Locus 2320

Sequence ID	X_DroMel_CAF1
Location	6,249,986 – 6,250,143
Length	157
Max. P	0.820806

overview

Window 0

Location	6,249,986 – 6,250,105
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.82
Mean single sequence MFE	-28.00
Consensus MFE	-21.62
Energy contribution	-22.38
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.56
Structure conservation index	0.77
SVM decision value	-0.01
SVM RNA-class probability	0.529311
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6249986 119 - 22224390
AGU-GUGUGCGUGUAAGCUUUUAGCUAGCUAAUUGCGGCCAAUUGGCCAAAACAAAACCACCGCAAAAAUUGCACAAAAAUUCAAAAUGUACUGCAAUGUAUGCAUUUAACUCAACCAGA
(((-..((((((((((((..((((....))))..))((((....)))).....................)))))).............((((......))))))))...)))........ ( -29.10)
>DroSec_CAF1 16773 119 - 1
AUA-GUGUGCGUGUAAGCUUUUAGCUAGCUAAUUGCGGCCAAUUGGCCAAAACAAAACCACCGCAAAAAUUGCACAAAAAUUCAACAUGUACUGCAAUGUAUGCAUUUAACUCAACCAGA
...-..((((((((..((..((((....))))..))((((....))))..............(((.....)))...........))))))))((((.....))))............... ( -28.70)
>DroEre_CAF1 11442 119 - 1
ACU-GUGUGCGUGUAAGCUUUUAGCUAGCUAAUUGCGUCCAAUUGGCCAAAACAAAACCACCGCAAAAAUUGCACAAAAAUUCAGCAUGUACUGCAAUGUAUGCAUUUAACUCAACCGGA
.((-(.((((((((.(((.....))).((((((((....))))))))...............(((.....)))...........))))))))((((.....))))...........))). ( -25.60)
>DroYak_CAF1 23907 120 - 1
ACUGGUGUGCGUGUAAGCUUUUAGCUAGCUAAUUGCGUCCAAUUGGCCAAAACAAAACCACCGCAAAAAUUUCACAAAAAUUCAACAUGUACCGCAAUGUAUGCAUUUAACUCAACCAGA
.(((((((((((((.(((.....))).((((((((....)))))))).....................................)))))))).(((.....)))..........))))). ( -28.60)
>consensus
ACU_GUGUGCGUGUAAGCUUUUAGCUAGCUAAUUGCGGCCAAUUGGCCAAAACAAAACCACCGCAAAAAUUGCACAAAAAUUCAACAUGUACUGCAAUGUAUGCAUUUAACUCAACCAGA
......((((((((((((..((((....))))..))((((....)))).....................)))))).............((((......)))))))).............. (-21.62 = -22.38 +   0.75)

alignment

secondary structure

dotplot

Window 1

Location	6,250,026 – 6,250,143
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.11
Mean single sequence MFE	-33.53
Consensus MFE	-23.24
Energy contribution	-25.30
Covariance contribution	2.06
Combinations/Pair	1.03
Mean z-score	-1.49
Structure conservation index	0.69
SVM decision value	-0.01
SVM RNA-class probability	0.529027
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6250026 117 + 22224390
UUUUUGUGCAAUUUUUGCGGUGGUUUUGUUUUGGCCAAUUGGCCGCAAUUAGCUAGCUAAAAGCUUACACGCACAC-ACUUUCG--GCCGCACUCACACAAGUGCCGCCGUCUAGCACAC
....(((((......((((((((.........((((....))))((..((((....))))..)))))).))))...-.....((--((.(((((......))))).))))....))))). ( -40.10)
>DroSec_CAF1 16813 119 + 1
UUUUUGUGCAAUUUUUGCGGUGGUUUUGUUUUGGCCAAUUGGCCGCAAUUAGCUAGCUAAAAGCUUACACGCACAC-UAUGGCAGCGCUGCACGCACACAAGUGCCGCCGACUAGCACAC
....(((((......((((((((.........((((....))))((..((((....))))..)))))).))))...-..((((.(((((...........))))).))))....))))). ( -38.60)
>DroEre_CAF1 11482 112 + 1
UUUUUGUGCAAUUUUUGCGGUGGUUUUGUUUUGGCCAAUUGGACGCAAUUAGCUAGCUAAAAGCUUACACGCACAC-AGUGGCG--CCCGCACUCACACAAACGCAGCGAU-----ACAC
..((((((.......((((((((((((...(((((.(((((....))))).)))))...))))).))).))))...-.((((..--.)))).....)))))).........-----.... ( -26.60)
>DroYak_CAF1 23947 113 + 1
UUUUUGUGAAAUUUUUGCGGUGGUUUUGUUUUGGCCAAUUGGACGCAAUUAGCUAGCUAAAAGCUUACACGCACACCAGUGCCG--GUUGCACUCACACAAACGCAGCGAU-----ACAC
..((((((.......((((((((((((...(((((.(((((....))))).)))))...))))).))).))))....(((((..--...)))))..)))))).........-----.... ( -28.80)
>consensus
UUUUUGUGCAAUUUUUGCGGUGGUUUUGUUUUGGCCAAUUGGACGCAAUUAGCUAGCUAAAAGCUUACACGCACAC_AGUGGCG__GCCGCACUCACACAAACGCAGCCAU_____ACAC
....(((((......((((((((((((...(((((.(((((....))))).)))))...))))).))).)))).............((.((((........)))).))......))))). (-23.24 = -25.30 +   2.06)

