Locus 836

Sequence ID	3R_DroMel_CAF1
Location	2,870,895 – 2,871,054
Length	159
Max. P	0.967067

overview

Window 7

Location	2,870,895 – 2,871,014
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.97
Mean single sequence MFE	-41.80
Consensus MFE	-35.66
Energy contribution	-34.98
Covariance contribution	-0.69
Combinations/Pair	1.24
Mean z-score	-1.75
Structure conservation index	0.85
SVM decision value	0.68
SVM RNA-class probability	0.820995
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2870895 119 - 27905053
AAAGUGGGGGAAGUGCAAAUUGUGUUGCAAAGGUGAGGCAAGAACAGAAGGCUCAGGUCGGGGUCACCCCG-AAAUUGGAUGGAUUCGGGGUUUGGUGGGAUGGUUCAUUCGCCGGCGGA
...((.((.(((.......((((.(..(....)..).))))((((....(((((......)))))((((((-((.((....)).))))))))...........)))).))).)).))... ( -37.50)
>DroSec_CAF1 1872 120 - 1
AAAGUGGGGGAAGUGCAAAUUGUGUUGCGAAGGUGAGGCAAGAACAGAAGGAUCAGGUCGGGGUCACCACUUGGCUCGGAUGGAUUUCGGGCUUGCCUGGAUGGUUCAUUCGCCGGCGGA
...((.((.(((.......((((.(..(....)..).))))((((...(((..(((((.((.....)))))))(((((((.....)))))))...))).....)))).))).)).))... ( -42.00)
>DroSim_CAF1 2253 120 - 1
AAAGUGGGGGAAGUGCAAAUUGUGUUGCGAAGGUGAGGCAAGAACAGAAGGAUCAGGUCGGGGUCACCACUUGGCUCGGAUGGAUUUCGGGCUUGCCUGGAUGGUUCAUUCGCCGGCGGA
...((.((.(((.......((((.(..(....)..).))))((((...(((..(((((.((.....)))))))(((((((.....)))))))...))).....)))).))).)).))... ( -42.00)
>DroEre_CAF1 2811 120 - 1
AAAGUGGGGGGAGUGCAAAUUGUGUUGCGAAGGUGAAGCAAGAGCAGAAGGCUCAGGUCGGGGUCACCACUUGGCUCGGAUGAAUUCCGGGCUUGCCUCGAUGGUUUAUUCGCCGGCGGA
...((.((.(((..((...((((.(..(....)..).))))((((.....))))..((((((((........((((((((.....)))))))).)))))))).))...))).)).))... ( -45.70)
>consensus
AAAGUGGGGGAAGUGCAAAUUGUGUUGCGAAGGUGAGGCAAGAACAGAAGGAUCAGGUCGGGGUCACCACUUGGCUCGGAUGGAUUCCGGGCUUGCCUGGAUGGUUCAUUCGCCGGCGGA
...((.((.(((.......((((.(..(....)..).))))((((....(((((......))))).(((...((((((((.....))))))))....)))...)))).))).)).))... (-35.66 = -34.98 +  -0.69)

alignment

secondary structure

dotplot

Window 8

Location	2,870,935 – 2,871,054
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.78
Mean single sequence MFE	-32.77
Consensus MFE	-28.38
Energy contribution	-29.38
Covariance contribution	1.00
Combinations/Pair	1.13
Mean z-score	-2.45
Structure conservation index	0.87
SVM decision value	1.60
SVM RNA-class probability	0.967067
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2870935 119 - 27905053
ACCCAAAAAUAUAAGAGAAAUGGAUAAGGGAACCGAGUGCAAAGUGGGGGAAGUGCAAAUUGUGUUGCAAAGGUGAGGCAAGAACAGAAGGCUCAGGUCGGGGUCACCCCG-AAAUUGGA
.(((.....(((.......))).....)))..((((........(((((...((.....((((.(..(....)..).))))..))....(((((......))))).)))))-...)))). ( -26.90)
>DroSec_CAF1 1912 120 - 1
ACCCAAAAAUAUAAGAGAAAUGGAUAAGGGAACCGAGUGCAAAGUGGGGGAAGUGCAAAUUGUGUUGCGAAGGUGAGGCAAGAACAGAAGGAUCAGGUCGGGGUCACCACUUGGCUCGGA
.(((.....(((.......))).....)))..((((((...((((((.....((.....((((.(..(....)..).))))..)).....((((.......)))).)))))).)))))). ( -33.90)
>DroSim_CAF1 2293 120 - 1
ACCCAAAAAUAUAAGAGAAAUGGAUAAGGGAACCGAGUGCAAAGUGGGGGAAGUGCAAAUUGUGUUGCGAAGGUGAGGCAAGAACAGAAGGAUCAGGUCGGGGUCACCACUUGGCUCGGA
.(((.....(((.......))).....)))..((((((...((((((.....((.....((((.(..(....)..).))))..)).....((((.......)))).)))))).)))))). ( -33.90)
>DroEre_CAF1 2851 119 - 1
ACCCAAAAAUAUAAG-GAAAAGGAUAGGGGAGCCGGGUGCAAAGUGGGGGGAGUGCAAAUUGUGUUGCGAAGGUGAAGCAAGAGCAGAAGGCUCAGGUCGGGGUCACCACUUGGCUCGGA
.(((...........-..........)))...((((((...((((((...((.(.(...((((.(..(....)..).))))((((.....)))).....).).)).)))))).)))))). ( -36.40)
>consensus
ACCCAAAAAUAUAAGAGAAAUGGAUAAGGGAACCGAGUGCAAAGUGGGGGAAGUGCAAAUUGUGUUGCGAAGGUGAGGCAAGAACAGAAGGAUCAGGUCGGGGUCACCACUUGGCUCGGA
.(((.....(((.......))).....)))..((((((...((((((.....((.....((((.(..(....)..).))))..))....(((((......))))).)))))).)))))). (-28.38 = -29.38 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:18 2006