Locus 10174

Sequence ID	3R_DroMel_CAF1
Location	27,303,904 – 27,304,039
Length	135
Max. P	0.910383

overview

Window 9

Location	27,303,904 – 27,304,008
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.88
Mean single sequence MFE	-35.69
Consensus MFE	-23.59
Energy contribution	-23.46
Covariance contribution	-0.13
Combinations/Pair	1.30
Mean z-score	-2.21
Structure conservation index	0.66
SVM decision value	1.07
SVM RNA-class probability	0.910383
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27303904 104 + 27905053
GGCUAGCGGAAUUCUUAAAAAUGC--------------AGAAGCCGCAUUUCUUGUCUCGAGAAUCCACUGAAAGAUUCUGGGGCAGAAUG--CUGGCGGUUCCCAGAACUGUGAGUAUU
.....((((..((((.........--------------)))).)))).....(((((((.((((((........)))))))))))))((((--((.(((((((...))))))).)))))) ( -34.60)
>DroSec_CAF1 8874 104 + 1
GGCUAGCGGAAUUCCUAAAAACGC--------------AGAAGCCGCAUUUCUUGUCUCGAGAAUCCAGUGAAAGAUUCUGGGGCAGAAUG--CUGGCGGUUCCCAGAACUGUCAGCAUU
((((.(((.............)))--------------...)))).......(((((((.((((((........)))))))))))))((((--((((((((((...)))))))))))))) ( -40.72)
>DroSim_CAF1 9297 104 + 1
GGCUAGCGGAAUUCUUAAAAACGC--------------AGAAGCCGCAUUUCUUGUCUCGAGCAUCCAGUGAAAGAUUCUGGGGCAGAAUG--CUGGCGGUUCCCAGAACUGUCAGCAUU
((((.(((.............)))--------------...)))).......(((((((.((.(((........))).)))))))))((((--((((((((((...)))))))))))))) ( -36.32)
>DroEre_CAF1 9114 104 + 1
GGCUAUCGGAAUUCUUUAAAAUGC--------------AGAAGCCGCAUUUCUCGUCUCGGGAAUCCAGCGCCAGAUUCUGGGUCAGAAUG--CUGACGGUUCCCAGAACUGUCAGCAUU
((((..(((((((.........((--------------....))(((..((((((...))))))....)))...)))))))))))..((((--((((((((((...)))))))))))))) ( -35.70)
>DroYak_CAF1 5174 104 + 1
GGCUAGCGGAAUUCUUUAAAAAGC--------------AGAAGCCGCAUUUCUUGUCUCGAGAAUCCAGCGCCAGAUUCUGGGGCAGAAUG--UUGACGGUUCUCAGAACUGUCAGCAUU
.....((((..((((.........--------------)))).)))).....(((((((.((((((........)))))))))))))((((--((((((((((...)))))))))))))) ( -38.00)
>DroAna_CAF1 10279 120 + 1
GUCUAGACGAGUUCCCUAAAACGCCAAGACAGUUAUGCGGCAGAAGCUUUUAUUCUCCUGGGAAUCCAUCGUCGGAUUCUGGGGCAUGUUUAUCCGUCACUUCCAAGAACUGUCAGCACC
......................((...(((((((....((.((..((...((..(.(((.(((((((......))))))).)))...)..))...))..)).))...))))))).))... ( -28.80)
>consensus
GGCUAGCGGAAUUCUUAAAAACGC______________AGAAGCCGCAUUUCUUGUCUCGAGAAUCCAGCGAAAGAUUCUGGGGCAGAAUG__CUGGCGGUUCCCAGAACUGUCAGCAUU
((((.....................................))))((..((((.(((((.((((((........))))))))))))))).....(((((((((...)))))))))))... (-23.59 = -23.46 +  -0.13)

alignment

secondary structure

dotplot

Window 0

Location	27,303,930 – 27,304,039
Length	109
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.49
Mean single sequence MFE	-32.92
Consensus MFE	-22.80
Energy contribution	-22.80
Covariance contribution	0.00
Combinations/Pair	1.32
Mean z-score	-1.68
Structure conservation index	0.69
SVM decision value	0.14
SVM RNA-class probability	0.604708
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27303930 109 + 27905053
AAGCCGCAUUUCUUGUCUCGAGAAUCCACUGAAAGAUUCUGGGGCAGAAUG--CUGGCGGUUCCCAGAACUGUGAGUAUUGCUGAUG---------UCUCCUUUUACAGAUCAAUAACAC
..(((((((((..((((((.((((((........)))))))))))))))))--).)))........((.(((((((....((....)---------).....))))))).))........ ( -32.30)
>DroSec_CAF1 8900 109 + 1
AAGCCGCAUUUCUUGUCUCGAGAAUCCAGUGAAAGAUUCUGGGGCAGAAUG--CUGGCGGUUCCCAGAACUGUCAGCAUUGCUGAUG---------UCUCCUUUUACAGAUCAAUAACAC
.(((........(((((((.((((((........)))))))))))))((((--((((((((((...)))))))))))))))))...(---------(((........))))......... ( -35.30)
>DroSim_CAF1 9323 109 + 1
AAGCCGCAUUUCUUGUCUCGAGCAUCCAGUGAAAGAUUCUGGGGCAGAAUG--CUGGCGGUUCCCAGAACUGUCAGCAUUGCUGAAG---------UCUCCUUUUACAGAUCAAUAACAC
..((((((.....))...)).)).....(((((((...((..((((..(((--((((((((((...)))))))))))))))))..))---------....)))))))............. ( -32.80)
>DroEre_CAF1 9140 109 + 1
AAGCCGCAUUUCUCGUCUCGGGAAUCCAGCGCCAGAUUCUGGGUCAGAAUG--CUGACGGUUCCCAGAACUGUCAGCAUUGCUGAUG---------UCUCCUUUUAUAGAUCAAUAACAC
....(((..((((((...))))))....)))((((...))))(((((((((--((((((((((...)))))))))))))).)))))(---------(((........))))......... ( -37.30)
>DroYak_CAF1 5200 109 + 1
AAGCCGCAUUUCUUGUCUCGAGAAUCCAGCGCCAGAUUCUGGGGCAGAAUG--UUGACGGUUCUCAGAACUGUCAGCAUUGCUGAUG---------UCUCCUUUUAUAGAUCAAUAACAC
.(((........(((((((.((((((........)))))))))))))((((--((((((((((...)))))))))))))))))...(---------(((........))))......... ( -33.40)
>DroAna_CAF1 10319 120 + 1
CAGAAGCUUUUAUUCUCCUGGGAAUCCAUCGUCGGAUUCUGGGGCAUGUUUAUCCGUCACUUCCAAGAACUGUCAGCACCGUAGAUGAAGCCGCGUUCCCCGUUUGUGGAUCAAUAAUGC
((.((((.............(((((((......)))))))((((.(((((((((((...((..((.....))..))...))..)))))....)))).)))))))).))............ ( -26.40)
>consensus
AAGCCGCAUUUCUUGUCUCGAGAAUCCAGCGAAAGAUUCUGGGGCAGAAUG__CUGGCGGUUCCCAGAACUGUCAGCAUUGCUGAUG_________UCUCCUUUUACAGAUCAAUAACAC
.....(((.((((.(((((.((((((........)))))))))))))))....((((((((((...))))))))))...)))...................................... (-22.80 = -22.80 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:50:38 2006