((....))).))).)))))))... ( -23.40)
>DroAna_CAF1 20077 119 + 1
UUUAUUCACUUUCCUCUGUUUUUCAGGCAAAAAUCUUUACAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCUAUGAAGUCAAAGGCUCCGCAACUACACUUAGAGUAUAGGUUUUAUA
..............((((.....))))..(((((((.(((..........................(((((((.((....)).)))))))....(((....))).))).)))))))... ( -24.00)
>consensus
UUUUUU___________CUUUUGCAGGAAAAAAUCUUUACAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCUAUGAAGUCAAAGGCUCCGCAACUACACUUAGAGUAUAGGUUUUAUA
.............................(((((((.(((.........................((((((((.((....)).))))))))...(((....))).))).)))))))... (-22.63 = -22.38 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,118,430 – 12,118,538
Length 108
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 89.82
Mean single sequence MFE -27.93
Consensus MFE -24.53
Energy contribution -24.83
Covariance contribution 0.31
Combinations/Pair 1.10
Mean z-score -2.66
Structure conservation index 0.88
SVM decision value 2.14
SVM RNA-class probability 0.989001
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12118430 108 - 27905053
UAUAAAACCUAUACUCUAAGUGUAGUUGCGGAGCCUUUGACUUCAUAGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUGUAAAGGUUUUUGCCUGAAAUAA-----------AAGAAA
........((((((.....))))))....(((((((.((....)).))))))).((((((((((.(((.......))).))..((((....))))..)))))-----------)))... ( -28.70)
>DroVir_CAF1 30023 108 - 1
UAUAAAACCUAUACUCUAAGUGUAGUUGCGGAGCCUUUGACUUCAUAGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUGUAAAGAUUUUUUCCUGCAAAAG-----------AAAAGA
........((((((.....))))))(((((((((((.((....)).)))))))((((((((....(((.......))).))))))))........))))...-----------...... ( -28.30)
>DroGri_CAF1 32513 108 - 1
UAUAAAACCUAUACUCUAAGUGUAGUUGCGGAGCCUUUGACUUCAUCGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUGUAAAGAUUUUUUCCUGCAAAAG-----------AGAGAA
.............((((...(((((....((((((..((....))..))))))((((((((....(((.......))).))))))))......)))))....-----------)))).. ( -28.00)
>DroWil_CAF1 28978 112 - 1
UAUAAAACCUAUACUCUAAGUGUAGUUGCGGAGCCUUUGACUUCAUAGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUGUAAAGAUUUUUGCCUGUAAAAA----GAAAUU---GAAA
........((((((.....))))))(((((((((((.((....)).)))))))((((((((....(((.......))).))))))))........))))...----......---.... ( -26.30)
>DroMoj_CAF1 30010 108 - 1
UAUAAAACCUAUACUCUAAGUGUAGUUGUGGAGCCUUCGACUUCAUAGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUGUAAAGAUUUUUUCCUGCAAAAG-----------AAAGAG
.............((((..(((((((.(((((((((..(....)..))))))))).......))))))).(((....(((((..((.....)).)))))..)-----------)))))) ( -27.40)
>DroAna_CAF1 20077 119 - 1
UAUAAAACCUAUACUCUAAGUGUAGUUGCGGAGCCUUUGACUUCAUAGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUGUAAAGAUUUUUGCCUGAAAAACAGAGGAAAGUGAAUAAA
.((((((.((((((.....))))))....(((((((.((....)).)))))))..)))))).......((((((((...(((((....)))))(((.....))).....)))))))).. ( -28.90)
>consensus
UAUAAAACCUAUACUCUAAGUGUAGUUGCGGAGCCUUUGACUUCAUAGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUGUAAAGAUUUUUGCCUGCAAAAG___________AAAAAA
........((((((.....))))))(((((((((((.((....)).)))))))((((((((....(((.......))).))))))))........)))).................... (-24.53 = -24.83 +   0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,118,458 – 12,118,574
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 91.67
Mean single sequence MFE -26.87
Consensus MFE -24.19
Energy contribution -24.42
Covariance contribution 0.22
Combinations/Pair 1.08
Mean z-score -2.29
Structure conservation index 0.90
SVM decision value 2.34
SVM RNA-class probability 0.992569
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12118458 116 + 27905053
CAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCUAUGAAGUCAAAGGCUCCGCAACUACACUUAGAGUAUAGGUUUUAUAAACUAUUAGGAUCACAUGGUAUGUAAU---CUA-UCGCUU
............(((((.........((((((((.((....)).))))))))...)))))....((((((((((..((((.(((((.........))))).))))))---)))-).)))) ( -25.10)
>DroVir_CAF1 30051 115 + 1
CAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCUAUGAAGUCAAAGGCUCCGCAACUACACUUAGAGUAUAGGUUUUAUAAGCUAUUAGGAUCACAUGGUAUGUUAAAU-----UGUCUU
..(((((.((((((((((.((((((..(((((((.((....)).)))))))....(((.((.....)).))).))))))..)))))....(((....))))))))..))-----)))... ( -27.60)
