Locus 430

Sequence ID	X_DroMel_CAF1
Location	1,260,331 – 1,260,521
Length	190
Max. P	0.948847

overview

Window 3

Location	1,260,331 – 1,260,428
Length	97
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	70.23
Mean single sequence MFE	-33.06
Consensus MFE	-18.50
Energy contribution	-20.20
Covariance contribution	1.70
Combinations/Pair	1.24
Mean z-score	-1.84
Structure conservation index	0.56
SVM decision value	1.39
SVM RNA-class probability	0.948847
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1260331 97 - 22224390
AAGGGGAGGGUGGAGGUGGCGGCUU--CAGCGGGG------------------GGACUGCGAAUGAGGCAAGGCUGCGG-CGCUUGAUUGAUGGACUGCAGCGAAGGAGGAGCUGCCA
................(((((((((--(.((((..------------------...))))............(((((((-..((........)).)))))))......)))))))))) ( -35.10)
>DroSec_CAF1 14523 96 - 1
AGAGGAGGG-GGGAGGUGGCGGCUU--CAGCGGGG------------------GAACUGCGAAUGAGGCAAGGCUGCGG-CGCUUGAGUGAUGGACUGCAGAGAAGGAGGAGCUGCCA
.........-......(((((((((--(.((((..------------------...)))).............((((((-(((....))).....)))))).......)))))))))) ( -31.60)
>DroSim_CAF1 13202 97 - 1
AGGGGAGGGGGGGAGGUGGCGGCUU--CAGCGGGG------------------GAACUGCGAAUGAGGCAAGGCUGCGG-CGCUUGAUUGAUGGACUGCAGCGAAGGAGGAGCUGCCA
................(((((((((--(.((((..------------------...))))............(((((((-..((........)).)))))))......)))))))))) ( -35.10)
>DroEre_CAF1 16256 90 - 1
AAGUAGAGGG-------GGCGGCUU--CCGCGGGG------------------GGACUGCAAAUGAGGCAAGGCUGCGG-CGCUUGAUUGAUGGACUGCAGCGAAGGAGGAGCUGCCA
.......((.-------(((..(((--((((((..------------------...))))............(((((((-..((........)).)))))))...))))).))).)). ( -34.60)
>DroYak_CAF1 15803 108 - 1
ACGGGAAGAG-------GGCAGCUG--CCGCAAGGAGGGGGAGGUGAGGGGGUCGGCUGCAAAUGAGGCAAGGCUGCGG-CGCUUGAUUGAUGGACUGCAGCGUAGGAGGAGCUGUCG
..........-------(((((((.--((((........(.((.(((.....))).)).).......))...(((((((-..((........)).)))))))......))))))))). ( -33.16)
>DroAna_CAF1 13764 82 - 1
AGGG------CUGGGGCGGCGGCCUUCCGGCAGGU------------------G-----C-----AGUUAAGAUUACGGACAGUUGAUUGAUUGACUGCGGCG--GGAAGAUGUGGCA
....------.....((.(((..(((((.((....------------------(-----(-----((((((((((((.....).)))))..)))))))).)).--))))).))).)). ( -28.80)
>consensus
AGGGGAAGGG_GGAGGUGGCGGCUU__CAGCGGGG__________________GGACUGCGAAUGAGGCAAGGCUGCGG_CGCUUGAUUGAUGGACUGCAGCGAAGGAGGAGCUGCCA
.................((((((((....((((.......................))))............(((((((...((........)).))))))).......)))))))). (-18.50 = -20.20 +   1.70)

alignment

secondary structure

dotplot

Window 4

Location	1,260,428 – 1,260,521
Length	93
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	76.19
Mean single sequence MFE	-34.83
Consensus MFE	-19.56
Energy contribution	-20.66
Covariance contribution	1.10
Combinations/Pair	1.40
Mean z-score	-1.55
Structure conservation index	0.56
SVM decision value	0.07
SVM RNA-class probability	0.567560
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1260428 93 + 22224390
UUUGGGCGACCUUUUGUGCAAUUUGCGUUGGU-------AGUGGGUUCACGGUUCCCCAGGGAGGCGGAGAAGGUGGGCUUAGGUGC---AGGGUUGGUCUAA
.(((((((((((..((..(...((((....))-------))(((((((((..((((((.....)).))))...))))))))).)..)---)))))).)))))) ( -30.90)
>DroPse_CAF1 27579 73 + 1
UAGGGGCGACCUUUUAUGCAAUUUGCAUAGCC-------AGCAGCUGCUC-------UAGUG----------GGUG---CUGUGUGU---GUGGGCGGUUCAA
..(((.((.(((..(((((.....)))))(((-------((((.(..(..-------..)..----------).))---))).))..---..))))).))).. ( -25.80)
>DroSec_CAF1 14619 93 + 1
UUGGAGCGACCUUUUGUGCAAUUUGCGUGGGC-------AGUGGGUUCACGGUUCCCCAGGGAGGCGGAGAAGGUGGGCUUAGGCGC---AGGGGUGGCCUAA
.(((.((.((((((.((((...((((....))-------))(((((((((..((((((.....)).))))...))))))))).))))---)))))).))))). ( -37.30)
>DroSim_CAF1 13299 93 + 1
UUGGGGCGACCUUUUGUGCAAUUUGCGUGGGC-------AGUGGGUUCACGGUUCCCCAGGGAGGCGGAGAAGGUGGGCUUAGGCGC---AGGGGUGGCCUAA
...((((.((((((.((((...((((....))-------))(((((((((..((((((.....)).))))...))))))))).))))---)))))).)))).. ( -40.20)
>DroEre_CAF1 16346 98 + 1
UU-GGGCGACCUUUUGUGCAAUUUGCGUGGGCAGUGGGCAGUGGGUUCACGGUUCCCCAGGGAGGCAGAGAAGGUGGGCUUCUGCGCG----GGGUGGCCUAA
.(-((((.((((..((((((.(((((.......((((((.....))))))..((((....)))))))))((((.....))))))))))----)))).))))). ( -40.00)
>DroYak_CAF1 15911 96 + 1
UUGGGGCGACCUUUUGUGCAAUUUGCGUGGGC-------AGUGGCUUCGUGGUUCCCCAGGGAGGCAGAGACGGUGGGCUUUGGGGCGGCAGGGGUGGCCUAA
...((((.(((((...(((...(..((.((((-------....))))))..)..((((((((..((.......))...))))))))..)))))))).)))).. ( -34.80)
>consensus
UUGGGGCGACCUUUUGUGCAAUUUGCGUGGGC_______AGUGGGUUCACGGUUCCCCAGGGAGGCGGAGAAGGUGGGCUUAGGCGC___AGGGGUGGCCUAA
...((((.((((((.((((.....((....)).........((((((((((.((((....)))).).......))))))))).))))...)))))).)))).. (-19.56 = -20.66 +   1.10)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:25 2006