Locus 1924

Sequence ID	3L_DroMel_CAF1
Location	5,379,203 – 5,379,378
Length	175
Max. P	0.913308

overview

Window 9

Location	5,379,203 – 5,379,307
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	92.68
Mean single sequence MFE	-26.52
Consensus MFE	-23.64
Energy contribution	-23.87
Covariance contribution	0.22
Combinations/Pair	1.04
Mean z-score	-1.68
Structure conservation index	0.89
SVM decision value	1.09
SVM RNA-class probability	0.913308
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5379203 104 + 23771897
---------AG-------GGAACAUCAUCAACAGCAACUUAAGUAGCUCAAUAAAUCUUGAGCUUAACAUUUGUUGAAGCUUUUGCCAGUUGGCAAACGUGACUUGUGUGCGACACAAAU
---------.(-------....)........((((((.......(((((((......)))))))......))))))..((.((((((....)))))).))...(((((.....))))).. ( -26.62)
>DroSec_CAF1 28479 104 + 1
---------AG-------GGAACAUCAUCAACAGCAACUUAAGUAGCACAAUAAAUCUUGAGCUUAACAUUUGUUGAAGCUUUUGCCAGUUGGCAAACGUGACUUGUGUGCGACACAAAU
---------.(-------....)..........(((...(((((..(((..........(((((((((....)))).)))))(((((....)))))..))))))))..)))......... ( -23.20)
>DroSim_CAF1 26651 104 + 1
---------AG-------GGAACAUCAUCAACAGCAACUUAAGUAGCUCAAUAAAUCUUGAGCUUAACAUUUGUUGAAGCUUUUGCCAGUUGGCAAACGUGACUUGUGUGCGACACAAAU
---------.(-------....)........((((((.......(((((((......)))))))......))))))..((.((((((....)))))).))...(((((.....))))).. ( -26.62)
>DroEre_CAF1 28541 104 + 1
---------AG-------GGAACAUCAUCAACAGCAACUUAAGUAGCUCAAUAAAUCUUGAGCUUAACAUUUGUUGAAGCUUUUGCCAGUUGGCAAACGUGACUUGUGUGCGACACAAAU
---------.(-------....)........((((((.......(((((((......)))))))......))))))..((.((((((....)))))).))...(((((.....))))).. ( -26.62)
>DroYak_CAF1 27032 104 + 1
---------AA-------GGAACAUCAUCAACAGCAACUUAAGUAGCUCAAUAAAUCUUGAGCUUAACAUUUGUUGAAGCUUUUGCCAGUUGGCAAACGUGACUUGUGUGCGACACCAAU
---------((-------(..((........((((((.......(((((((......)))))))......)))))).....((((((....)))))).))..)))(((.....))).... ( -25.82)
>DroAna_CAF1 26485 120 + 1
GCGAGUGGCAGGGCAAAAAGAACAUCAUCAACAGCAACUUAAGUAGCUCAAUAAAUCUUGGGCUUAACAUUUGUUGAAGCUUUUGCCAGUUGGCAAACGUGACUGGAGUGCGACAGAAAU
.(((.(((((((((.....((......))..((((((.......(((((((......)))))))......))))))..)).))))))).)))..........(((........))).... ( -30.22)
>consensus
_________AG_______GGAACAUCAUCAACAGCAACUUAAGUAGCUCAAUAAAUCUUGAGCUUAACAUUUGUUGAAGCUUUUGCCAGUUGGCAAACGUGACUUGUGUGCGACACAAAU
.................................(((...(((((.((((((......))))))(((((....))))).((.((((((....)))))).)).)))))..)))......... (-23.64 = -23.87 +   0.22)

