Locus 1834

Sequence ID	2L_DroMel_CAF1
Location	5,068,548 – 5,068,695
Length	147
Max. P	0.994372

overview

Window 2

Location	5,068,548 – 5,068,659
Length	111
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	72.25
Mean single sequence MFE	-32.10
Consensus MFE	-23.49
Energy contribution	-23.80
Covariance contribution	0.31
Combinations/Pair	1.09
Mean z-score	-2.14
Structure conservation index	0.73
SVM decision value	2.28
SVM RNA-class probability	0.991650
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5068548 111 + 22407834
UGCAUACGUAUGUAUUAUACAUGUAUGAU--CACAUUGGCUUGUGGGCGUGGCACUUCAAUUGGGCUGACUUUGCCUGGCUGGAAAAGCGG-CACCUAAUUGAAAUGCCCGCCG
..(((((((.(((...))).)))))))..--((((......))))((((.((((.(((((((((((((.((((.((.....)).)))))))-).)).))))))).)))))))). ( -44.60)
>DroPse_CAF1 1569 95 + 1
UCUGUAUGUCU---------GUGU----G-CG-CAUUGGGUUG-GGGCGUGGCACUUCAAUUUGGC--GCUUUGCCUGGCUGUAAAAGCUG-CAACUAAUUGAAAUGUCCGCCA
...((((....---------..))----)-).-..........-.((((.((((.(((((((..((--(((((..(.....)..))))).)-)....))))))).)))))))). ( -27.80)
>DroEre_CAF1 1728 89 + 1
---------------------UUUAUGAU--C-CAUUGGCUUGUGGGCGUGGCACUUCAAUUGGUCUGACUUUGCCCGGCUGGAAAAGCGG-CACCUAAUUGAAAUGCCCGCCA
---------------------........--.-(((......)))((((.((((.(((((((((((((.((((.((.....)).)))))))-.))).))))))).)))))))). ( -33.00)
>DroYak_CAF1 1708 91 + 1
---------------------UAUACUAUAAU-CAUUGGCUUGUGGGCGUGGCACUUCAAUUGGUCUGACUUUGCCCGACUGGAAAAGCGG-CACCUAAUUGAAAUGCCCGCCA
---------------------...........-(((......)))((((.((((.(((((((((((((.((((.((.....)).)))))))-.))).))))))).)))))))). ( -32.80)
>DroAna_CAF1 1752 86 + 1
UGUAU--------------------------A-CAUAUG-UUGUGGGCGUGGCACUUCAAUUGGUCUAACUUUCCCGGAAUGGUAAAGCAGUCACUUAAUUGAAAUGCCCGCCA
....(--------------------------(-((....-.))))((((.((((.((((((((((....((((.((.....)).)))).....)).)))))))).)))))))). ( -26.60)
>DroPer_CAF1 1569 95 + 1
UCUGUAUGUCU---------GUGU----G-CG-CAUUGGGUUG-GGGCGUGGCACUUCAAUUUGGC--GCUUUGCCUGGCUGUAAAAGCUG-CAACUAAUUGAAAUGUCCGCCA
...((((....---------..))----)-).-..........-.((((.((((.(((((((..((--(((((..(.....)..))))).)-)....))))))).)))))))). ( -27.80)
>consensus
U_U_U________________UGU____U__C_CAUUGGCUUGUGGGCGUGGCACUUCAAUUGGGCUGACUUUGCCUGGCUGGAAAAGCGG_CACCUAAUUGAAAUGCCCGCCA
.............................................((((.((((.(((((((((.....((((.((.....)).)))).......))))))))).)))))))). (-23.49 = -23.80 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	5,068,548 – 5,068,659
Length	111
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	72.25
Mean single sequence MFE	-30.63
Consensus MFE	-24.52
Energy contribution	-25.13
Covariance contribution	0.61
Combinations/Pair	1.04
Mean z-score	-2.96
Structure conservation index	0.80
SVM decision value	2.13
SVM RNA-class probability	0.988689
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5068548 111 - 22407834
CGGCGGGCAUUUCAAUUAGGUG-CCGCUUUUCCAGCCAGGCAAAGUCAGCCCAAUUGAAGUGCCACGCCCACAAGCCAAUGUG--AUCAUACAUGUAUAAUACAUACGUAUGCA
.((((((((((((((((.(((.-..(((((.((.....)).)))))..))).)))))))))))).))))((((......))))--..((((((((((...)))))..))))).. ( -42.50)
>DroPse_CAF1 1569 95 - 1
UGGCGGACAUUUCAAUUAGUUG-CAGCUUUUACAGCCAGGCAAAGC--GCCAAAUUGAAGUGCCACGCCC-CAACCCAAUG-CG-C----ACAC---------AGACAUACAGA
.(((((.((((((((((.....-..(((.....)))..(((.....--))).)))))))))).).)))).-..........-..-.----....---------........... ( -22.80)
>DroEre_CAF1 1728 89 - 1
UGGCGGGCAUUUCAAUUAGGUG-CCGCUUUUCCAGCCGGGCAAAGUCAGACCAAUUGAAGUGCCACGCCCACAAGCCAAUG-G--AUCAUAAA---------------------
.((((((((((((((((.(((.-..((((((((....))).)))))...))))))))))))))).))))............-.--........--------------------- ( -33.50)
>DroYak_CAF1 1708 91 - 1
UGGCGGGCAUUUCAAUUAGGUG-CCGCUUUUCCAGUCGGGCAAAGUCAGACCAAUUGAAGUGCCACGCCCACAAGCCAAUG-AUUAUAGUAUA---------------------
.((((((((((((((((.(((.-..((((((((....))).)))))...))))))))))))))).))))............-...........--------------------- ( -33.50)
>DroAna_CAF1 1752 86 - 1
UGGCGGGCAUUUCAAUUAAGUGACUGCUUUACCAUUCCGGGAAAGUUAGACCAAUUGAAGUGCCACGCCCACAA-CAUAUG-U--------------------------AUACA
.((((((((((((((((..((....(((((.((.....)).)))))...)).)))))))))))).)))).....-......-.--------------------------..... ( -28.70)
>DroPer_CAF1 1569 95 - 1
UGGCGGACAUUUCAAUUAGUUG-CAGCUUUUACAGCCAGGCAAAGC--GCCAAAUUGAAGUGCCACGCCC-CAACCCAAUG-CG-C----ACAC---------AGACAUACAGA
.(((((.((((((((((.....-..(((.....)))..(((.....--))).)))))))))).).)))).-..........-..-.----....---------........... ( -22.80)
>consensus
UGGCGGGCAUUUCAAUUAGGUG_CCGCUUUUCCAGCCAGGCAAAGUCAGACCAAUUGAAGUGCCACGCCCACAAGCCAAUG_C__A____ACA________________A_A_A
.((((((((((((((((.(......(((((.((.....)).)))))....).)))))))))))).))))............................................. (-24.52 = -25.13 +   0.61)

