Locus 6822

Sequence ID 2L_DroMel_CAF1
Location 19,073,052 – 19,073,159
Length 107
Max. P 0.998690
window10883 window10884

overview

Window 3

Location 19,073,052 – 19,073,159
Length 107
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 75.86
Mean single sequence MFE -24.22
Consensus MFE -10.29
Energy contribution -10.41
Covariance contribution 0.12
Combinations/Pair 1.29
Mean z-score -2.90
Structure conservation index 0.42
SVM decision value 3.19
SVM RNA-class probability 0.998690
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19073052 107 + 22407834
AAAAUGAGCUUUUUAUAGCAGCACAAAGCUUUGAGUCGAAUUUU----AUU-------CGAAUGUUAAUACAAAGCUUUUAUUAACAGAAUUA-GUUAACAGAAUUAGUUAACAGAGCA
.......(((......))).((..(((((((((..((((((...----)))-------)))((....)).)))))))))..............-((((((.......))))))...)). ( -21.50)
>DroSec_CAF1 5993 104 + 1
AAAAUGAGCUUUUUAUAGCAGCAGAAAGCUUUGAGUUGAAUUUUCGACAUUCGAAAUUCGAAUGUUAAUUCAAAGCUUUUAUUAACAGAAUUC-GUUAAC--------------GAGCA
.......(((......))).((.((((((((((((((((....))((((((((.....))))))))))))))))))))))...........((-(....)--------------)))). ( -31.40)
>DroSim_CAF1 6007 98 + 1
AAAAUGAGCUUUUUAUAGCAGCAGAAAGCUUUGAGUCGAAUUUUCGACAUU-------CGAAUGUUAAUUCAAAGCUUUUAUUAACAGAAUUC-GUUAAC-------------AGAGCA
.......(((......))).((.(((((((((((((..(...((((.....-------))))..)..))))))))))))).(((((.......-))))).-------------...)). ( -26.90)
>DroEre_CAF1 5347 94 + 1
AAAGAGAGCUUUUUAUAGCACUACUAAGCUUUGAGUC-AAUGUU----AUA-------CGAAUGUUAAUGCAAAGCUUGCAUUAACAGAACAUAGCUAAC-------------AGACCA
....(((((((..((......))..)))))))(.(((-...(((----((.-------....((((((((((.....))))))))))....)))))....-------------.)))). ( -21.90)
>DroYak_CAF1 5627 94 + 1
AAACGGAGCUUUUUAUAGCACUGCUGAGCUUAACGCCGAACGUU----AUU-------CGAAUGUUAACGCAAAGCUUUUAUUAACAGAACAU-GUUAUA-------------AGACCA
....((.(((......)))...(((..((((((((.((((....----.))-------))..)))))).))..)))((((((.((((.....)-))))))-------------))))). ( -19.40)
>consensus
AAAAUGAGCUUUUUAUAGCAGCACAAAGCUUUGAGUCGAAUUUU____AUU_______CGAAUGUUAAUGCAAAGCUUUUAUUAACAGAAUUC_GUUAAC_____________AGAGCA
.......(((......))).....(((((((((((...(((......................)))..)))))))))))........................................ (-10.29 = -10.41 +   0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,073,052 – 19,073,159
Length 107
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 75.86
Mean single sequence MFE -20.96
Consensus MFE -8.05
Energy contribution -9.17
Covariance contribution 1.12
Combinations/Pair 1.16
Mean z-score -2.01
Structure conservation index 0.38
SVM decision value 0.73
SVM RNA-class probability 0.835979
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19073052 107 - 22407834
UGCUCUGUUAACUAAUUCUGUUAAC-UAAUUCUGUUAAUAAAAGCUUUGUAUUAACAUUCG-------AAU----AAAAUUCGACUCAAAGCUUUGUGCUGCUAUAAAAAGCUCAUUUU
.((.(.((((((.......))))))-..............(((((((((.........(((-------(((----...))))))..)))))))))).)).(((......)))....... ( -19.30)
>DroSec_CAF1 5993 104 - 1
UGCUC--------------GUUAAC-GAAUUCUGUUAAUAAAAGCUUUGAAUUAACAUUCGAAUUUCGAAUGUCGAAAAUUCAACUCAAAGCUUUCUGCUGCUAUAAAAAGCUCAUUUU
.((..--------------((((((-(.....))))))).((((((((((....(((((((.....))))))).((....))...))))))))))..)).(((......)))....... ( -24.50)
>DroSim_CAF1 6007 98 - 1
UGCUCU-------------GUUAAC-GAAUUCUGUUAAUAAAAGCUUUGAAUUAACAUUCG-------AAUGUCGAAAAUUCGACUCAAAGCUUUCUGCUGCUAUAAAAAGCUCAUUUU
.((..(-------------((((((-(.....))))))))((((((((((.....(....)-------...(((((....)))))))))))))))..)).(((......)))....... ( -21.60)
>DroEre_CAF1 5347 94 - 1
UGGUCU-------------GUUAGCUAUGUUCUGUUAAUGCAAGCUUUGCAUUAACAUUCG-------UAU----AACAUU-GACUCAAAGCUUAGUAGUGCUAUAAAAAGCUCUCUUU
.(((((-------------((((..((((...((((((((((.....))))))))))..))-------)))----))))..-))))...(((((..((......))..)))))...... ( -22.40)
>DroYak_CAF1 5627 94 - 1
UGGUCU-------------UAUAAC-AUGUUCUGUUAAUAAAAGCUUUGCGUUAACAUUCG-------AAU----AACGUUCGGCGUUAAGCUCAGCAGUGCUAUAAAAAGCUCCGUUU
.((.((-------------(.((((-(.....)))))......(((..((.(((((..(((-------(((----...)))))).)))))))..)))...........)))..)).... ( -17.00)
>consensus
UGCUCU_____________GUUAAC_AAAUUCUGUUAAUAAAAGCUUUGAAUUAACAUUCG_______AAU____AAAAUUCGACUCAAAGCUUUGUGCUGCUAUAAAAAGCUCAUUUU
...................((((((........)))))).((((((((((...................................)))))))))).....(((......)))....... ( -8.05 =  -9.17 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:41 2006