alignment

secondary structure

dotplot

Window 0

Location	5,379,203 – 5,379,307
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	92.68
Mean single sequence MFE	-25.88
Consensus MFE	-23.28
Energy contribution	-24.28
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.54
Structure conservation index	0.90
SVM decision value	0.96
SVM RNA-class probability	0.889814
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5379203 104 - 23771897
AUUUGUGUCGCACACAAGUCACGUUUGCCAACUGGCAAAAGCUUCAACAAAUGUUAAGCUCAAGAUUUAUUGAGCUACUUAAGUUGCUGUUGAUGAUGUUCC-------CU---------
..(((((.....)))))((((..((((((....))))))(((..((((....((..(((((((......)))))))))....))))..)))..)))).....-------..--------- ( -27.50)
>DroSec_CAF1 28479 104 - 1
AUUUGUGUCGCACACAAGUCACGUUUGCCAACUGGCAAAAGCUUCAACAAAUGUUAAGCUCAAGAUUUAUUGUGCUACUUAAGUUGCUGUUGAUGAUGUUCC-------CU---------
(((((.((.(((((.(((((...((((((....))))))(((((.(((....))))))))...)))))..))))).)).)))))..................-------..--------- ( -24.70)
>DroSim_CAF1 26651 104 - 1
AUUUGUGUCGCACACAAGUCACGUUUGCCAACUGGCAAAAGCUUCAACAAAUGUUAAGCUCAAGAUUUAUUGAGCUACUUAAGUUGCUGUUGAUGAUGUUCC-------CU---------
..(((((.....)))))((((..((((((....))))))(((..((((....((..(((((((......)))))))))....))))..)))..)))).....-------..--------- ( -27.50)
>DroEre_CAF1 28541 104 - 1
AUUUGUGUCGCACACAAGUCACGUUUGCCAACUGGCAAAAGCUUCAACAAAUGUUAAGCUCAAGAUUUAUUGAGCUACUUAAGUUGCUGUUGAUGAUGUUCC-------CU---------
..(((((.....)))))((((..((((((....))))))(((..((((....((..(((((((......)))))))))....))))..)))..)))).....-------..--------- ( -27.50)
>DroYak_CAF1 27032 104 - 1
AUUGGUGUCGCACACAAGUCACGUUUGCCAACUGGCAAAAGCUUCAACAAAUGUUAAGCUCAAGAUUUAUUGAGCUACUUAAGUUGCUGUUGAUGAUGUUCC-------UU---------
....(((.....)))..((((..((((((....))))))(((..((((....((..(((((((......)))))))))....))))..)))..)))).....-------..--------- ( -25.70)
>DroAna_CAF1 26485 120 - 1
AUUUCUGUCGCACUCCAGUCACGUUUGCCAACUGGCAAAAGCUUCAACAAAUGUUAAGCCCAAGAUUUAUUGAGCUACUUAAGUUGCUGUUGAUGAUGUUCUUUUUGCCCUGCCACUCGC
......((.(((...((((.((.((((((....))))))((((.(((.((((.((......)).)))).)))))))......)).))))..((......)).........))).)).... ( -22.40)
>consensus
AUUUGUGUCGCACACAAGUCACGUUUGCCAACUGGCAAAAGCUUCAACAAAUGUUAAGCUCAAGAUUUAUUGAGCUACUUAAGUUGCUGUUGAUGAUGUUCC_______CU_________
..(((((.....)))))((((..((((((....))))))(((..((((....((..(((((((......)))))))))....))))..)))..))))....................... (-23.28 = -24.28 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	5,379,267 – 5,379,378
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.60
Mean single sequence MFE	-29.14
Consensus MFE	-17.88
Energy contribution	-18.93
Covariance contribution	1.06
Combinations/Pair	1.08
Mean z-score	-1.85
Structure conservation index	0.61
SVM decision value	0.34
SVM RNA-class probability	0.695635
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5379267 111 - 23771897
CAUGGGGCUCGCUAUCCUAUCCAACCAAAUGCGAGGGGACUGGCAAACAGACAGAGCUCC--GAAGUA-------CCCACAUUUGUGUCGCACACAAGUCACGUUUGCCAACUGGCAAAA
..((((((((....((((.((((......)).)).))))(((.....)))...)))))))--).....-------.....(((((((.....)))))))....((((((....)))))). ( -34.80)
>DroSec_CAF1 28543 95 - 1
CAAGGGGCUCGCUAUCCUAUCCA----------------CUGGCAAACAGACAGAGCUCC--GAAGUA-------CCCACAUUUGUGUCGCACACAAGUCACGUUUGCCAACUGGCAAAA
...(((((((.((..((......----------------..)).....))...)))))))--......-------.....(((((((.....)))))))....((((((....)))))). ( -26.40)
>DroSim_CAF1 26715 95 - 1
CAAGGGGCUCGCUAUCCUAUCCA----------------CUGGCAAACAGACAGAGCUCC--GAAGUA-------CCCACAUUUGUGUCGCACACAAGUCACGUUUGCCAACUGGCAAAA
...(((((((.((..((......----------------..)).....))...)))))))--......-------.....(((((((.....)))))))....((((((....)))))). ( -26.40)
>DroEre_CAF1 28605 107 - 1
CAAGGGGCUCGCUAUCCUAUCCAACCAAAUGCGA----GCUGGCAAACAGACAGAGCUCC--GAAGUA-------CCCACAUUUGUGUCGCACACAAGUCACGUUUGCCAACUGGCAAAA
...(((((((((..................))..----((((.....))).).)))))))--......-------.....(((((((.....)))))))....((((((....)))))). ( -29.57)
>DroYak_CAF1 27096 107 - 1
CAAGGGGCUCGCUAUCCUAUCCCACCAAAUGCGA----ACUGGCAAACAGACAGAGCUCC--GAAGUA-------CUCACAUUGGUGUCGCACACAAGUCACGUUUGCCAACUGGCAAAA
...(((((((((..................))..----.(((.....)))...)))))))--......-------.........(((.(........).))).((((((....)))))). ( -27.47)
>DroAna_CAF1 26565 99 - 1
C--GUGGCUCACAUGCCGGU-------------------CGGUUAGACAGACAGACUUCUUGGUAAUAUCCAGCUCACACAUUUCUGUCGCACUCCAGUCACGUUUGCCAACUGGCAAAA
(--((((((....(((..((-------------------(.....))).((((((.....(((......)))(......)...)))))))))....)))))))((((((....)))))). ( -30.20)
>consensus
CAAGGGGCUCGCUAUCCUAUCCA________________CUGGCAAACAGACAGAGCUCC__GAAGUA_______CCCACAUUUGUGUCGCACACAAGUCACGUUUGCCAACUGGCAAAA
...((((((((.....)......................(((.....)))...)))))))....................(((((((.....)))))))....((((((....)))))). (-17.88 = -18.93 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:05 2006