Locus 4709

Sequence ID 3R_DroMel_CAF1
Location 12,371,487 – 12,371,617
Length 130
Max. P 0.979146
window7737 window7738 window7739

overview

Window 7

Location 12,371,487 – 12,371,596
Length 109
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 75.91
Mean single sequence MFE -28.20
Consensus MFE -10.67
Energy contribution -11.79
Covariance contribution 1.12
Combinations/Pair 1.10
Mean z-score -2.37
Structure conservation index 0.38
SVM decision value 1.83
SVM RNA-class probability 0.979146
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12371487 109 + 27905053
CUUGAUUUAUUGCUUAAACAUUUA--CAUACAUGUGUACACACAAA---CUGAAUGCAGAACAGGUUUUGCUCCUAAUGAGCGGGCAUAAAUCAGAGAA-ACCCAAACGGGUUCG
.(((((((((.((((((((.....--......((((....))))..---(((....))).....)))).((((.....))))))))))))))))).(((-.(((....)))))). ( -27.60)
>DroSim_CAF1 39189 112 + 1
CUUGAUUUAUUGCUUACACAUUUA--CAUACAUGUGUACACAUACGUAUGUAUAUGCAGAACAGGUUUUUCUCCUAAUGAACAGGCAUAAAUCAGAGAA-ACCCAAACGGGUUCG
.(((((((((.((((...(((.((--(((((.((((....)))).))))))).)))......(((.......))).......))))))))))))).(((-.(((....)))))). ( -31.20)
>DroEre_CAF1 40182 108 + 1
GUUGAUUUACUGAUGUACCAUAUAUAUAUACAUGUGU------AUAUACGAGUAUGCAGAACAGGUUUUUCUCCUAAUGAGCAGGCAUAAAUCAGAGAA-ACCCAAACGGGUUCG
.(((((((((((.((((((.(((((((((....))))------))))).).)))))))).....((((..(((.....))).)))).)))))))).(((-.(((....)))))). ( -25.90)
>DroYak_CAF1 36560 109 + 1
CUUGAUUUACUGCUUGAGCAUAUA--CAUACAUGUGUAC---UAUAUAUGCAUAUGCAGAACAGGUUUUACUCCUAAUGAGCAGGCAUAAAUCAGAGAA-GCCCAAACGGGUUCG
.((((((((.((((((..(((...--....((((((((.---......))))))))......(((.......))).)))..)))))))))))))).(((-.(((....)))))). ( -31.60)
>DroAna_CAF1 21680 96 + 1
ACUGAUUUAUGGCAGA--CGU-----------UGUGUA------AAUAUGCAGAGGCAUAACCUGUUUUCGUCCUAAUGAGCAGGCAUAAAUUACAGAGGACCGAAACGGGUUCU
.((((((((((.....--...-----------......------..(((((....))))).(((((((..........))))))))))))))..)))((((((......)))))) ( -24.70)
>consensus
CUUGAUUUAUUGCUUAAACAUAUA__CAUACAUGUGUAC____AAAUAUGCAUAUGCAGAACAGGUUUUUCUCCUAAUGAGCAGGCAUAAAUCAGAGAA_ACCCAAACGGGUUCG
.((((((((.((((....(((...........(((((................)))))....(((.......))).)))....)))))))))))).((..((((....)))))). (-10.67 = -11.79 +   1.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,371,487 – 12,371,596
Length 109
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 75.91
Mean single sequence MFE -27.50
Consensus MFE -10.22
Energy contribution -10.90
Covariance contribution 0.68
Combinations/Pair 1.17
Mean z-score -2.24
Structure conservation index 0.37
SVM decision value 1.44
SVM RNA-class probability 0.953809
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12371487 109 - 27905053
CGAACCCGUUUGGGU-UUCUCUGAUUUAUGCCCGCUCAUUAGGAGCAAAACCUGUUCUGCAUUCAG---UUUGUGUGUACACAUGUAUG--UAAAUGUUUAAGCAAUAAAUCAAG
.((((((....))))-))...((((((((((.....((((.((((((.....))))))((((.((.---..((((....)))))).)))--).)))).....)).)))))))).. ( -27.20)
>DroSim_CAF1 39189 112 - 1
CGAACCCGUUUGGGU-UUCUCUGAUUUAUGCCUGUUCAUUAGGAGAAAAACCUGUUCUGCAUAUACAUACGUAUGUGUACACAUGUAUG--UAAAUGUGUAAGCAAUAAAUCAAG
.((((((....))))-))...((((((((.((((.....))))..............(((.((((((((((((((((....))))))))--))..)))))).))))))))))).. ( -33.20)
>DroEre_CAF1 40182 108 - 1