alignment

secondary structure

dotplot

Window 2

Location	6,250,026 – 6,250,143
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.11
Mean single sequence MFE	-37.88
Consensus MFE	-25.56
Energy contribution	-27.00
Covariance contribution	1.44
Combinations/Pair	1.10
Mean z-score	-2.35
Structure conservation index	0.67
SVM decision value	0.68
SVM RNA-class probability	0.820806
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6250026 117 - 22224390
GUGUGCUAGACGGCGGCACUUGUGUGAGUGCGGC--CGAAAGU-GUGUGCGUGUAAGCUUUUAGCUAGCUAAUUGCGGCCAAUUGGCCAAAACAAAACCACCGCAAAAAUUGCACAAAAA
.(((((....((((.((((((....)))))).))--))...((-(.(((.((....((..((((....))))..))((((....))))........)))))))).......))))).... ( -46.90)
>DroSec_CAF1 16813 119 - 1
GUGUGCUAGUCGGCGGCACUUGUGUGCGUGCAGCGCUGCCAUA-GUGUGCGUGUAAGCUUUUAGCUAGCUAAUUGCGGCCAAUUGGCCAAAACAAAACCACCGCAAAAAUUGCACAAAAA
.(((((.....((((((.((.((......)))).))))))...-.((((.(((...((..((((....))))..))((((....))))..........)))))))......))))).... ( -42.20)
>DroEre_CAF1 11482 112 - 1
GUGU-----AUCGCUGCGUUUGUGUGAGUGCGGG--CGCCACU-GUGUGCGUGUAAGCUUUUAGCUAGCUAAUUGCGUCCAAUUGGCCAAAACAAAACCACCGCAAAAAUUGCACAAAAA
....-----.........((((((..(.((((((--(((....-..)))).(((.(((.....))).((((((((....))))))))....)))......)))))....)..)))))).. ( -33.30)
>DroYak_CAF1 23947 113 - 1
GUGU-----AUCGCUGCGUUUGUGUGAGUGCAAC--CGGCACUGGUGUGCGUGUAAGCUUUUAGCUAGCUAAUUGCGUCCAAUUGGCCAAAACAAAACCACCGCAAAAAUUUCACAAAAA
(((.-----.....(((.........(((((...--..)))))((((....(((.(((.....))).((((((((....))))))))....)))....))))))).......)))..... ( -29.12)
>consensus
GUGU_____ACCGCGGCACUUGUGUGAGUGCAGC__CGCCACU_GUGUGCGUGUAAGCUUUUAGCUAGCUAAUUGCGGCCAAUUGGCCAAAACAAAACCACCGCAAAAAUUGCACAAAAA
((((........(((((((((....)))))))))...........((((.(((...((..((((....))))..))((((....))))..........)))))))......))))..... (-25.56 = -27.00 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:30 2006