Locus 2318

Sequence ID	X_DroMel_CAF1
Location	6,249,150 – 6,249,279
Length	129
Max. P	0.996578

overview

Window 5

Location	6,249,150 – 6,249,248
Length	98
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	71.13
Mean single sequence MFE	-21.98
Consensus MFE	-13.31
Energy contribution	-13.20
Covariance contribution	-0.11
Combinations/Pair	1.10
Mean z-score	-1.49
Structure conservation index	0.61
SVM decision value	0.55
SVM RNA-class probability	0.777394
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6249150 98 + 22224390
AUU-------GCCACAUGAAAAUUGCACACGGAAUGGACUCAUUAAACUUGCAACAUUUUGCGACUUUCGCAAUCAAUUUAUAAAAUAAUGUGCGC--AAGUACUUU-------------
.((-------(((((((.....(((((.....((((....)))).....)))))....(((((.....)))))...............))))).))--)).......------------- ( -21.20)
>DroSec_CAF1 15941 94 + 1
A-----------CCCAUGGAAACUGCACACGAAAUGGGCUCAUUAAACUUGCAACAUUUUGCGA--UUCGCAAUCAAUUUAUAUAAUAAAGUGCGCACAAGUACUUU-------------
.-----------((((((....)..........)))))..........((((((....))))))--.....................(((((((......)))))))------------- ( -15.10)
>DroYak_CAF1 23052 113 + 1
CCACUUCUGCGGCCCAUGAAUACUGCAGCGUGAAUGGGCUCAUUAAACUUGCAACAGU-UGCGA--UUCGCAAUCAAUUCAUAU--UAAUAUGCGC--AAGUACUUUAUGCUCGGCCACA
......((((((..........)))))).(((..(((((.......((((((....((-((((.--..)))))).....((((.--...)))).))--)))).......)))))..))). ( -29.64)
>consensus
A_________G_CCCAUGAAAACUGCACACGGAAUGGGCUCAUUAAACUUGCAACAUUUUGCGA__UUCGCAAUCAAUUUAUAUAAUAAUGUGCGC__AAGUACUUU_____________
...............(((((...((((.....((((....)))).....))))......((((.....)))).....)))))........((((......))))................ (-13.31 = -13.20 +  -0.11)

alignment

secondary structure

dotplot

Window 6

Location	6,249,183 – 6,249,279
Length	96
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	76.66
Mean single sequence MFE	-23.12
Consensus MFE	-15.20
Energy contribution	-15.95
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.54
Structure conservation index	0.66
SVM decision value	2.72
SVM RNA-class probability	0.996578
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6249183 96 + 22224390
CAUUAAACUUGCAACAUUUUGCGACUUUCGCAAUCAAUUUAUAAAAUAAUGUGCGC--AAGUACUUU-------------------AGCUGCAUUUUUAAUGACGAACUA---UUAGUGA
(((((((..((((.(...(((((.....))))).............(((.((((..--..)))).))-------------------)).))))..)))))))........---....... ( -23.30)
>DroSec_CAF1 15970 99 + 1
CAUUAAACUUGCAACAUUUUGCGA--UUCGCAAUCAAUUUAUAUAAUAAAGUGCGCACAAGUACUUU-------------------AGCUGCAUUUUUAAUGGCGCACUAUUAUUAGUGA
(((((((..((((.(...(((((.--..))))).............((((((((......)))))))-------------------)).))))..)))))))...(((((....))))). ( -27.10)
>DroEre_CAF1 10676 110 + 1
CAUUAAACUUGCAACAGU-UGCCA--CUCGCAAUCAAUUCAUAU--UAAUAUGCGC--AAGUACUUAAUACUCGGCCACAAUAAACAGCUGCAUUUUUAAUGGCAAACUA---UUAGAGA
.(((((((((((....((-(((..--...))))).....((((.--...)))).))--))))..)))))...((((...........))))..((((((((((....)))---))))))) ( -19.00)
>DroYak_CAF1 23092 110 + 1
CAUUAAACUUGCAACAGU-UGCGA--UUCGCAAUCAAUUCAUAU--UAAUAUGCGC--AAGUACUUUAUGCUCGGCCACAAUGAAGAGCUGCAGUUUUAAUGCCAAACUA---UUAGAGA
(((((((.(((((...((-((((.--..))))))..........--(((..(((..--..)))..))).((((..(......)..))))))))).)))))))........---....... ( -23.10)
>consensus
CAUUAAACUUGCAACAGU_UGCGA__UUCGCAAUCAAUUCAUAU__UAAUAUGCGC__AAGUACUUU___________________AGCUGCAUUUUUAAUGGCAAACUA___UUAGAGA
(((((((..((((.(....((((.....))))..................((((......)))).......................).))))..))))))).................. (-15.20 = -15.95 +   0.75)

alignment

secondary structure

dotplot

Window 7

Location	6,249,183 – 6,249,279
Length	96
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	76.66
Mean single sequence MFE	-23.90
Consensus MFE	-15.75
Energy contribution	-16.00
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.72
Structure conservation index	0.66
SVM decision value	0.46
SVM RNA-class probability	0.746464
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6249183 96 - 22224390
UCACUAA---UAGUUCGUCAUUAAAAAUGCAGCU-------------------AAAGUACUU--GCGCACAUUAUUUUAUAAAUUGAUUGCGAAAGUCGCAAAAUGUUGCAAGUUUAAUG
.......---........(((((((..((((((.-------------------...((((((--.((((.((((..........)))))))).)))).)).....))))))..))))))) ( -21.10)
>DroSec_CAF1 15970 99 - 1
UCACUAAUAAUAGUGCGCCAUUAAAAAUGCAGCU-------------------AAAGUACUUGUGCGCACUUUAUUAUAUAAAUUGAUUGCGAA--UCGCAAAAUGUUGCAAGUUUAAUG
.(((((....)))))...(((((((..(((((((-------------------(((((.(......).)))))).............(((((..--.)))))...))))))..))))))) ( -22.40)
>DroEre_CAF1 10676 110 - 1
UCUCUAA---UAGUUUGCCAUUAAAAAUGCAGCUGUUUAUUGUGGCCGAGUAUUAAGUACUU--GCGCAUAUUA--AUAUGAAUUGAUUGCGAG--UGGCA-ACUGUUGCAAGUUUAAUG
.......---........(((((((..((((((.((....(((.(((((((((...))))))--)((((.((((--((....)))))))))).)--).)))-)).))))))..))))))) ( -28.60)
>DroYak_CAF1 23092 110 - 1
UCUCUAA---UAGUUUGGCAUUAAAACUGCAGCUCUUCAUUGUGGCCGAGCAUAAAGUACUU--GCGCAUAUUA--AUAUGAAUUGAUUGCGAA--UCGCA-ACUGUUGCAAGUUUAAUG
.......---........(((((((..((((((......((((((....(((.........)--))(((.((((--((....)))))))))...--)))))-)..))))))..))))))) ( -23.50)
>consensus
UCACUAA___UAGUUCGCCAUUAAAAAUGCAGCU___________________AAAGUACUU__GCGCACAUUA__AUAUAAAUUGAUUGCGAA__UCGCA_AAUGUUGCAAGUUUAAUG
..................(((((((..((((((.......................(..(....)..)....................((((.....))))....))))))..))))))) (-15.75 = -16.00 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:26 2006