alignment

secondary structure

dotplot

Window 4

Location	5,068,585 – 5,068,695
Length	110
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	74.66
Mean single sequence MFE	-34.72
Consensus MFE	-23.78
Energy contribution	-23.95
Covariance contribution	0.17
Combinations/Pair	1.13
Mean z-score	-2.77
Structure conservation index	0.69
SVM decision value	2.47
SVM RNA-class probability	0.994372
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5068585 110 + 22407834
CUUGUGGGCGUGGCACUUCAAUUGGGCUGACUUUGCCUGGCUGGAAAAGCGG-CACCUAAUUGAAAUGCCCGCCGAUCAGUGCUCGAUUACGAUCGACACAAGCGACAUUU
((((((((((.((((.(((((((((((((.((((.((.....)).)))))))-).)).))))))).))))))))((((.(((......)))))))..))))))........ ( -47.30)
>DroPse_CAF1 1593 105 + 1
GUUG-GGGCGUGGCACUUCAAUUUGGC--GCUUUGCCUGGCUGUAAAAGCUG-CAACUAAUUGAAAUGUCCGCCAAUCAAU--UAAGCAAUAAACAACAUAAGCAACACUU
((((-.((((.((((.(((((((..((--(((((..(.....)..))))).)-)....))))))).)))))))).......--..(....)...))))............. ( -27.50)
>DroSec_CAF1 1727 84 + 1
CUUGUGGGCGUGGCACUUCGAUUGGGCUGACUUUGCCUGGCUGGAAAAGCGG-CACCUAAUUGAAAUGCCCGCCAAU--------------------------CGACAUUU
.(((..((((.((((.(((((((((((((.((((.((.....)).)))))))-).)).))))))).))))))))...--------------------------)))..... ( -36.10)
>DroEre_CAF1 1743 110 + 1
CUUGUGGGCGUGGCACUUCAAUUGGUCUGACUUUGCCCGGCUGGAAAAGCGG-CACCUAAUUGAAAUGCCCGCCAAACAGUGCUCGACCAUGAUCGGCACAAGCGACAUUU
.((((.((((.((((.(((((((((((((.((((.((.....)).)))))))-.))).))))))).)))))))).....((((.(((......)))))))..))))..... ( -42.30)
>DroAna_CAF1 1764 90 + 1
-UUGUGGGCGUGGCACUUCAAUUGGUCUAACUUUCCCGGAAUGGUAAAGCAGUCACUUAAUUGAAAUGCCCGCCAAUC--------------------ACGAGCAACAUUU
-(((((((((.((((.((((((((((....((((.((.....)).)))).....)).)))))))).))))))))...)--------------------))))......... ( -27.60)
>DroPer_CAF1 1593 105 + 1
GUUG-GGGCGUGGCACUUCAAUUUGGC--GCUUUGCCUGGCUGUAAAAGCUG-CAACUAAUUGAAAUGUCCGCCAAUCAAU--UAAGCAAUAAACAACAUAAGCAACAAUU
((((-.((((.((((.(((((((..((--(((((..(.....)..))))).)-)....))))))).)))))))).......--..(....)...))))............. ( -27.50)
>consensus
CUUGUGGGCGUGGCACUUCAAUUGGGCUGACUUUGCCUGGCUGGAAAAGCGG_CACCUAAUUGAAAUGCCCGCCAAUCA_U__U___C_AU_A_C_ACACAAGCAACAUUU
......((((.((((.(((((((((.....((((.((.....)).)))).......))))))))).))))))))..................................... (-23.78 = -23.95 +   0.17)

