Locus 1703

Sequence ID	2L_DroMel_CAF1
Location	4,660,141 – 4,660,236
Length	95
Max. P	0.965225

overview

Window 1

Location	4,660,141 – 4,660,236
Length	95
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	91.57
Mean single sequence MFE	-35.96
Consensus MFE	-27.40
Energy contribution	-27.64
Covariance contribution	0.24
Combinations/Pair	1.05
Mean z-score	-1.57
Structure conservation index	0.76
SVM decision value	0.04
SVM RNA-class probability	0.553462
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4660141 95 + 22407834
AAGGCGCUUCCUGCCGCUCCAAAGUGGCCCGCUGUGGCGUUUGUUUGCCACACGCAAUCAAUGGAUGUGGAUGUGGUUAGGG-----AUUGGUUUGGAAU
(((.((.((((((((((((((.........(((((((((......))))))).)).(((....))).)))).)))).)))))-----).)).)))..... ( -33.20)
>DroSec_CAF1 96375 94 + 1
AAGGCGCUUCCUGCCGCUCCAAAGUGGCCCGCUGUGGCGUUUGUUUGCCACACGCAAUCAAUGGUUGUGGAUGUGGUUAGGG-----AUUGGGUUGGAA-
..(((.(.((((((((((....))))))(((((((((((......)))))))((((((.....))))))...))))...)))-----)..).)))....- ( -36.20)
>DroSim_CAF1 88052 95 + 1
AAGGCGCUUCCUGCCGCUCCAAAGUGGCCCGCUGUGGCGUUUGUUUGCCACACGCAAUCAAUGGUUGUGGAUGUGGUUAGGG-----AUUGGGUUGGAAU
..(((.(.((((((((((....))))))(((((((((((......)))))))((((((.....))))))...))))...)))-----)..).)))..... ( -36.20)
>DroEre_CAF1 99974 100 + 1
AAGGCGCUUCCUGCCGAACCAAAGUGGCCCGCUGUGGCGUUUGUUUGCCACACGCAAUCAAUGGAUGUGGAUGUGGCUAGGGAGCGGAUUGGGUUGGGUU
....((((((((((((..(((.........(((((((((......))))))).)).(((....))).)))...)))).)))))))).............. ( -37.10)
>DroYak_CAF1 100166 100 + 1
AAGGCGCUUCCUGCCGAACCAAAGUGGCCCGCUGUGGCGUUUGUUUGCCACACGCAAUCACUGGAUGUGGAUGUGGUUAAGGUUUGGAUUGGGUUGGGUU
..(((.(..(((.(((((((....(((((((((((((((......))))))).))..((((.....))))..).))))).)))))))...)))..).))) ( -37.10)
>consensus
AAGGCGCUUCCUGCCGCUCCAAAGUGGCCCGCUGUGGCGUUUGUUUGCCACACGCAAUCAAUGGAUGUGGAUGUGGUUAGGG_____AUUGGGUUGGAAU
.((.(((.(((.(((((......)))))..(((((((((......))))))).)).............))).))).))...................... (-27.40 = -27.64 +   0.24)

alignment

secondary structure

dotplot

Window 2

Location	4,660,141 – 4,660,236
Length	95
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	91.57
Mean single sequence MFE	-26.72
Consensus MFE	-22.82
Energy contribution	-22.66
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.81
Structure conservation index	0.85
SVM decision value	1.58
SVM RNA-class probability	0.965225
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4660141 95 - 22407834
AUUCCAAACCAAU-----CCCUAACCACAUCCACAUCCAUUGAUUGCGUGUGGCAAACAAACGCCACAGCGGGCCACUUUGGAGCGGCAGGAAGCGCCUU
.(((((((.....-----(((............((.....))...((.((((((........)))))))))))....))))))).(((.(....)))).. ( -26.10)
>DroSec_CAF1 96375 94 - 1
-UUCCAACCCAAU-----CCCUAACCACAUCCACAACCAUUGAUUGCGUGUGGCAAACAAACGCCACAGCGGGCCACUUUGGAGCGGCAGGAAGCGCCUU
-((((((......-----(((............((.....))...((.((((((........))))))))))).....)))))).(((.(....)))).. ( -23.90)
>DroSim_CAF1 88052 95 - 1
AUUCCAACCCAAU-----CCCUAACCACAUCCACAACCAUUGAUUGCGUGUGGCAAACAAACGCCACAGCGGGCCACUUUGGAGCGGCAGGAAGCGCCUU
.((((((......-----(((............((.....))...((.((((((........))))))))))).....)))))).(((.(....)))).. ( -24.20)
>DroEre_CAF1 99974 100 - 1
AACCCAACCCAAUCCGCUCCCUAGCCACAUCCACAUCCAUUGAUUGCGUGUGGCAAACAAACGCCACAGCGGGCCACUUUGGUUCGGCAGGAAGCGCCUU
..............((((.(((.(((...................((.((((((........))))))))(((((.....))))))))))).)))).... ( -33.70)
>DroYak_CAF1 100166 100 - 1
AACCCAACCCAAUCCAAACCUUAACCACAUCCACAUCCAGUGAUUGCGUGUGGCAAACAAACGCCACAGCGGGCCACUUUGGUUCGGCAGGAAGCGCCUU
............(((................(((.....)))..(((.((((((........)))))).((((((.....))))))))))))........ ( -25.70)
>consensus
AUUCCAACCCAAU_____CCCUAACCACAUCCACAUCCAUUGAUUGCGUGUGGCAAACAAACGCCACAGCGGGCCACUUUGGAGCGGCAGGAAGCGCCUU
........((((......(((............((.....))...((.((((((........))))))))))).....))))...(((.(....)))).. (-22.82 = -22.66 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:58 2006