Locus 3290

Sequence ID	X_DroMel_CAF1
Location	8,758,834 – 8,758,932
Length	98
Max. P	0.967913

overview

Window 6

Location	8,758,834 – 8,758,932
Length	98
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	76.62
Mean single sequence MFE	-29.58
Consensus MFE	-9.14
Energy contribution	-9.18
Covariance contribution	0.04
Combinations/Pair	1.19
Mean z-score	-2.07
Structure conservation index	0.31
SVM decision value	0.90
SVM RNA-class probability	0.877369
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8758834 98 + 22224390
CUUUUAUUA--UUUCAUAGCCUACAAAACGGGG------CUGGCAAAUUGAAAUGUUUCAAGUUUUGCGGUUCGCUUUGCUUUGGCCAAAAUGUCGAAAUAAUGAA
..(((((((--((((....((........))((------((((((((.((((.(((..........))).)))).))))))..))))........))))))))))) ( -25.10)
>DroSec_CAF1 7090 103 + 1
CUUUUAUUA--UUUCAUAGCCUACAAAACGGGGCCGCUGCUGGCGAAUUGAAAUGUUUCAAGUUCUGCGGUUCGCUUUGCU-UGGCCAGAAAGUCGAAAUAAUGAA
..(((((((--((((....((........))(((((..((.(((((((((.(((.......)))...)))))))))..)).-)))))........))))))))))) ( -31.30)
>DroSim_CAF1 7915 104 + 1
CUUUUAUUA--UUUCAUAGCCUACAAAACGGGGCCGCUGCUGGCGAAUUGAAAUGUUUCAAGUUCUGCGGUUCGCUUUGCUUUGGCCAGAAAAUCGAAAUAAUGAA
..(((((((--((((....((........))(((((..((.(((((((((.(((.......)))...)))))))))..))..)))))........))))))))))) ( -32.50)
>DroEre_CAF1 6122 93 + 1
CUUUUAUUA--UUUUAUAGCCUACAAAACGGGGCCG---CUGGCAUAUUGAAAUGUUUGAAGUUUUGCGGUUCCGU-----UUGGCCAGAAACUCAAA---AUGAA
......(((--((((...(((....(((((((((((---(.(((((......))))).........))))))))))-----)))))..(.....))))---)))). ( -24.40)
>DroAna_CAF1 3841 94 + 1
CCCUCAGUGCGGCCCUCAGCCCACGACUCCGGGCCG---CAGGCGAAUUGAAAUGUUUCAAGUUGUGCGGCUGCGU-----UUGGACAGAAAGCCAA----ACGAG
..(((...((((((....((((........)))).(---(..((((.(((((....))))).))))))))))))((-----((((........))))----))))) ( -34.60)
>consensus
CUUUUAUUA__UUUCAUAGCCUACAAAACGGGGCCG___CUGGCGAAUUGAAAUGUUUCAAGUUCUGCGGUUCGCUUUGCUUUGGCCAGAAAGUCGAAAUAAUGAA
..................((((........))))........(((..(((((....)))))....)))((((...........))))................... ( -9.14 =  -9.18 +   0.04)

alignment

secondary structure

dotplot

Window 7

Location	8,758,834 – 8,758,932
Length	98
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	76.62
Mean single sequence MFE	-27.75
Consensus MFE	-9.36
Energy contribution	-12.04
Covariance contribution	2.68
Combinations/Pair	1.21
Mean z-score	-2.34
Structure conservation index	0.34
SVM decision value	1.62
SVM RNA-class probability	0.967913
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8758834 98 - 22224390
UUCAUUAUUUCGACAUUUUGGCCAAAGCAAAGCGAACCGCAAAACUUGAAACAUUUCAAUUUGCCAG------CCCCGUUUUGUAGGCUAUGAAA--UAAUAAAAG
...(((((((((......(((((...((((((((....(((((..(((((....))))))))))...------...)))))))).))))))))))--))))..... ( -24.40)
>DroSec_CAF1 7090 103 - 1
UUCAUUAUUUCGACUUUCUGGCCA-AGCAAAGCGAACCGCAGAACUUGAAACAUUUCAAUUCGCCAGCAGCGGCCCCGUUUUGUAGGCUAUGAAA--UAAUAAAAG
...(((((((((......(((((.-.((((((((..((((.(((.(((((....))))))))(....).))))...)))))))).))))))))))--))))..... ( -30.00)
>DroSim_CAF1 7915 104 - 1
UUCAUUAUUUCGAUUUUCUGGCCAAAGCAAAGCGAACCGCAGAACUUGAAACAUUUCAAUUCGCCAGCAGCGGCCCCGUUUUGUAGGCUAUGAAA--UAAUAAAAG
...(((((((((......(((((...((((((((..((((.(((.(((((....))))))))(....).))))...)))))))).))))))))))--))))..... ( -29.80)
>DroEre_CAF1 6122 93 - 1
UUCAU---UUUGAGUUUCUGGCCAA-----ACGGAACCGCAAAACUUCAAACAUUUCAAUAUGCCAG---CGGCCCCGUUUUGUAGGCUAUAAAA--UAAUAAAAG
....(---((((..(((.(((((((-----((((..((((..........................)---)))..))))))....))))).))).--...))))). ( -18.67)
>DroAna_CAF1 3841 94 - 1
CUCGU----UUGGCUUUCUGUCCAA-----ACGCAGCCGCACAACUUGAAACAUUUCAAUUCGCCUG---CGGCCCGGAGUCGUGGGCUGAGGGCCGCACUGAGGG
(((((----.((((((((.(((((.-----((.(.((((((....(((((....)))))......))---))))...).))..))))).)))))))).)).))).. ( -35.90)
>consensus
UUCAUUAUUUCGACUUUCUGGCCAAAGCAAAGCGAACCGCAAAACUUGAAACAUUUCAAUUCGCCAG___CGGCCCCGUUUUGUAGGCUAUGAAA__UAAUAAAAG
...............((((((((...((((((((...........(((((....)))))...(((......)))..)))))))).))))).)))............ ( -9.36 = -12.04 +   2.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:41 2006