Locus 9960

Sequence ID	3R_DroMel_CAF1
Location	26,683,289 – 26,683,439
Length	150
Max. P	0.999096

overview

Window 3

Location	26,683,289 – 26,683,401
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.88
Mean single sequence MFE	-37.48
Consensus MFE	-37.26
Energy contribution	-37.26
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.98
Structure conservation index	0.99
SVM decision value	3.37
SVM RNA-class probability	0.999096
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26683289 112 - 27905053
CAUCGAAAUAAUGCGGGCAAUUGCUACUUUCUUGAGGUUAAACGCAAGUUGCUCUCAAGAUUCUUCGAGGACAUUGUUCGCCGGA--------UCGGCGGCUCAGCGGAUUUGCCCUUAA
..............(((((((((((....((((((((...(((....)))..))))))))......(((........((((((..--------.))))))))))))))..)))))).... ( -36.50)
>DroSec_CAF1 274019 112 - 1
CAUCGAAAUAAUGCGGGCAAUUGCUACUUUCUUGAGGUUAAACGCAAGUUGCUCUCAAGAUUCUUCGAGGACAUUGUUCGCCGGA--------UCGGCGGCUCAGCGGAUUUGCCCUUAA
..............(((((((((((....((((((((...(((....)))..))))))))......(((........((((((..--------.))))))))))))))..)))))).... ( -36.50)
>DroSim_CAF1 270761 112 - 1
CAUCGAAAUAAUGCGGGCAAUUGCUACUUUCUUGAGGUUAAACGCAAGUUGCUCUCAAGAUUCUUCGAGGACAUUGUUCGCCGGA--------UCGGCGGCUCAGCGGAUUUGCCCUUAA
..............(((((((((((....((((((((...(((....)))..))))))))......(((........((((((..--------.))))))))))))))..)))))).... ( -36.50)
>DroEre_CAF1 289948 120 - 1
CAUCGAAAUAAUGCGGGCAAUUGCUACUUUCUUGAGGUUAAACGCAAGUUGCUCUCAAGAUUCUUCGAGGACAUUGUUCGCCGGAUCGCCAGAUCGGCGGCUCAGCGGAUUUGCCCUUAA
..(((((........(((....)))....((((((((...(((....)))..))))))))...)))))((.((..((((((.(..(((((.....)))))..).)))))).)).)).... ( -41.40)
>DroYak_CAF1 278930 112 - 1
CAUCGAAAUAAUGCGGGCAAUUGCUACUUUCUUGAGGUUAAACGCAAGUUGCUCUCAAGAUUCAUCGAGGACAUUGUUCGCCGGA--------UCGGCGGCUCAGCGGAUUUGCCCUUAA
..............(((((((((((....((((((((...(((....)))..))))))))......(((........((((((..--------.))))))))))))))..)))))).... ( -36.50)
>consensus
CAUCGAAAUAAUGCGGGCAAUUGCUACUUUCUUGAGGUUAAACGCAAGUUGCUCUCAAGAUUCUUCGAGGACAUUGUUCGCCGGA________UCGGCGGCUCAGCGGAUUUGCCCUUAA
..............(((((((((((....((((((((...(((....)))..))))))))......(((........(((((((.........)))))))))))))))..)))))).... (-37.26 = -37.26 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	26,683,321 – 26,683,439
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.13
Mean single sequence MFE	-33.34
Consensus MFE	-27.62
Energy contribution	-27.78
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-1.70
Structure conservation index	0.83
SVM decision value	0.61
SVM RNA-class probability	0.799910
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26683321 118 - 27905053
CCAGCAAACUGCAUUCCUCGAACAAAGGAC--UCGUCGAUCAUCGAAAUAAUGCGGGCAAUUGCUACUUUCUUGAGGUUAAACGCAAGUUGCUCUCAAGAUUCUUCGAGGACAUUGUUCG
...((.....))......(((((((.(..(--(((..((................(((....)))....((((((((...(((....)))..)))))))).))..))))..).))))))) ( -34.80)
>DroSec_CAF1 274051 118 - 1
CCAUCAAACUGCAUCCCUCGAACAAAGGAC--UCGUCGAUCAUCGAAAUAAUGCGGGCAAUUGCUACUUUCUUGAGGUUAAACGCAAGUUGCUCUCAAGAUUCUUCGAGGACAUUGUUCG
..................(((((((.(..(--(((..((................(((....)))....((((((((...(((....)))..)))))))).))..))))..).))))))) ( -33.30)
>DroSim_CAF1 270793 118 - 1
CCAGCAAACUGCAUCCCUCGAACAAAGGAC--UCGUCGAUCAUCGAAAUAAUGCGGGCAAUUGCUACUUUCUUGAGGUUAAACGCAAGUUGCUCUCAAGAUUCUUCGAGGACAUUGUUCG
...((.....))......(((((((.(..(--(((..((................(((....)))....((((((((...(((....)))..)))))))).))..))))..).))))))) ( -34.80)
>DroEre_CAF1 289988 118 - 1
CCAGCGAACUGCAUCCCUCGUUCAAAGGAC--UCGUCGAUCAUCGAAAUAAUGCGGGCAAUUGCUACUUUCUUGAGGUUAAACGCAAGUUGCUCUCAAGAUUCUUCGAGGACAUUGUUCG
....(((((......(((((....(((((.--...(((.....))).........(((....)))....((((((((...(((....)))..)))))))))))))))))).....))))) ( -30.90)
>DroYak_CAF1 278962 120 - 1
CCAGCGAACUCCAUCCCUCGAACAAAGGAGGAACGUCGAUCAUCGAAAUAAUGCGGGCAAUUGCUACUUUCUUGAGGUUAAACGCAAGUUGCUCUCAAGAUUCAUCGAGGACAUUGUUCG
....(((((......((((((......(((.....(((.....))).........(((....))).)))((((((((...(((....)))..))))))))....)))))).....))))) ( -32.90)
>consensus
CCAGCAAACUGCAUCCCUCGAACAAAGGAC__UCGUCGAUCAUCGAAAUAAUGCGGGCAAUUGCUACUUUCUUGAGGUUAAACGCAAGUUGCUCUCAAGAUUCUUCGAGGACAUUGUUCG
(((((((.((((((.(((.......))).......(((.....)))....))))))....)))))....((((((((...(((....)))..))))))))........)).......... (-27.62 = -27.78 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:45:46 2006