Locus 1877

Sequence ID	X_DroMel_CAF1
Location	5,198,749 – 5,198,849
Length	100
Max. P	0.999470

overview

Window 8

Location	5,198,749 – 5,198,849
Length	100
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	77.98
Mean single sequence MFE	-23.32
Consensus MFE	-11.53
Energy contribution	-11.85
Covariance contribution	0.32
Combinations/Pair	1.35
Mean z-score	-2.17
Structure conservation index	0.49
SVM decision value	0.94
SVM RNA-class probability	0.886427
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5198749 100 + 22224390
UUGG-GUUGAAGGCUGGUAGAGUUUUAUGGGUUUCAAGUUUAAUAAGAAAACGUAACAAUUAAAAAUAUGUUUCGAAACCUUAAGUGACCAGCCUUUCGA-A
....-.((((((((((((.....((((.(((((((..((((.......))))(.((((..........)))).))))))))))))..))))))).)))))-. ( -27.10)
>DroSec_CAF1 19472 98 + 1
UUGGGGUUGAAGGCUGGUCGAGUUUUAUAGGG-UCAAGCUUAAUAAGAAAACGUAACAAUUAAAAA--UGUUUCGAAACCUAAAGUGACCAGCCUUGCUA-A
....(((..(((((((((((..((((((..((-.....))..))))))...((.((((........--)))).))..........)))))))))))))).-. ( -26.70)
>DroSim_CAF1 13251 97 + 1
UUGG-GUUGAAGGCUGGUCGAGUUUUAUAGGG-UCAAGCUUAAUAAGAAAACGUAACAAUUAAAAA--UGUUUCGAAACCUAAAGUGACCAGCCUUGCUA-A
...(-((..(((((((((((..((((((..((-.....))..))))))...((.((((........--)))).))..........)))))))))))))).-. ( -26.70)
>DroEre_CAF1 22369 86 + 1
UUGG-GUUGAUGGCUGGUCCAGAUUUAUGGCA-UCAAGUUAAAUAUUAAAACAUAACAAUUAA--------------ACCUGAAAUGACCAGACAUUUUAAA
.((.-.(((((((((((((((......))).)-)).)))....))))))..))..........--------------...(((((((......))))))).. ( -13.10)
>DroYak_CAF1 19859 97 + 1
UUGG-CUUGAAGGCCGGUCGAGUCUUCUAGCC-UCAAGUUAAAUAUUAAAGUGUAAGAAUUAAAAA--UAUUUUAAAACUUAAAGGGACCAGCCCUGCUG-A
..((-((.(((((((....).)))))).))))-..(((((.....(((((((((...........)--)))))))))))))..((((.....))))....-. ( -23.00)
>consensus
UUGG_GUUGAAGGCUGGUCGAGUUUUAUAGGG_UCAAGUUUAAUAAGAAAACGUAACAAUUAAAAA__UGUUUCGAAACCUAAAGUGACCAGCCUUGCUA_A
.........((((((((((....(((.((((...............................................))))))).))))))))))...... (-11.53 = -11.85 +   0.32)

alignment

secondary structure

dotplot

Window 9

Location	5,198,749 – 5,198,849
Length	100
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	77.98
Mean single sequence MFE	-22.78
Consensus MFE	-14.29
Energy contribution	-13.97
Covariance contribution	-0.32
Combinations/Pair	1.35
Mean z-score	-3.37
Structure conservation index	0.63
SVM decision value	3.63
SVM RNA-class probability	0.999470
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5198749 100 - 22224390
U-UCGAAAGGCUGGUCACUUAAGGUUUCGAAACAUAUUUUUAAUUGUUACGUUUUCUUAUUAAACUUGAAACCCAUAAAACUCUACCAGCCUUCAAC-CCAA
.-..(((.(((((((.......((((((((((((..........))))..((((.......))))))))))))...........))))))))))...-.... ( -23.07)
>DroSec_CAF1 19472 98 - 1
U-UAGCAAGGCUGGUCACUUUAGGUUUCGAAACA--UUUUUAAUUGUUACGUUUUCUUAUUAAGCUUGA-CCCUAUAAAACUCGACCAGCCUUCAACCCCAA
.-..(.((((((((((....((((..((((((((--........))))..((((.......))))))))-.))))........)))))))))))........ ( -23.80)
>DroSim_CAF1 13251 97 - 1
U-UAGCAAGGCUGGUCACUUUAGGUUUCGAAACA--UUUUUAAUUGUUACGUUUUCUUAUUAAGCUUGA-CCCUAUAAAACUCGACCAGCCUUCAAC-CCAA
.-..(.((((((((((....((((..((((((((--........))))..((((.......))))))))-.))))........)))))))))))...-.... ( -23.80)
>DroEre_CAF1 22369 86 - 1
UUUAAAAUGUCUGGUCAUUUCAGGU--------------UUAAUUGUUAUGUUUUAAUAUUUAACUUGA-UGCCAUAAAUCUGGACCAGCCAUCAAC-CCAA
......(((.((((((...((((((--------------(....(((((.....)))))...)))))))-...((......)))))))).)))....-.... ( -18.50)
>DroYak_CAF1 19859 97 - 1
U-CAGCAGGGCUGGUCCCUUUAAGUUUUAAAAUA--UUUUUAAUUCUUACACUUUAAUAUUUAACUUGA-GGCUAGAAGACUCGACCGGCCUUCAAG-CCAA
.-..((((((((((((.(((((((((...(((((--((.................))))))))))))))-))...((....))))))))))))...)-)... ( -24.73)
>consensus
U_UAGCAAGGCUGGUCACUUUAGGUUUCGAAACA__UUUUUAAUUGUUACGUUUUCUUAUUAAACUUGA_CCCUAUAAAACUCGACCAGCCUUCAAC_CCAA
......((((((((((...(((((((....................................)))))))..............))))))))))......... (-14.29 = -13.97 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:48 2006