Locus 8463

Sequence ID 3L_DroMel_CAF1
Location 22,269,508 – 22,269,662
Length 154
Max. P 0.983763
window13837 window13838 window13839

overview

Window 7

Location 22,269,508 – 22,269,622
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.76
Mean single sequence MFE -34.73
Consensus MFE -29.62
Energy contribution -30.07
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -2.09
Structure conservation index 0.85
SVM decision value 0.40
SVM RNA-class probability 0.721805
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22269508 114 - 23771897
AAACAAAAAUGCCAAGCAAAUGGCUUAGAAUAGCUGGCUAGGGUAGCUUGGGUA---UCUACUAGCUACCCACACAU--ACACAUAGGAGAAGUGGGGGGCAGUAGAA-UGAAUGGGUUC
.(((.......((((((...(((((.((.....))))))).....))))))...---((((((.((..(((((....--.(.....).....)))))..)))))))).-.......))). ( -33.50)
>DroSec_CAF1 27901 120 - 1
AAACAAAAAUGCCAAGCAAAUGGCUUAGAAUAGCUGGUUAGGGUAGCUUGGGUACUAGCUCCUAGCUACCCACACACUCACACACAGAAGAAGUGGGGCCCAGUGGAAAGGAAUGGGUUC
..........(((((((.....))))......(((((...((((((((.((((....)).)).)))))))).....(((((...........)))))..)))))...........))).. ( -35.50)
>DroSim_CAF1 19510 117 - 1
AAACAAAAAUGCCAAGCAAAUGGCUUAGAAUAGCUGGCUAGGGUAGCUUGGGUACUAGCUGCUAGCUACCCACACAC--ACACACAGAAGAAGUGGGGGCCAGUGGAA-UGAAUGGGUUC
..........(((((((.....))))......(((((((.((((((((..(((....)))...))))))))......--...(((.......)))..)))))))....-......))).. ( -35.20)
>consensus
AAACAAAAAUGCCAAGCAAAUGGCUUAGAAUAGCUGGCUAGGGUAGCUUGGGUACUAGCUACUAGCUACCCACACAC__ACACACAGAAGAAGUGGGGGCCAGUGGAA_UGAAUGGGUUC
..........(((((((.....))))......(((((((.((((((((..((......))...))))))))...........(((.......)))..)))))))...........))).. (-29.62 = -30.07 +   0.45)

alignment

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secondary structure

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dotplot

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Window 8

Location 22,269,547 – 22,269,662
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.91
Mean single sequence MFE -29.48
Consensus MFE -18.21
Energy contribution -19.84
Covariance contribution 1.63
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.62
SVM decision value 0.79
SVM RNA-class probability 0.851004
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22269547 115 + 23771897
U--AUGUGUGGGUAGCUAGUAGA---UACCCAAGCUACCCUAGCCAGCUAUUCUAAGCCAUUUGCUUGGCAUUUUUGUUUUGUGCAGCCGGGUAGCAUUAUUUUAAUUAACGUAUUUAUA
(--((((.((((((.(.....).---)))))).(((((((..((((((...............)).))))....((((.....))))..))))))).............)))))...... ( -32.46)
>DroSec_CAF1 27941 120 + 1
UGAGUGUGUGGGUAGCUAGGAGCUAGUACCCAAGCUACCCUAACCAGCUAUUCUAAGCCAUUUGCUUGGCAUUUUUGUUUUGUGCAGCCGGGUAACAUUAUUUUAAUUAACAUACUUAUA
(((((((((((((((((.((.(......))).))))))))...((.(((....(((((.....)))))((((.........))))))).))..................))))))))).. ( -37.70)
>DroSim_CAF1 19549 118 + 1
U--GUGUGUGGGUAGCUAGCAGCUAGUACCCAAGCUACCCUAGCCAGCUAUUCUAAGCCAUUUGCUUGGCAUUUUUGUUUUGUGCAGCCGGGUAACAUUAUUUUAAUUAACAUAUUUAUA
.--(((((((((((.((((...)))))))))..(.(((((..((((((...............)).))))....((((.....))))..))))).).............))))))..... ( -29.66)
>DroEre_CAF1 26849 96 + 1
-------------------CCACUUGUACCCC-UCUACC----CCAGCUAUUCUAAGCCAUUGGCUUGGCAUUUUUGUUCUGUGCAGCCGGGUAACAUUAUUUUAAUUAACAUAUUUAUA
-------------------.............-..((((----(..(((....((((((...))))))((((.........))))))).))))).......................... ( -18.10)
>consensus
U__GUGUGUGGGUAGCUAGCAGCUAGUACCCAAGCUACCCUAGCCAGCUAUUCUAAGCCAUUUGCUUGGCAUUUUUGUUUUGUGCAGCCGGGUAACAUUAUUUUAAUUAACAUAUUUAUA
.........((((((((...............))))))))...((.(((....(((((.....)))))((((.........))))))).))............................. (-18.21 = -19.84 +   1.63)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,269,547 – 22,269,662
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.91
Mean single sequence MFE -29.75
Consensus MFE -19.26
Energy contribution -20.95
Covariance contribution 1.69
Combinations/Pair 1.04
Mean z-score -2.98
Structure conservation index 0.65
SVM decision value 1.95
SVM RNA-class probability 0.983763
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22269547 115 - 23771897
UAUAAAUACGUUAAUUAAAAUAAUGCUACCCGGCUGCACAAAACAAAAAUGCCAAGCAAAUGGCUUAGAAUAGCUGGCUAGGGUAGCUUGGGUA---UCUACUAGCUACCCACACAU--A
........................((((((((((................))).(((....((((......)))).))).))))))).((((((---.(.....).)))))).....--. ( -31.29)
>DroSec_CAF1 27941 120 - 1
UAUAAGUAUGUUAAUUAAAAUAAUGUUACCCGGCUGCACAAAACAAAAAUGCCAAGCAAAUGGCUUAGAAUAGCUGGUUAGGGUAGCUUGGGUACUAGCUCCUAGCUACCCACACACUCA
....(((.(((..................(((((((..............((((......))))......)))))))...((((((((.((((....)).)).))))))))))).))).. ( -32.45)
>DroSim_CAF1 19549 118 - 1
UAUAAAUAUGUUAAUUAAAAUAAUGUUACCCGGCUGCACAAAACAAAAAUGCCAAGCAAAUGGCUUAGAAUAGCUGGCUAGGGUAGCUUGGGUACUAGCUGCUAGCUACCCACACAC--A
........................((((((((((................))).(((....((((......)))).))).))))))).((((((((((...)))).)))))).....--. ( -32.09)
>DroEre_CAF1 26849 96 - 1
UAUAAAUAUGUUAAUUAAAAUAAUGUUACCCGGCUGCACAGAACAAAAAUGCCAAGCCAAUGGCUUAGAAUAGCUGG----GGUAGA-GGGGUACAAGUGG-------------------
.......................(((.((((..((((.(((.........((((......)))).........))).----.)))).-.))))))).....------------------- ( -23.17)
>consensus
UAUAAAUAUGUUAAUUAAAAUAAUGUUACCCGGCUGCACAAAACAAAAAUGCCAAGCAAAUGGCUUAGAAUAGCUGGCUAGGGUAGCUUGGGUACUAGCUGCUAGCUACCCACACAC__A
.............................(((((((((...........))).((((.....)))).....))))))...((((((((..((......))...))))))))......... (-19.26 = -20.95 +   1.69)

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 13:16:01 2006