Locus 4395

Sequence ID	2L_DroMel_CAF1
Location	12,642,090 – 12,642,243
Length	153
Max. P	0.867171

overview

Window 5

Location	12,642,090 – 12,642,203
Length	113
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	93.51
Mean single sequence MFE	-24.42
Consensus MFE	-19.73
Energy contribution	-20.85
Covariance contribution	1.12
Combinations/Pair	1.06
Mean z-score	-2.36
Structure conservation index	0.81
SVM decision value	0.83
SVM RNA-class probability	0.861291
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12642090 113 + 22407834
UGGGGUUUUCAUAUUUUUCGAAUAUUUACCAUCGAUUAUGUGGUUAAUUUUCCAUUGAUAUUCAGGCACAUAAAGUUUCCGACCUGUUCAUAAAUUUUUAUGAACAUUUUAAA
..(((((...(((((..(.(((.(((.(((((.......))))).))).))).)..)))))...((.((.....))..)))))))((((((((....))))))))........ ( -20.30)
>DroSec_CAF1 23172 113 + 1
UGGGGUUUUCAUAUUUUUGGAAUAUUUACCAUCGAUUAUAUGGUUAAUUUUCCAUUGAUAUUCAGGCUCAUAAAGUUUCGGACCUGUUCAUAAAUGUUUAUGAAAAUUUUUAA
.((((((((((((....(((((.(((.(((((.......))))).))).))))).(((....((((..(..........)..)))).)))........))))))))))))... ( -24.70)
>DroSim_CAF1 23892 113 + 1
UCGGGUUUUCAUAUUUUUGGAAUAUUUACCAUCGAUUAUGUGGUUAAUUUUCCAUUGAUAUUCAGGCUCAUAAAGUUUCCGACCUGUUCAUAAAUGUUUAUGAACAUUUUUAA
..((((((..(((((..(((((.(((.(((((.......))))).))).)))))..)))))..))))))...............(((((((((....)))))))))....... ( -28.80)
>DroYak_CAF1 23945 112 + 1
UGGGGUUUUCAUAUU-UUGGAAUAUUUACCGUCGAUUAUGUGCUUAAUUUUCCAUUGAUAUUCCGGGUCAUAAAAUUUCCGACCUGUUCAUAAAUUUUUAUGAACAUUUUAAA
.(..(((((.((..(-((((((((((....(..(((((......)))))..)....)))))))))))..)))))))..).....(((((((((....)))))))))....... ( -23.90)
>consensus
UGGGGUUUUCAUAUUUUUGGAAUAUUUACCAUCGAUUAUGUGGUUAAUUUUCCAUUGAUAUUCAGGCUCAUAAAGUUUCCGACCUGUUCAUAAAUGUUUAUGAACAUUUUAAA
..((((((..(((((..(((((.(((.(((((.......))))).))).)))))..)))))..))))))...............(((((((((....)))))))))....... (-19.73 = -20.85 +   1.12)

alignment

secondary structure

dotplot

Window 6

Location	12,642,129 – 12,642,243
Length	114
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	86.01
Mean single sequence MFE	-19.62
Consensus MFE	-14.15
Energy contribution	-15.28
Covariance contribution	1.13
Combinations/Pair	1.15
Mean z-score	-2.13
Structure conservation index	0.72
SVM decision value	0.85
SVM RNA-class probability	0.867171
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12642129 114 - 22407834
UCGCAAGGAAACGAGACAGCUUCAUAAACAUAAAUAAGUUUUUAAAAUGUUCAUAAAAAUUUAUGAACAGGUCGGAAACUUUAUGUGCCUGAAUAUCAAUGGAAAAUUAACCAC
......(....)........((((...((((((...((((((..(..(((((((((....)))))))))..)..))))))))))))...))))......(((........))). ( -24.90)
>DroSec_CAF1 23211 110 - 1
----AAGAAGACAAGAUAGCCUUAUAAACAUAAAUAAGUUUUAAAAAUUUUCAUAAACAUUUAUGAACAGGUCCGAAACUUUAUGAGCCUGAAUAUCAAUGGAAAAUUAACCAU
----..........((((..(((((........)))))...........(((((((....)))))))((((..((........))..))))..)))).((((........)))) ( -15.60)
>DroSim_CAF1 23931 110 - 1
----AAGAAGACAAGAUAGCCUUAUAAACAUAAAUAAGUUUUAAAAAUGUUCAUAAACAUUUAUGAACAGGUCGGAAACUUUAUGAGCCUGAAUAUCAAUGGAAAAUUAACCAC
----............(((.(((((((.........((((((..(..(((((((((....)))))))))..)..))))))))))))).)))........(((........))). ( -19.90)
>DroYak_CAF1 23983 104 - 1
----AAGGCGUAAAGAU------AUAAAGAUAUAUAAGUUUUUAAAAUGUUCAUAAAAAUUUAUGAACAGGUCGGAAAUUUUAUGACCCGGAAUAUCAAUGGAAAAUUAAGCAC
----..((((((((.((------(((....)))))..(((((..(..(((((((((....)))))))))..)..))))))))))).)).......................... ( -18.10)
>consensus
____AAGAAGACAAGAUAGCCUUAUAAACAUAAAUAAGUUUUAAAAAUGUUCAUAAAAAUUUAUGAACAGGUCGGAAACUUUAUGAGCCUGAAUAUCAAUGGAAAAUUAACCAC
................(((.(((((((.........((((((..(..(((((((((....)))))))))..)..))))))))))))).)))....................... (-14.15 = -15.28 +   1.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:51 2006