Locus 3628

Sequence ID 3L_DroMel_CAF1
Location 10,678,425 – 10,678,533
Length 108
Max. P 0.871488
window5656 window5657

overview

Window 6

Location 10,678,425 – 10,678,533
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.45
Mean single sequence MFE -31.52
Consensus MFE -16.74
Energy contribution -17.66
Covariance contribution 0.92
Combinations/Pair 1.10
Mean z-score -3.18
Structure conservation index 0.53
SVM decision value 0.87
SVM RNA-class probability 0.871488
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10678425 108 + 23771897
UUUUUGCCAGGGAGCUGGC---GUGGUAUAAAAAGCAGCG-------UACAUUUU--GGGUGUGGGUUCGAGUGUAAAUAAAACCCAUUUAAAAAAUUACGCUGUUUUUAUAAGGUAACA
.....(((((....)))))---((..((((((((.(((((-------((.(((((--....(((((((..(.......)..)))))))....)))))))))))))))))))).....)). ( -36.50)
>DroSec_CAF1 12830 107 + 1
UUUUUGCCAGCGAGCUGGC---CUCGUAUAA-AAGCAGCG-------AACAUUUU--UGGUGUGGGUUCGAGUGUAAAUAAAACCCAUUUAAAAAAUUACGCUGUUUUUAUAAGGUAACA
...(((((.(((((.....---)))))((((-((((((((-------...(((((--(...(((((((..(.......)..)))))))...))))))..))))))))))))..))))).. ( -36.00)
>DroEre_CAF1 13364 103 + 1
UUUUUGC-AGGGAGCU------CUGGGAUAA-AAGCAGUG-------AACAUUUU--GGGUGUGGGUUCGAGUGUAAAUAAAACCCAUUUAAAAAAUUACGCUGUUUUUAUAAGGUAACA
.......-..(..((.------((...((((-((((((((-------...(((((--....(((((((..(.......)..)))))))....)))))..)))))))))))).))))..). ( -26.10)
>DroYak_CAF1 24761 106 + 1
UUUUUGCCAGGGAGCU------CUGGGAUAA-AAGCAGCG-------AACAUUUUUGGGGUGUGGGUUCGAGUGUAAAUAAAACCCAUUUAAAAAAUUACGCUGUUUUUAUAAGGUAACA
......(((((....)------)))).((((-((((((((-------...((((((.....(((((((..(.......)..)))))))...))))))..))))))))))))......... ( -30.70)
>DroAna_CAF1 13086 117 + 1
UUUUUGCCAGCGUACCGGGGAUAUGGGAUAA-AAGCGGCGAGAGCUGAAAAUUCA--CAGAACGGGAAAGUGUGUAAAUAAAACCCAUUUAAAAAAUUACGCUGUUUUUAUAAGGUAACA
...(((((......(((......))).((((-((((((((.(..(((........--)))..)(((....(((....)))...))).............))))))))))))..))))).. ( -28.30)
>consensus
UUUUUGCCAGGGAGCUGG____CUGGGAUAA_AAGCAGCG_______AACAUUUU__GGGUGUGGGUUCGAGUGUAAAUAAAACCCAUUUAAAAAAUUACGCUGUUUUUAUAAGGUAACA
...(((((((....))...........((((.((((((((........(((((.....)))))(((((...((....))..))))).............))))))))))))..))))).. (-16.74 = -17.66 +   0.92)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,678,425 – 10,678,533
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.45
Mean single sequence MFE -24.51
Consensus MFE -9.42
Energy contribution -10.10
Covariance contribution 0.68
Combinations/Pair 1.09
Mean z-score -3.34
Structure conservation index 0.38
SVM decision value 0.26
SVM RNA-class probability 0.659486
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10678425 108 - 23771897
UGUUACCUUAUAAAAACAGCGUAAUUUUUUAAAUGGGUUUUAUUUACACUCGAACCCACACCC--AAAAUGUA-------CGCUGCUUUUUAUACCAC---GCCAGCUCCCUGGCAAAAA
........((((((((((((((((((((.....(((((((...........))))))).....--))))).))-------))))).))))))))....---(((((....)))))..... ( -31.00)
>DroSec_CAF1 12830 107 - 1
UGUUACCUUAUAAAAACAGCGUAAUUUUUUAAAUGGGUUUUAUUUACACUCGAACCCACACCA--AAAAUGUU-------CGCUGCUU-UUAUACGAG---GCCAGCUCGCUGGCAAAAA
......(.(((((((.(((((..((((((....(((((((...........)))))))....)--)))))...-------))))).))-))))).)..---(((((....)))))..... ( -31.40)
>DroEre_CAF1 13364 103 - 1
UGUUACCUUAUAAAAACAGCGUAAUUUUUUAAAUGGGUUUUAUUUACACUCGAACCCACACCC--AAAAUGUU-------CACUGCUU-UUAUCCCAG------AGCUCCCU-GCAAAAA
.(((.....((((((.(((.(..(((((.....(((((((...........))))))).....--)))))...-------).))).))-)))).....------))).....-....... ( -15.40)
>DroYak_CAF1 24761 106 - 1
UGUUACCUUAUAAAAACAGCGUAAUUUUUUAAAUGGGUUUUAUUUACACUCGAACCCACACCCCAAAAAUGUU-------CGCUGCUU-UUAUCCCAG------AGCUCCCUGGCAAAAA
.........((((((.(((((..((((((....(((((((...........)))))))......))))))...-------))))).))-)))).((((------......))))...... ( -23.30)
>DroAna_CAF1 13086 117 - 1
UGUUACCUUAUAAAAACAGCGUAAUUUUUUAAAUGGGUUUUAUUUACACACUUUCCCGUUCUG--UGAAUUUUCAGCUCUCGCCGCUU-UUAUCCCAUAUCCCCGGUACGCUGGCAAAAA
................(((((((.........(((((....(((((((.((......))..))--)))))....(((.......))).-....)))))........)))))))....... ( -21.43)
>consensus
UGUUACCUUAUAAAAACAGCGUAAUUUUUUAAAUGGGUUUUAUUUACACUCGAACCCACACCC__AAAAUGUU_______CGCUGCUU_UUAUCCCAG____CCAGCUCCCUGGCAAAAA
.........((((.((((((((((....)))..(((((((...........)))))))......................))))).)).))))............((......))..... ( -9.42 = -10.10 +   0.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:39 2006