alignment

secondary structure

dotplot

Window 5

Location	5,068,585 – 5,068,695
Length	110
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	74.66
Mean single sequence MFE	-33.88
Consensus MFE	-23.78
Energy contribution	-24.39
Covariance contribution	0.61
Combinations/Pair	1.04
Mean z-score	-2.52
Structure conservation index	0.70
SVM decision value	2.33
SVM RNA-class probability	0.992526
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5068585 110 - 22407834
AAAUGUCGCUUGUGUCGAUCGUAAUCGAGCACUGAUCGGCGGGCAUUUCAAUUAGGUG-CCGCUUUUCCAGCCAGGCAAAGUCAGCCCAAUUGAAGUGCCACGCCCACAAG
........(((((((((((....))))).........((((((((((((((((.(((.-..(((((.((.....)).)))))..))).)))))))))))).)))))))))) ( -44.70)
>DroPse_CAF1 1593 105 - 1
AAGUGUUGCUUAUGUUGUUUAUUGCUUA--AUUGAUUGGCGGACAUUUCAAUUAGUUG-CAGCUUUUACAGCCAGGCAAAGC--GCCAAAUUGAAGUGCCACGCCC-CAAC
..(((..((((..(((((.....(((((--(((((((((........)))))))))))-.)))....)))))..(((.....--)))......))))..)))....-.... ( -27.20)
>DroSec_CAF1 1727 84 - 1
AAAUGUCG--------------------------AUUGGCGGGCAUUUCAAUUAGGUG-CCGCUUUUCCAGCCAGGCAAAGUCAGCCCAAUCGAAGUGCCACGCCCACAAG
........--------------------------...((((((((((((.(((.(((.-..(((((.((.....)).)))))..))).))).)))))))).))))...... ( -31.00)
>DroEre_CAF1 1743 110 - 1
AAAUGUCGCUUGUGCCGAUCAUGGUCGAGCACUGUUUGGCGGGCAUUUCAAUUAGGUG-CCGCUUUUCCAGCCGGGCAAAGUCAGACCAAUUGAAGUGCCACGCCCACAAG
...........((((((((....)))).))))(((..((((((((((((((((.(((.-..((((((((....))).)))))...))))))))))))))).)))).))).. ( -45.10)
>DroAna_CAF1 1764 90 - 1
AAAUGUUGCUCGU--------------------GAUUGGCGGGCAUUUCAAUUAAGUGACUGCUUUACCAUUCCGGGAAAGUUAGACCAAUUGAAGUGCCACGCCCACAA-
...........((--------------------(...((((((((((((((((..((....(((((.((.....)).)))))...)).)))))))))))).)))))))..- ( -31.00)
>DroPer_CAF1 1593 105 - 1
AAUUGUUGCUUAUGUUGUUUAUUGCUUA--AUUGAUUGGCGGACAUUUCAAUUAGUUG-CAGCUUUUACAGCCAGGCAAAGC--GCCAAAUUGAAGUGCCACGCCC-CAAC
....((((.....(((((.....(((((--(((((((((........)))))))))))-.)))....)))))..(((...((--((.........))))...))).-)))) ( -24.30)
>consensus
AAAUGUCGCUUGUGU_G_U_AU_G___A__A_UGAUUGGCGGGCAUUUCAAUUAGGUG_CCGCUUUUCCAGCCAGGCAAAGUCAGCCCAAUUGAAGUGCCACGCCCACAAG
.....................................((((((((((((((((........(((((.((.....)).)))))......)))))))))))).))))...... (-23.78 = -24.39 +   0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:22 2006