Locus 887

Sequence ID	X_DroMel_CAF1
Location	2,503,134 – 2,503,231
Length	97
Max. P	0.999451

overview

Window 0

Location	2,503,134 – 2,503,231
Length	97
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.37
Mean single sequence MFE	-28.88
Consensus MFE	-25.46
Energy contribution	-25.38
Covariance contribution	-0.08
Combinations/Pair	1.15
Mean z-score	-3.65
Structure conservation index	0.88
SVM decision value	3.61
SVM RNA-class probability	0.999451
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2503134 97 + 22224390
GAAAAUCACGAAAAGA--------GCUAUCAACAU---GGCCUAAAGUGACCAAUGAAUUGGAGUUUAUUUCACGGCGUUGUGAAAUAUGCUCCAACUUUAAC------CC--A----AA
.....((((....((.--------(((((....))---)))))...))))....(((((((((((.(((((((((....))))))))).))))))).))))..------..--.----.. ( -27.80)
>DroSec_CAF1 1820 97 + 1
GAAAAUCACGAAAAGA--------GCUAUCAACAU---GGCCCAAAGUGGCCAAUGAAUUGGAGUUUAUUUCACGUCGUUGUGAAAUGUGCUCCAACUUUAAC------CC--A----AA
...........((((.--------........(((---((((......)))).)))..(((((((.(((((((((....))))))))).)))))))))))...------..--.----.. ( -29.30)
>DroSim_CAF1 2794 97 + 1
GAAAAUCACGAAAAGA--------GCUAUCAACAU---GGCCUAAAGUGGCCAAUGAAUUGGAGUUUAUUUCACGGCGUUGUGAAAUGUGCUCCAACUUUAAC------CC--A----AA
...........((((.--------........(((---((((......)))).)))..(((((((.(((((((((....))))))))).)))))))))))...------..--.----.. ( -29.40)
>DroEre_CAF1 1891 107 + 1
AAAAAUCACGCAAAGA--------GCCGUCGACAUAGUGGCCCAAAGUGGCCAAUGAAUUGGAGUUUGUUUCACGGCAUUGUGAAAUAUGCUCCAACUUUAACUUUAACCC-----AAAA
...........((((.--------.............(((((......))))).(((((((((((.(((((((((....))))))))).))))))).)))).)))).....-----.... ( -28.80)
>DroYak_CAF1 2953 118 + 1
GAAAAUCACAAAAAGAUAGAAAUCACUAUCAGCAU--UAGUCUAAAGUGGCCAAUGAAAUGGAGUUUAUUUCACAGCGUUGUGAAAUAUGCUCCAACUUUAACUUUGCCCCUCAAAAAAA
..............(((((......))))).(((.--.(((.((((((...........((((((.((((((((......)))))))).))))))))))))))).)))............ ( -29.10)
>consensus
GAAAAUCACGAAAAGA________GCUAUCAACAU___GGCCUAAAGUGGCCAAUGAAUUGGAGUUUAUUUCACGGCGUUGUGAAAUAUGCUCCAACUUUAAC______CC__A____AA
...........((((.................(((...((((......)))).)))..(((((((.(((((((((....))))))))).))))))))))).................... (-25.46 = -25.38 +  -0.08)

alignment

secondary structure

dotplot

Window 1

Location	2,503,134 – 2,503,231
Length	97
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.37
Mean single sequence MFE	-29.46
Consensus MFE	-20.30
Energy contribution	-21.26
Covariance contribution	0.96
Combinations/Pair	1.11
Mean z-score	-2.90
Structure conservation index	0.69
SVM decision value	2.13
SVM RNA-class probability	0.988673
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2503134 97 - 22224390
UU----U--GG------GUUAAAGUUGGAGCAUAUUUCACAACGCCGUGAAAUAAACUCCAAUUCAUUGGUCACUUUAGGCC---AUGUUGAUAGC--------UCUUUUCGUGAUUUUC
..----.--((------((((..(((((((..((((((((......))))))))..)))))))(((.(((((......))))---)...)))))))--------)).............. ( -30.00)
>DroSec_CAF1 1820 97 - 1
UU----U--GG------GUUAAAGUUGGAGCACAUUUCACAACGACGUGAAAUAAACUCCAAUUCAUUGGCCACUUUGGGCC---AUGUUGAUAGC--------UCUUUUCGUGAUUUUC
..----.--((------((((..(((((((...(((((((......)))))))...)))))))(((.(((((......))))---)...)))))))--------)).............. ( -30.50)
>DroSim_CAF1 2794 97 - 1
UU----U--GG------GUUAAAGUUGGAGCACAUUUCACAACGCCGUGAAAUAAACUCCAAUUCAUUGGCCACUUUAGGCC---AUGUUGAUAGC--------UCUUUUCGUGAUUUUC
..----.--((------((((..(((((((...(((((((......)))))))...)))))))(((.(((((......))))---)...)))))))--------)).............. ( -30.60)
>DroEre_CAF1 1891 107 - 1
UUUU-----GGGUUAAAGUUAAAGUUGGAGCAUAUUUCACAAUGCCGUGAAACAAACUCCAAUUCAUUGGCCACUUUGGGCCACUAUGUCGACGGC--------UCUUUGCGUGAUUUUU
....-----((((....(((..((((((((....((((((......))))))....))))))))...(((((......))))).......))).))--------)).............. ( -26.40)
>DroYak_CAF1 2953 118 - 1
UUUUUUUGAGGGGCAAAGUUAAAGUUGGAGCAUAUUUCACAACGCUGUGAAAUAAACUCCAUUUCAUUGGCCACUUUAGACUA--AUGCUGAUAGUGAUUUCUAUCUUUUUGUGAUUUUC
....((((((((((...........(((((..(((((((((....)))))))))..)))))........))).)))))))...--.....(((((......))))).............. ( -29.81)
>consensus
UU____U__GG______GUUAAAGUUGGAGCAUAUUUCACAACGCCGUGAAAUAAACUCCAAUUCAUUGGCCACUUUAGGCC___AUGUUGAUAGC________UCUUUUCGUGAUUUUC
.................(((((((((((((..((((((((......))))))))..))))))))(((.((((......))))...))))))))........................... (-20.30 = -21.26 +   0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:19 2006