Locus 1364

Sequence ID	X_DroMel_CAF1
Location	4,083,683 – 4,083,779
Length	96
Max. P	0.960281

overview

Window 9

Location	4,083,683 – 4,083,779
Length	96
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	77.64
Mean single sequence MFE	-26.51
Consensus MFE	-14.25
Energy contribution	-14.83
Covariance contribution	0.59
Combinations/Pair	1.10
Mean z-score	-1.95
Structure conservation index	0.54
SVM decision value	0.55
SVM RNA-class probability	0.776882
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4083683 96 + 22224390
------UGUGUCCCGCACUCGGAACAUCCGCUUACAUCCCCUCGUACACAUCC------------GCACACAUCGGAUGUUGCUUUGUUUGGGCAACUAAAUGCGCGUUUCCGA
------.(((.....)))((((((.((.(((............(((.((((((------------(.......))))))))))...((((((....))))))))).)))))))) ( -29.10)
>DroSec_CAF1 96216 94 + 1
------UGUGUUCCGCACUCGGAACAACCGCUAACAUC--CUCGUACACAUCC------------ACACACAUCGGAUGUUGCUUUGUUUGGGCAACUAAAUGCGCGUUUCCUA
------..(((((((....)))))))(((((.......--...(((.((((((------------.........)))))))))...((((((....))))))))).))...... ( -27.00)
>DroSim_CAF1 97041 94 + 1
------UGUGUUCCGCACUCGGAACAUCCGCUAACAUC--CUCGUACACAUCC------------GCACACAUCGGAUGUUGCUUUGUUUGGGCAACUAAAUGCGCGUUUCCGA
------.((((((((....)))))))).(((.......--...(((.((((((------------(.......))))))))))...((((((....))))))..)))....... ( -29.20)
>DroEre_CAF1 101676 104 + 1
------U-UGCCCCGCACUCGGAGCAUCCGCUUACAUC--CUUGUACACAUCCGCACACACAUCCGCACACAUCGGAUGUUGCUUUGUUUGGCCAACUAAAUG-GCGUUUCCGA
------.-..........((((((((..((..((((..--..))))..)....(((...(((((((.......))))))))))...)..))((((......))-))..)))))) ( -25.00)
>DroYak_CAF1 95090 104 + 1
------U-UGCCCCGCACUCGGAGCAUCCGCUUACAUC--CUUGUACACAUCCGCACUCACAUCUGCACACAUCGGAUGUUGCUUUGUUUGGCCAACUAAAUG-GCGUUUCCGA
------.-..........((((((((((((..((((..--..)))).......(((........)))......)))))))...........((((......))-))...))))) ( -24.40)
>DroAna_CAF1 115182 106 + 1
GUUUGCUGUUUUCCGCA----AAAUAUCCGCAAACACC--CAC--ACACACCCACACACACACAUCCGCAUGUCGGAUGUUGCUUUGUUUGUGGAUCUAAAUUGGCAUUUCCGU
((((((((((((....)----)))))...))))))..(--((.--......(((((.(((((((((((.....)))))).))...))).)))))........)))......... ( -24.36)
>consensus
______UGUGUCCCGCACUCGGAACAUCCGCUAACAUC__CUCGUACACAUCC____________GCACACAUCGGAUGUUGCUUUGUUUGGGCAACUAAAUGCGCGUUUCCGA
........(((.(((....))).)))..............................................(((((...(((...((((((....))))))..)))..))))) (-14.25 = -14.83 +   0.59)

alignment

secondary structure

dotplot

Window 0

Location	4,083,683 – 4,083,779
Length	96
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	77.64
Mean single sequence MFE	-34.88
Consensus MFE	-18.21
Energy contribution	-17.80
Covariance contribution	-0.41
Combinations/Pair	1.24
Mean z-score	-2.55
Structure conservation index	0.52
SVM decision value	1.51
SVM RNA-class probability	0.960281
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4083683 96 - 22224390
UCGGAAACGCGCAUUUAGUUGCCCAAACAAAGCAACAUCCGAUGUGUGC------------GGAUGUGUACGAGGGGAUGUAAGCGGAUGUUCCGAGUGCGGGACACA------
((((((.(((((.(((.(((.....)))))))).((((((....(((((------------(....))))))...))))))..)))....))))))(((.....))).------ ( -29.90)
>DroSec_CAF1 96216 94 - 1
UAGGAAACGCGCAUUUAGUUGCCCAAACAAAGCAACAUCCGAUGUGUGU------------GGAUGUGUACGAG--GAUGUUAGCGGUUGUUCCGAGUGCGGAACACA------
..(....)(.(((......))).).(((...(((((((((..((((..(------------....)..)))).)--)))))).)).)))((((((....))))))...------ ( -29.80)
>DroSim_CAF1 97041 94 - 1
UCGGAAACGCGCAUUUAGUUGCCCAAACAAAGCAACAUCCGAUGUGUGC------------GGAUGUGUACGAG--GAUGUUAGCGGAUGUUCCGAGUGCGGAACACA------
.((....)).(((......))).........(((((((((..((((..(------------....)..)))).)--)))))).))...(((((((....)))))))..------ ( -31.70)
>DroEre_CAF1 101676 104 - 1
UCGGAAACGC-CAUUUAGUUGGCCAAACAAAGCAACAUCCGAUGUGUGCGGAUGUGUGUGCGGAUGUGUACAAG--GAUGUAAGCGGAUGCUCCGAGUGCGGGGCA-A------
..(....)((-((......))))........((.((((((....((((((.((.((....)).)).)))))).)--)))))..))...(((((((....)))))))-.------ ( -39.00)
>DroYak_CAF1 95090 104 - 1
UCGGAAACGC-CAUUUAGUUGGCCAAACAAAGCAACAUCCGAUGUGUGCAGAUGUGAGUGCGGAUGUGUACAAG--GAUGUAAGCGGAUGCUCCGAGUGCGGGGCA-A------
..(....)((-((......))))........((.((((((..((((..((..(((....)))..))..)))).)--)))))..))...(((((((....)))))))-.------ ( -39.50)
>DroAna_CAF1 115182 106 - 1
ACGGAAAUGCCAAUUUAGAUCCACAAACAAAGCAACAUCCGACAUGCGGAUGUGUGUGUGUGGGUGUGU--GUG--GGUGUUUGCGGAUAUUU----UGCGGAAAACAGCAAAC
.((.(((((((....((.(((((((.(((.....(((((((.....))))))).))).))))))).)).--...--))))))).)).....((----(((........))))). ( -39.40)
>consensus
UCGGAAACGCGCAUUUAGUUGCCCAAACAAAGCAACAUCCGAUGUGUGC____________GGAUGUGUACGAG__GAUGUAAGCGGAUGUUCCGAGUGCGGAACACA______
.......(((.((((..(((.....)))...(((.(((((.....................)))))))).......))))...)))..(((((((....)))))))........ (-18.21 = -17.80 +  -0.41)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:24 2006