Locus 3341

Sequence ID	X_DroMel_CAF1
Location	8,934,871 – 8,935,029
Length	158
Max. P	0.941432

overview

Window 1

Location	8,934,871 – 8,934,989
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	92.19
Mean single sequence MFE	-31.46
Consensus MFE	-24.84
Energy contribution	-25.44
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.15
Structure conservation index	0.79
SVM decision value	1.32
SVM RNA-class probability	0.941432
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8934871 118 - 22224390
CACGUGCAAGCCGCCUGUCAAAAUGGCUUGCGCUUCGUUCACACACACACCCGGCAAAUGAAAACGCCGAAUUGGCCACAAUUAUCAAUGAAAAGUGGGCGAAUUCACGCAACGCCAA
...((((((((((..........))))))))))(((((((((.........((((..........))))(((((....)))))...........)))))))))............... ( -35.50)
>DroSec_CAF1 5146 118 - 1
CACGUGCAAGCCGCCUGUCAAAAUGGCUUGCGCUUCGUUCACACACACACCCGGCAAAUGAAAACGCCGAAUUGGCCACAAUUAUCAAUGAAAAUACGGCGAAUUCACGCAACGCCAA
...((((((((((..........))))))))))...................(((...((((..((((((((((....)))))....((....)).)))))..))))......))).. ( -32.80)
>DroSim_CAF1 5379 118 - 1
CACGUGCAAGCCGCCUGUCAAAAUGGCUUGCGCUUCGUUCACACACACACCCGGCAAAUGAAAACGCCGAAUUGGCCACAAUUAUCAAUGAAAAUAUGGCGAAUUCACGCAACGCCAA
...((((((((((..........))))))))))((((((............((((..........))))(((((....)))))...))))))....(((((...........))))). ( -32.50)
>DroEre_CAF1 4171 116 - 1
CACGUGCAAGCCGCCUGUCAAAAUGGCUUGCGCUUCUAUCACA--CACACCCGGCAAAUGAAAACGCCGAAUUGGCGGAAAUUAUCAAUGAAAACUGUCCAAAGUCACGUAACGCCAC
...((((((((((..........))))))))))..........--......((((..........))))...(((((((.....)).(((...(((......)))..)))..))))). ( -29.10)
>DroYak_CAF1 4250 116 - 1
CACGUGCAAGCCGCCUGUCAAAAUGGCUUGCGCUUCGUUCACA--CACACCCGGCAAAUGAAAACGCCGAAUUGGCCGGAAUUAUCAAUGAAAACUGCCCGAAAUCACGCAACGCCAC
...((((((((((..........))))))))))..........--.......(((...(((.((..(((.......)))..)).)))........(((..(....)..)))..))).. ( -27.40)
>consensus
CACGUGCAAGCCGCCUGUCAAAAUGGCUUGCGCUUCGUUCACACACACACCCGGCAAAUGAAAACGCCGAAUUGGCCACAAUUAUCAAUGAAAACUGGGCGAAUUCACGCAACGCCAA
...((((((((((..........))))))))))...................(((..........(((.....)))......................(((......)))...))).. (-24.84 = -25.44 +   0.60)

alignment

secondary structure

dotplot

Window 2

Location	8,934,909 – 8,935,029
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.07
Mean single sequence MFE	-38.72
Consensus MFE	-32.92
Energy contribution	-33.32
Covariance contribution	0.40
Combinations/Pair	1.06
Mean z-score	-1.34
Structure conservation index	0.85
SVM decision value	0.27
SVM RNA-class probability	0.662602
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8934909 120 - 22224390
AAGGUUCUGGAAGUGGCAGGCGAAAUCGGAGUCCAUGGCUCACGUGCAAGCCGCCUGUCAAAAUGGCUUGCGCUUCGUUCACACACACACCCGGCAAAUGAAAACGCCGAAUUGGCCACA
............(((((.((((((....((((.....))))..((((((((((..........))))))))))))))))............((((..........)))).....))))). ( -40.30)
>DroSec_CAF1 5184 120 - 1
AAGGUUCUGGAAGUGGCAGGCGAAAUCGGAGUCCAUGGCUCACGUGCAAGCCGCCUGUCAAAAUGGCUUGCGCUUCGUUCACACACACACCCGGCAAAUGAAAACGCCGAAUUGGCCACA
............(((((.((((((....((((.....))))..((((((((((..........))))))))))))))))............((((..........)))).....))))). ( -40.30)
>DroSim_CAF1 5417 120 - 1
AAGGUUCUGGAAGUGGCAGGCGAAAUCGGAGUCCAUGGCUCACGUGCAAGCCGCCUGUCAAAAUGGCUUGCGCUUCGUUCACACACACACCCGGCAAAUGAAAACGCCGAAUUGGCCACA
............(((((.((((((....((((.....))))..((((((((((..........))))))))))))))))............((((..........)))).....))))). ( -40.30)
>DroEre_CAF1 4209 117 - 1
AAUGUUCUGGAAGUGA-AACCGAAAUCGGAGUCCAUGGCUCACGUGCAAGCCGCCUGUCAAAAUGGCUUGCGCUUCUAUCACA--CACACCCGGCAAAUGAAAACGCCGAAUUGGCGGAA
..(((..(((((((((-..(((....))).((.....))))))((((((((((..........)))))))))))))))..)))--...................((((.....))))... ( -34.50)
>DroYak_CAF1 4288 117 - 1
AAUGUUCUCGAAGUGG-AAGCGAAAUCGGUGUCCAUGGCUCACGUGCAAGCCGCCUGUCAAAAUGGCUUGCGCUUCGUUCACA--CACACCCGGCAAAUGAAAACGCCGAAUUGGCCGGA
............(((.-.((((((....(((.(....)..)))((((((((((..........))))))))))))))))..))--)....(((((.(((...........))).))))). ( -38.20)
>consensus
AAGGUUCUGGAAGUGGCAGGCGAAAUCGGAGUCCAUGGCUCACGUGCAAGCCGCCUGUCAAAAUGGCUUGCGCUUCGUUCACACACACACCCGGCAAAUGAAAACGCCGAAUUGGCCACA
..((((......((((...(((((....((((.....))))..((((((((((..........))))))))))))))))))).........((((..........))))....))))... (-32.92 = -33.32 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:57 2006