Locus 6489

Sequence ID	3L_DroMel_CAF1
Location	17,255,870 – 17,256,026
Length	156
Max. P	0.997129

overview

Window 7

Location	17,255,870 – 17,255,986
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.56
Mean single sequence MFE	-28.62
Consensus MFE	-24.98
Energy contribution	-25.78
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.33
Structure conservation index	0.87
SVM decision value	0.44
SVM RNA-class probability	0.735762
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17255870 116 - 23771897
UGUGUUCCAUUCGAGACUUCCGGCUGGGCUUCUCGACUGGCCCAUAAUAAUAAACAUGCUAACAACAAUCACGACCCA----GCGAAUCCAUCAAGUUUUGGGUUCGACUUAAAGCCAAA
((((..(((.((((((..(((....)))..)))))).)))..))))...............................(----(((((((((........)))))))).)).......... ( -29.40)
>DroSec_CAF1 139585 116 - 1
UGUAUUCCAUUCGAGACUUCCGGCUGGGCUUCUCGACUGGCCCAUAAUAAUAAACAUGCAAACAACAAUCACGACCCA----GCGAAUCCAUCAAGUUUUGGGUUGGACUUAAAGCCAAA
.....................(((((((((........))))).........................((.(((((((----((...........))..))))))))).....))))... ( -25.80)
>DroSim_CAF1 134421 116 - 1
UGUGUUCCAUUCGAGACUUCCGGCUGGGCUUCUCGACUGGCCCAUAAUAAUAAACAUGCAAACAACAAUCACGACCCA----GCGAAUCCAUCAAGUUUUGGGUUCGACUUAAAGCCAAA
((((..(((.((((((..(((....)))..)))))).)))..))))...............................(----(((((((((........)))))))).)).......... ( -29.40)
>DroEre_CAF1 142711 115 - 1
UGUGUUCCAUUCGAGACUUCCGGCUGGGCUGCUCGACUGGCCCAUAAUAAUAAACAUGCAAACAACAAUCACGACCCA----GCGAAUCCAUCAAGUUUUGGGUUCGACU-UCAGCUCAG
((((..(((.(((((...(((....)))...))))).)))..))))..........................((...(----(((((((((........)))))))).))-))....... ( -27.90)
>DroYak_CAF1 146686 120 - 1
UGUGUUCCAUUCGAGACUUCCGGCUGGUCUUCUCGACUGGCCCAUAAUAAUAAACAUGCAAACAACAAUCACGACCCAUCGAGCGAAUCCAUCAAGUUUUGGGUUCGACUUUCAGCCAAA
((((..(((.((((((...((....))...)))))).)))..))))...........((............(((....)))((((((((((........)))))))).))....)).... ( -30.60)
>consensus
UGUGUUCCAUUCGAGACUUCCGGCUGGGCUUCUCGACUGGCCCAUAAUAAUAAACAUGCAAACAACAAUCACGACCCA____GCGAAUCCAUCAAGUUUUGGGUUCGACUUAAAGCCAAA
((((..(((.((((((..(((....)))..)))))).)))..)))).....................................((((((((........))))))))............. (-24.98 = -25.78 +   0.80)

alignment

secondary structure

dotplot

Window 8

Location	17,255,908 – 17,256,026
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.31
Mean single sequence MFE	-35.46
Consensus MFE	-32.74
Energy contribution	-33.34
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.92
SVM decision value	2.80
SVM RNA-class probability	0.997129
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17255908 118 - 23771897
CUCUUGGGUCUCAGUUAUGGCUCCCGAUUGGACGGCAUUUUGUGUUCCAUUCGAGACUUCCGGCUGGGCUUCUCGACUGGCCCAUAAUAAUAAACAUGCUAACAACAAUCACGACCCA--
....((((((..(((....)))...(((((...(((((.(((((..(((.((((((..(((....)))..)))))).)))..)))))........))))).....)))))..))))))-- ( -36.50)
>DroSec_CAF1 139623 118 - 1
CUCUUGGGUCUCAGUUAUGGCUCCCGAUUGGACGGCAUUUUGUAUUCCAUUCGAGACUUCCGGCUGGGCUUCUCGACUGGCCCAUAAUAAUAAACAUGCAAACAACAAUCACGACCCA--
....((((((..(((....)))...(((((....(((((((((((((((.((((((..(((....)))..)))))).))).....))).))))).))))......)))))..))))))-- ( -33.00)
>DroSim_CAF1 134459 118 - 1
CUCUUGGGUCUCAGUUAUGGCUCCCGAUUGGACGGCAUUUUGUGUUCCAUUCGAGACUUCCGGCUGGGCUUCUCGACUGGCCCAUAAUAAUAAACAUGCAAACAACAAUCACGACCCA--
....((((((..(((....)))...(((((....((((.(((((..(((.((((((..(((....)))..)))))).)))..)))))........))))......)))))..))))))-- ( -36.00)
>DroEre_CAF1 142748 118 - 1
CUCUUGGGUCUCAGUUAUGGGUCCCGAUUGGACGGCAUUUUGUGUUCCAUUCGAGACUUCCGGCUGGGCUGCUCGACUGGCCCAUAAUAAUAAACAUGCAAACAACAAUCACGACCCA--
....((((((..((((..(((((.(((.((((..((.....))..)))).))).)))))..))))(((((........))))).............................))))))-- ( -36.50)
>DroYak_CAF1 146726 120 - 1
CUCUUGGGUCUCCGUUAUGGCUCCCGAUUGGACGGCAUUUUGUGUUCCAUUCGAGACUUCCGGCUGGUCUUCUCGACUGGCCCAUAAUAAUAAACAUGCAAACAACAAUCACGACCCAUC
....((((((...((((((..((.(((.((((..((.....))..)))).))).)).....(((..(((.....)))..)))))))))........((....))........)))))).. ( -35.30)
>consensus
CUCUUGGGUCUCAGUUAUGGCUCCCGAUUGGACGGCAUUUUGUGUUCCAUUCGAGACUUCCGGCUGGGCUUCUCGACUGGCCCAUAAUAAUAAACAUGCAAACAACAAUCACGACCCA__
....((((((........((...))(((((....((((.(((((..(((.((((((..(((....)))..)))))).)))..)))))........))))......)))))..)))))).. (-32.74 = -33.34 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:59 2006