Locus 1406

Sequence ID X_DroMel_CAF1
Location 4,231,056 – 4,231,188
Length 132
Max. P 0.990686
window2243 window2244

overview

Window 3

Location 4,231,056 – 4,231,162
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.10
Mean single sequence MFE -20.53
Consensus MFE -13.36
Energy contribution -13.42
Covariance contribution 0.06
Combinations/Pair 1.22
Mean z-score -1.22
Structure conservation index 0.65
SVM decision value 0.25
SVM RNA-class probability 0.653618
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4231056 106 - 22224390
UCUCGGGGAUCAUUCGCUUGGGGUCUCCUAACCAUCCGUACCUUAACAAAAAAAAAAA----AAAAAAG-----UAAAAAUGUCGGCAUAUUUCUUGUUUUGGUUAUGCCACAUU-----
....(((((((..........)))))))..............................----.......-----....(((((.((((((...((......)).)))))))))))----- ( -19.70)
>DroSec_CAF1 18337 107 - 1
UCUCGGGGAUCAUUCGCUUUGGGUCUCCUAACCAUCCGUACCUUAACAAAAAA---AAGAUGAAAAAAA-----CAAAAAUGUCGGCAUAUUUCUGGUUUUGGUUAUGCCACAUU-----
....(((((((..........)))))))....((((.................---..)))).......-----....(((((.((((((...((......)).)))))))))))----- ( -20.41)
>DroSim_CAF1 24009 110 - 1
UCUCGGGGAUCAUUCGCUACGGGUCUCCCAACCAUCCGUACCUUAACAAAAAAAAAAAGAAGCAAAAAC-----CAAAAAUGUCGGCAUAUUUCUUGUUUUGGUUAUGCCACAUU-----
....((.((....))(((((((((.........))))))..(((............))).))).....)-----)...(((((.((((((...((......)).)))))))))))----- ( -19.70)
>DroEre_CAF1 24055 109 - 1
UCUCUGGGAUCAUUCGCUUGGGGUCUCCAUACCAUCCGAGCCUUGACAAAAAAAA--A----GAAUAAC-----CAAAAAUGUCGGCAUAUUUCUUGUUUCCAUUAUGCCACAUUUCAUU
....(((((....))(((((((((......)))..))))))..............--.----......)-----)).((((((.((((((..............)))))))))))).... ( -23.34)
>DroYak_CAF1 18210 97 - 1
UCUCUGGGAUCAUUCGCUUGGGGUCUCCAUACCAUCCGAACCUUAACAAAA---A--A----GGAAAAC-----CAAAUAUGUCGGCAUAUUUCU---------UAUGCCACAUUUCAUU
....(((.....((((..(((..........)))..))))((((.......---)--)----))....)-----))...((((.((((((.....---------))))))))))...... ( -22.20)
>DroAna_CAF1 21303 108 - 1
UCCUUUGGAACCUACGCUUGAGGUCUCC---------GUACCUCACAAUAAAA-A--ACGUAAAAAAAAUAUGAAAAAACUGUCGGCAUAUUUCUUGUUUUCAUUAUGCCACAUUUCAUU
(((...))).........((((((....---------..))))))........-.--.............((((((....(((.((((((..............))))))))))))))). ( -17.84)
>consensus
UCUCGGGGAUCAUUCGCUUGGGGUCUCCAAACCAUCCGUACCUUAACAAAAAA_A__A____AAAAAAC_____CAAAAAUGUCGGCAUAUUUCUUGUUUUGGUUAUGCCACAUU_____
.(((((((........))))))).......................................................(((((.((((((..............)))))))))))..... (-13.36 = -13.42 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,231,091 – 4,231,188
Length 97
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 73.59
Mean single sequence MFE -24.30
Consensus MFE -15.23
Energy contribution -17.15
Covariance contribution 1.92
Combinations/Pair 1.05
Mean z-score -2.30
Structure conservation index 0.63
SVM decision value 2.23
SVM RNA-class probability 0.990686
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4231091 97 - 22224390
--UUAGGUCC--UACAAACCUAGGCGGUGGUCUCGGGGAUCAUUCGCUUGGGGUCUCCUAACCAUCCGUACCUUAACAAAAAAAAAAA----AAAAAAG-----UAAAAA
--((((((..--.....))))))((((((((...(((((((..........)))))))..)))).))))...................----.......-----...... ( -23.00)
>DroSec_CAF1 18372 97 - 1
--UAAGGACC--UACA-ACCUAGGCGGUGGUCUCGGGGAUCAUUCGCUUUGGGUCUCCUAACCAUCCGUACCUUAACAAAAAA---AAGAUGAAAAAAA-----CAAAAA
--(((((.((--((..-...))))(((((((...(((((((..........)))))))..)))).)))..)))))........---.............-----...... ( -23.70)
>DroSim_CAF1 24044 100 - 1
--UAAGGACC--UACA-ACCUAGGCGGUGGUCUCGGGGAUCAUUCGCUACGGGUCUCCCAACCAUCCGUACCUUAACAAAAAAAAAAAGAAGCAAAAAC-----CAAAAA
--(((((.((--((..-...))))(((((((...(((((((..........)))))))..)))).)))..)))))........................-----...... ( -23.70)
>DroEre_CAF1 24095 94 - 1
--AAGGGUCC--UAAA-AACUAGGCGGUGGUCUCUGGGAUCAUUCGCUUGGGGUCUCCAUACCAUCCGAGCCUUGACAAAAAAAA--A----GAAUAAC-----CAAAAA
--((((.((.--....-..(((((((((((((.....))))).))))))))(((......)))....)).))))...........--.----.......-----...... ( -24.30)
>DroYak_CAF1 18241 91 - 1
--UAGGGCCC--UAAA-AACUAGGCGGUGGUCUCUGGGAUCAUUCGCUUGGGGUCUCCAUACCAUCCGAACCUUAACAAAA---A--A----GGAAAAC-----CAAAUA
--..((((((--((..-.....((((((((((.....))))).)))))))))))))..............((((.......---)--)----)).....-----...... ( -23.21)
>DroAna_CAF1 21343 97 - 1
AAAAGGGGCGGGGAAA-ACCUAGGCGGUGGUCCUUUGGAACCUACGCUUGAGGUCUCC---------GUACCUCACAAUAAAA-A--ACGUAAAAAAAAUAUGAAAAAAC
...(((..((((((..-.((((((((..(((((...)).)))..))))).))))))))---------)..)))..........-.--.((((.......))))....... ( -27.90)
>consensus
__UAAGGACC__UAAA_ACCUAGGCGGUGGUCUCGGGGAUCAUUCGCUUGGGGUCUCCAAACCAUCCGUACCUUAACAAAAAA_A__A____AAAAAAC_____CAAAAA
..(((((............(((((((((((((.....)))))).)))))))(((......))).......)))))................................... (-15.23 = -17.15 +   1.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:42 2006