>DroGri_CAF1 32541 119 + 1
CAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCGAUGAAGUCAAAGGCUCCGCAACUACACUUAGAGUAUAGGUUUUAUAAGCUAUUAGGAUCACAUGGUAUGUUGAAU-UGAAUGUUUC
.......((((((....((((......((((((..((....))..)))))).(((((((((.....))...(((((((........))))))).....))).)))).))-)).)))))). ( -27.60)
>DroWil_CAF1 29010 114 + 1
CAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCUAUGAAGUCAAAGGCUCCGCAACUACACUUAGAGUAUAGGUUUUAUAAACUAUUAGGAUCACAUGGUAUGUUGAAA-UUA-UC----
(((((.....(((((............(((((((.((....)).)))))))....................(((((((........))))))))))))...)))))...-...-..---- ( -28.10)
>DroMoj_CAF1 30038 115 + 1
CAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCUAUGAAGUCGAAGGCUCCACAACUACACUUAGAGUAUAGGUUUUAUAAGCUAUUAGGAUCACAUGGUAUGUUAAAA-----UGUUUU
.((((...((((((((((.((((((.((((((((.((....)).))))))))...(((.((.....)).))).))))))..)))))....(((....))))))))....-----)))).. ( -26.70)
>DroAna_CAF1 20116 119 + 1
CAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCUAUGAAGUCAAAGGCUCCGCAACUACACUUAGAGUAUAGGUUUUAUAAACUAUUAGGAUCACAUGGUAUGUAAAAAAAAA-UCUCUU
............(((((.........((((((((.((....)).))))))))...)))))...((((......(((((((.(((((.........))))).))))))).....-.)))). ( -26.10)
>consensus
CAACAAUGAACAUGUAGCAAUAAAAAUGGAGCCUAUGAAGUCAAAGGCUCCGCAACUACACUUAGAGUAUAGGUUUUAUAAACUAUUAGGAUCACAUGGUAUGUUAAAA___A_UCUCUU
.((((.....(((((...........((((((((.((....)).))))))))...................(((((((........))))))))))))...))))............... (-24.19 = -24.42 +   0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,118,458 – 12,118,574
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 91.67
Mean single sequence MFE -29.85
Consensus MFE -27.27
Energy contribution -27.47
Covariance contribution 0.19
Combinations/Pair 1.06
Mean z-score -3.39
Structure conservation index 0.91
SVM decision value 3.97
SVM RNA-class probability 0.999735
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12118458 116 - 27905053
AAGCGA-UAG---AUUACAUACCAUGUGAUCCUAAUAGUUUAUAAAACCUAUACUCUAAGUGUAGUUGCGGAGCCUUUGACUUCAUAGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUG
.(((((-(.(---(((((((...))))))))....((((..((((((.((((((.....))))))....(((((((.((....)).)))))))..)))))).)))).......)))))). ( -34.20)
>DroVir_CAF1 30051 115 - 1
AAGACA-----AUUUAACAUACCAUGUGAUCCUAAUAGCUUAUAAAACCUAUACUCUAAGUGUAGUUGCGGAGCCUUUGACUUCAUAGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUG
..((((-----((..(((((..(....).......((((..((((((.((((((.....))))))....(((((((.((....)).)))))))..)))))).)))).))))).)))))). ( -30.70)
>DroGri_CAF1 32541 119 - 1
GAAACAUUCA-AUUCAACAUACCAUGUGAUCCUAAUAGCUUAUAAAACCUAUACUCUAAGUGUAGUUGCGGAGCCUUUGACUUCAUCGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUG
..........-...(((((...(((((.........(((..((((((.((((((.....))))))....((((((..((....))..))))))..)))))).)))))))).....))))) ( -29.10)
>DroWil_CAF1 29010 114 - 1
----GA-UAA-UUUCAACAUACCAUGUGAUCCUAAUAGUUUAUAAAACCUAUACUCUAAGUGUAGUUGCGGAGCCUUUGACUUCAUAGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUG
----..-...-...(((((...((((((....((((((..........((((((.....))))))....(((((((.((....)).)))))))....)))))).)))))).....))))) ( -29.20)
>DroMoj_CAF1 30038 115 - 1
AAAACA-----UUUUAACAUACCAUGUGAUCCUAAUAGCUUAUAAAACCUAUACUCUAAGUGUAGUUGUGGAGCCUUCGACUUCAUAGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUG
......-----...(((((...(((((.........(((..((((((.((((((.....))))))..(((((((((..(....)..))))))))))))))).)))))))).....))))) ( -28.40)
>DroAna_CAF1 20116 119 - 1
AAGAGA-UUUUUUUUUACAUACCAUGUGAUCCUAAUAGUUUAUAAAACCUAUACUCUAAGUGUAGUUGCGGAGCCUUUGACUUCAUAGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUG
..(((.-.......((((((...))))))......((((..((((((.((((((.....))))))....(((((((.((....)).)))))))..)))))).))))....)))....... ( -27.50)
>consensus
AAGACA_U___UUUUAACAUACCAUGUGAUCCUAAUAGCUUAUAAAACCUAUACUCUAAGUGUAGUUGCGGAGCCUUUGACUUCAUAGGCUCCAUUUUUAUUGCUACAUGUUCAUUGUUG
..............(((((...(((((.........(((..((((((.((((((.....))))))....(((((((.((....)).)))))))..)))))).)))))))).....))))) (-27.27 = -27.47 +   0.19)

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 11:34:34 2006