CGAACCCGUUUGGGU-UUCUCUGAUUUAUGCCUGCUCAUUAGGAGAAAAACCUGUUCUGCAUACUCGUAUAU------ACACAUGUAUAUAUAUAUGGUACAUCAGUAAAUCAAC
.((((((....))))-))..(((((...(((((((....((((.......))))....))).....((((((------((....))))))))....)))).)))))......... ( -26.20)
>DroYak_CAF1 36560 109 - 1
CGAACCCGUUUGGGC-UUCUCUGAUUUAUGCCUGCUCAUUAGGAGUAAAACCUGUUCUGCAUAUGCAUAUAUA---GUACACAUGUAUG--UAUAUGCUCAAGCAGUAAAUCAAG
.((((((....))).-)))..(((((((....(((((.....)))))....(((((..((((((((((((((.---(....))))))))--)))))))...)))))))))))).. ( -35.30)
>DroAna_CAF1 21680 96 - 1
AGAACCCGUUUCGGUCCUCUGUAAUUUAUGCCUGCUCAUUAGGACGAAAACAGGUUAUGCCUCUGCAUAUU------UACACA-----------ACG--UCUGCCAUAAAUCAGU
((((((.((((..(((((..(((.........))).....)))))..)))).)))(((((....)))))..------......-----------...--)))............. ( -15.60)
>consensus
CGAACCCGUUUGGGU_UUCUCUGAUUUAUGCCUGCUCAUUAGGAGAAAAACCUGUUCUGCAUAUACAUAUAU____GUACACAUGUAUG__UAAAUGUUUAAGCAAUAAAUCAAG
.((((((....))))..))..((((((((....((....((((.......))))....))...................................(((....))))))))))).. (-10.22 = -10.90 +   0.68)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,371,525 – 12,371,617
Length 92
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 77.61
Mean single sequence MFE -23.46
Consensus MFE -10.80
Energy contribution -10.56
Covariance contribution -0.24
Combinations/Pair 1.17
Mean z-score -2.12
Structure conservation index 0.46
SVM decision value 0.80
SVM RNA-class probability 0.854000
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12371525 92 + 27905053
CACAAA---CUGAAUGCAGAACAGGUUUUGCUCCUAAUGAGCGGGCAUAAAUCAGAGAA-ACCCAAACGGGUUCGCCC-------------------AUCUGAUAAUCACCAAAU
......---(((....)))..(((((...((((.....))))((((.....((...))(-((((....))))).))))-------------------)))))............. ( -22.50)
>DroSim_CAF1 39227 95 + 1
CAUACGUAUGUAUAUGCAGAACAGGUUUUUCUCCUAAUGAACAGGCAUAAAUCAGAGAA-ACCCAAACGGGUUCGCCC-------------------AUCUGAUAAUCACCAAAU
.((((....))))...((((...(((((((((....(((......))).....))))))-))).....(((....)))-------------------.))))............. ( -19.20)
>DroEre_CAF1 40219 92 + 1
---AUAUACGAGUAUGCAGAACAGGUUUUUCUCCUAAUGAGCAGGCAUAAAUCAGAGAA-ACCCAAACGGGUUCGCCC-------------------AUCUGAUAAUCACCAAAU
---......((.(((.((((...(((((((((....(((......))).....))))))-))).....(((....)))-------------------.))))))).))....... ( -21.00)
>DroYak_CAF1 36597 93 + 1
--UAUAUAUGCAUAUGCAGAACAGGUUUUACUCCUAAUGAGCAGGCAUAAAUCAGAGAA-GCCCAAACGGGUUCGCCC-------------------AUCUGAUAAUCACCAAAU
--....(((((...(((.....(((.......))).....))).))))).((((((..(-((((....))))).....-------------------.))))))........... ( -22.20)
>DroAna_CAF1 21705 111 + 1
----AAUAUGCAGAGGCAUAACCUGUUUUCGUCCUAAUGAGCAGGCAUAAAUUACAGAGGACCGAAACGGGUUCUCCCUCUCCCUCUCCGUCUCUGCCUGUGAUAAGCACCAAAU
----.(((.((((((((....(((((((..........)))))))...........(((((((......))))))).............)))))))).))).............. ( -32.40)
>consensus
___AAAUAUGCAUAUGCAGAACAGGUUUUUCUCCUAAUGAGCAGGCAUAAAUCAGAGAA_ACCCAAACGGGUUCGCCC___________________AUCUGAUAAUCACCAAAU
................((((...(((((....(((.......)))...)))))...((..((((....))))))........................))))............. (-10.80 = -10.56 +  -0.24)

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 11:37:07 2006