Locus 3903

Sequence ID 3L_DroMel_CAF1
Location 11,301,572 – 11,301,666
Length 94
Max. P 0.983737
window6077 window6078

overview

Window 7

Location 11,301,572 – 11,301,666
Length 94
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 66.00
Mean single sequence MFE -17.89
Consensus MFE -7.24
Energy contribution -7.44
Covariance contribution 0.20
Combinations/Pair 1.47
Mean z-score -2.40
Structure conservation index 0.40
SVM decision value 1.95
SVM RNA-class probability 0.983737
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11301572 94 + 23771897
UAUGCCAGGGCAUAAAUUUUACAA----------A--CACACACACAUCUCUGCCAUACAGAUAUAUAGAUAUAUAUGUUUGUAUAUAGCAUAUAUGUAGCUAUUG
(((((....)))))..........----------.--.......((((.(.(((.(((((((((((((....)))))))))))))...))).).))))........ ( -21.40)
>DroSec_CAF1 25710 92 + 1
UAUGCCAGGGCAUAAAUUUCACAG----------ACACACACACACAUCUCUGCCAAACAGAUAUAGAUAUGUAUAUGUUUGUAUAUGGCAUAU----AGCUAUUG
(((((((.((((............----------.................))))..(((((((((........)))))))))...))))))).----........ ( -19.55)
>DroSim_CAF1 29944 102 + 1
UAUGCCAGGGCAUAAAUUUCACAAAAACACAGACACACACACACACAUCUCUGCCAAACAGAAAUAUAGAUAUAUAUGUUUGUAUAUAGCAUAU----AGCUAUUG
(((((....)))))..............((((((...............((((.....)))).(((((....)))))))))))..(((((....----.))))).. ( -18.40)
>DroEre_CAF1 29303 82 + 1
UAUGCCAGGGCAUAAAUUUCACAA--ACAC--------------ACAUAUCUGC-AAAAAGAU--AUAGAUAUAUAAGUACCAGUAU-GUAUAU----AGCUAGUG
(((((....)))))..........--...(--------------((.(((((..-....))))--)(((.((((((.(((....)))-.)))))----).)))))) ( -16.80)
>DroPer_CAF1 32446 85 + 1
UAUGCCAGGGCAUAAAUUUCACGAACACACAC-------UCCACACA-------CUCCACACU--CCACACA-CCAUCCAUGGCCAUGGGGUUU----ACCUAUUG
(((((....)))))..................-------........-------......(((--(((....-(((....)))...))))))..----........ ( -13.30)
>consensus
UAUGCCAGGGCAUAAAUUUCACAA__ACAC____A__CACACACACAUCUCUGCCAAACAGAUAUAUAGAUAUAUAUGUUUGUAUAUAGCAUAU____AGCUAUUG
(((((....)))))........................................................((((((....))))))((((.........))))... ( -7.24 =  -7.44 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,301,572 – 11,301,666
Length 94
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 66.00
Mean single sequence MFE -24.52
Consensus MFE -5.02
Energy contribution -7.98
Covariance contribution 2.96
Combinations/Pair 1.16
Mean z-score -2.69
Structure conservation index 0.20
SVM decision value 1.02
SVM RNA-class probability 0.901143
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11301572 94 - 23771897
CAAUAGCUACAUAUAUGCUAUAUACAAACAUAUAUAUCUAUAUAUCUGUAUGGCAGAGAUGUGUGUGUG--U----------UUGUAAAAUUUAUGCCCUGGCAUA
..(((((.........))))).(((((((((((((((..((...((((.....)))).)))))))))))--)----------))))).....(((((....))))) ( -28.40)
>DroSec_CAF1 25710 92 - 1
CAAUAGCU----AUAUGCCAUAUACAAACAUAUACAUAUCUAUAUCUGUUUGGCAGAGAUGUGUGUGUGUGU----------CUGUGAAAUUUAUGCCCUGGCAUA
.....((.----....))((((.((..(((((((((((((....((((.....)))))))))))))))))))----------.)))).....(((((....))))) ( -27.20)
>DroSim_CAF1 29944 102 - 1
CAAUAGCU----AUAUGCUAUAUACAAACAUAUAUAUCUAUAUUUCUGUUUGGCAGAGAUGUGUGUGUGUGUGUCUGUGUUUUUGUGAAAUUUAUGCCCUGGCAUA
..(((((.----....)))))(((((.((((((((((.((((((((((.....)))))))))).)))))))))).)))))............(((((....))))) ( -35.30)
>DroEre_CAF1 29303 82 - 1
CACUAGCU----AUAUAC-AUACUGGUACUUAUAUAUCUAU--AUCUUUUU-GCAGAUAUGU--------------GUGU--UUGUGAAAUUUAUGCCCUGGCAUA
.......(----(((.((-((((.((((......)))).((--((((....-..))))))))--------------))))--.)))).....(((((....))))) ( -15.90)
>DroPer_CAF1 32446 85 - 1
CAAUAGGU----AAACCCCAUGGCCAUGGAUGG-UGUGUGG--AGUGUGGAG-------UGUGUGGA-------GUGUGUGUUCGUGAAAUUUAUGCCCUGGCAUA
........----..((.(((((((((....)))-).)))))--.)).....(-------(((..((.-------(((((.(((.....))).)))))))..)))). ( -15.80)
>consensus
CAAUAGCU____AUAUGCCAUAUACAAACAUAUAUAUCUAUAUAUCUGUUUGGCAGAGAUGUGUGUGUG__U____GUGU__UUGUGAAAUUUAUGCCCUGGCAUA
...........................((((((((((.......((((.....)))).))))))))))........................(((((....))))) ( -5.02 =  -7.98 +   2.96)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:37 2006