Locus 4975

Sequence ID 2R_DroMel_CAF1
Location 16,220,646 – 16,220,741
Length 95
Max. P 0.645013
window7963 window7964

overview

Window 3

Location 16,220,646 – 16,220,741
Length 95
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 79.24
Mean single sequence MFE -32.60
Consensus MFE -17.32
Energy contribution -18.27
Covariance contribution 0.95
Combinations/Pair 1.17
Mean z-score -1.98
Structure conservation index 0.53
SVM decision value 0.23
SVM RNA-class probability 0.645013
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16220646 95 + 20766785
UAUGCAACAUCGGCACUGCACUGCAACUGCGUGCAGCUGUGUGUGUG------------------CUGUGUGUAUUCGAGUGCAUUGGCAAGUGGCCAACAGUGGCAGAAACA
..(((.((((..(((((((((.((....)))))))).)))..))))(------------------((((((((((....))))))((((.....))))))))).)))...... ( -33.60)
>DroPse_CAF1 13926 81 + 1
UAUGCAACAGCGG--CGGUAAUGCAAU-G------UUUGUG--UG---------------------UGUGUGCGUGUGAGUGCAUUGGCAAGUGGCCAAGAGCGGCAACAGCU
...((....))((--((.(((((((..-.------((((..--((---------------------(....)))..))))))))))).)..((.(((......))).)).))) ( -21.50)
>DroSec_CAF1 1697 91 + 1
UAUGCAACAUCGG--CUGCACUGCAACUGCGUGCAGCUGUG--UGUG------------------CUGUGUGUAUUCGAGUGCAUUGGCAAGUGGCCAACAGUGGCAGAAACA
..(((.(((((((--((((((.((....))))))))))).)--)))(------------------((((((((((....))))))((((.....))))))))).)))...... ( -37.60)
>DroSim_CAF1 1701 91 + 1
UAUGCAACAUCGG--CUGCACUGCAACUGCGUGCAGCUGUG--UGUG------------------CUGUGUGUAUUCGAGUGCAUUGGCAAGUGGCCAACAGUGGCAGAAACA
..(((.(((((((--((((((.((....))))))))))).)--)))(------------------((((((((((....))))))((((.....))))))))).)))...... ( -37.60)
>DroEre_CAF1 6436 81 + 1
-AUGCAAC-----------ACUGCAACUGCGUGCAGCUGUG--UGUG------------------CUGUGUGUAUUCGAGUGCAUUGGCAAGUGGCCAACAGUGGCAAAAACA
-.(((..(-----------((((....((((..((((....--...)------------------)))..))))..........(((((.....)))))))))))))...... ( -26.20)
>DroYak_CAF1 12747 108 + 1
-AUGCAACAUCGG--CGGCACUGCAACUGCGUGCAGCUGUG--UGUGCUGUGAGUGCAGCGUGUGCUGUGUGUAUUCGAGUGCAUUGGCAAGUGGCCAACAGUGGUAAAAACA
-..((((((.(((--(.((((.((....)))))).))))))--).)))(((.((((((.((.((((.....)))).))..)))))).))).((.((((....))))....)). ( -39.10)
>consensus
UAUGCAACAUCGG__CUGCACUGCAACUGCGUGCAGCUGUG__UGUG__________________CUGUGUGUAUUCGAGUGCAUUGGCAAGUGGCCAACAGUGGCAAAAACA
..(((............((((.((....)))))).(((((.............................((((((....))))))((((.....))))))))).)))...... (-17.32 = -18.27 +   0.95)

alignment

Postscript

secondary structure

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dotplot

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Window 4

Location 16,220,646 – 16,220,741
Length 95
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 79.24
Mean single sequence MFE -25.40
Consensus MFE -14.10
Energy contribution -14.53
Covariance contribution 0.43
Combinations/Pair 1.12
Mean z-score -1.78
Structure conservation index 0.56
SVM decision value 0.09
SVM RNA-class probability 0.578465
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16220646 95 - 20766785
UGUUUCUGCCACUGUUGGCCACUUGCCAAUGCACUCGAAUACACACAG------------------CACACACACAGCUGCACGCAGUUGCAGUGCAGUGCCGAUGUUGCAUA
(((((((((....((((((.....)))))))))...))).)))....(------------------((.((((...(((((((((....)).)))))))...).))))))... ( -26.90)
>DroPse_CAF1 13926 81 - 1
AGCUGUUGCCGCUCUUGGCCACUUGCCAAUGCACUCACACGCACACA---------------------CA--CACAAA------C-AUUGCAUUACCG--CCGCUGUUGCAUA
.((....((.((..(((((.....)))))(((........)))....---------------------..--......------.-...........)--).))....))... ( -14.50)
>DroSec_CAF1 1697 91 - 1
UGUUUCUGCCACUGUUGGCCACUUGCCAAUGCACUCGAAUACACACAG------------------CACA--CACAGCUGCACGCAGUUGCAGUGCAG--CCGAUGUUGCAUA
(((((((((....((((((.....)))))))))...))).)))....(------------------((.(--(((.(((((((((....)).))))))--).).))))))... ( -29.00)
>DroSim_CAF1 1701 91 - 1
UGUUUCUGCCACUGUUGGCCACUUGCCAAUGCACUCGAAUACACACAG------------------CACA--CACAGCUGCACGCAGUUGCAGUGCAG--CCGAUGUUGCAUA
(((((((((....((((((.....)))))))))...))).)))....(------------------((.(--(((.(((((((((....)).))))))--).).))))))... ( -29.00)
>DroEre_CAF1 6436 81 - 1
UGUUUUUGCCACUGUUGGCCACUUGCCAAUGCACUCGAAUACACACAG------------------CACA--CACAGCUGCACGCAGUUGCAGU-----------GUUGCAU-
(((.((((.....((((((.....)))))).....)))).)))..(((------------------(((.--..((((((....))))))..))-----------))))...- ( -23.80)
>DroYak_CAF1 12747 108 - 1
UGUUUUUACCACUGUUGGCCACUUGCCAAUGCACUCGAAUACACACAGCACACGCUGCACUCACAGCACA--CACAGCUGCACGCAGUUGCAGUGCCG--CCGAUGUUGCAU-
.............((((((.....))))))(((((((........((((....))))........((((.--..((((((....))))))..))))..--.))).).)))..- ( -29.20)
>consensus
UGUUUCUGCCACUGUUGGCCACUUGCCAAUGCACUCGAAUACACACAG__________________CACA__CACAGCUGCACGCAGUUGCAGUGCAG__CCGAUGUUGCAUA
......(((.((.((((((.....))))))............................................((((((....))))))...............)).))).. (-14.10 = -14.53 +   0.43)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:32 2006