Locus 2464

Sequence ID	X_DroMel_CAF1
Location	6,578,468 – 6,578,585
Length	117
Max. P	0.587021

overview

Window 4

Location	6,578,468 – 6,578,585
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.94
Mean single sequence MFE	-31.75
Consensus MFE	-20.98
Energy contribution	-21.72
Covariance contribution	0.75
Combinations/Pair	1.21
Mean z-score	-1.69
Structure conservation index	0.66
SVM decision value	0.11
SVM RNA-class probability	0.587021
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6578468 117 + 22224390
UGGUAUCAUAUGAAAUGCAGGG-UAAAAUUUCAAGGUGUUUGGCCUGUAAUCCA--GCAUUAUUUGUAAAUUCGGUGGCUGGGUGCCGCCGAAUGAAAUGUAGAUCGGCUAAAAAUAAGU
.((..((....))..((((((.-((((...(....)..)))).))))))..))(--((...(((((((.((((((((((.....))))))))))....)))))))..))).......... ( -31.20)
>DroSec_CAF1 22956 119 + 1
UGGUAUCAUAUGAAAUGCAGUG-UAGAAUUUCAAGGUGUUCGCCCUGUAAUCCGGGGCCUUAUUUGUAAAUUCGGUGGCUGGUUGCUGCCGAAUGCAAUGUAGAUCGGCUAAAAAUAAGU
..........(((..((((.((-((((((((((((......((((((.....))))))....)))).))))))((..((.....))..))...)))).))))..)))............. ( -34.00)
>DroEre_CAF1 22268 118 + 1
UAUUAUCAUAUAAAACACAGGGAGAAACUUUUUAGGUUUUUGCCCUAUAAUCCG--ACAAUAUUUGUAAAUUCGGUGGCUGGGUGCCGCCGACUGCAAUAUAGAUCGGCUAAAAAUAACU
..................(((((((((((.....))))))).)))).....(((--((.(((((.(((...((((((((.....)))))))).)))))))).).))))............ ( -33.90)
>DroYak_CAF1 33489 117 + 1
UAUUAUCAUAUAAGACGCAGUG-GAGAAUUUCAAGGUGUUUGCCCUGUAAUCCG--GCAUUAUUUGUAAAUUCGGUGGCUGGCUGCCGUCGAAUGCAAUAUAGAUCGGCUAAAAAUAAGU
.(((((......((((((..((-((....))))..)))))).....)))))..(--((...(((((((.(((((..(((.....)))..)))))....)))))))..))).......... ( -27.90)
>consensus
UAGUAUCAUAUAAAACGCAGGG_GAAAAUUUCAAGGUGUUUGCCCUGUAAUCCG__GCAUUAUUUGUAAAUUCGGUGGCUGGGUGCCGCCGAAUGCAAUAUAGAUCGGCUAAAAAUAAGU
................((((((...((((........)))).))))))........((...(((((((.((((((((((.....))))))))))....)))))))..))........... (-20.98 = -21.72 +   0.75)

alignment

secondary structure

dotplot

Window 5

Location	6,578,468 – 6,578,585
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.94
Mean single sequence MFE	-25.08
Consensus MFE	-15.93
Energy contribution	-17.67
Covariance contribution	1.75
Combinations/Pair	1.14
Mean z-score	-1.74
Structure conservation index	0.64
SVM decision value	0.00
SVM RNA-class probability	0.534595
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6578468 117 - 22224390
ACUUAUUUUUAGCCGAUCUACAUUUCAUUCGGCGGCACCCAGCCACCGAAUUUACAAAUAAUGC--UGGAUUACAGGCCAAACACCUUGAAAUUUUA-CCCUGCAUUUCAUAUGAUACCA
...........(((((((((((((..((((((.(((.....))).))))))........)))).--))))))...)))....((...((((((.(..-....).))))))..))...... ( -23.10)
>DroSec_CAF1 22956 119 - 1
ACUUAUUUUUAGCCGAUCUACAUUGCAUUCGGCAGCAACCAGCCACCGAAUUUACAAAUAAGGCCCCGGAUUACAGGGCGAACACCUUGAAAUUCUA-CACUGCAUUUCAUAUGAUACCA
.(((((((.((((.(((....)))))((((((..((.....))..)))))).)).)))))))((((.(.....).))))...((...((((((.(..-....).))))))..))...... ( -24.30)
>DroEre_CAF1 22268 118 - 1
AGUUAUUUUUAGCCGAUCUAUAUUGCAGUCGGCGGCACCCAGCCACCGAAUUUACAAAUAUUGU--CGGAUUAUAGGGCAAAAACCUAAAAAGUUUCUCCCUGUGUUUUAUAUGAUAAUA
.((((((..((((((((..(((((....((((.(((.....))).)))).......))))).))--)))..(((((((...((((.......))))..)))))))..)))...)))))). ( -30.40)
>DroYak_CAF1 33489 117 - 1
ACUUAUUUUUAGCCGAUCUAUAUUGCAUUCGACGGCAGCCAGCCACCGAAUUUACAAAUAAUGC--CGGAUUACAGGGCAAACACCUUGAAAUUCUC-CACUGCGUCUUAUAUGAUAAUA
...............(((((((.((((((((..(((.....)))..))))..............--.(((((.(((((......))))).)))))..-...))))...)))).))).... ( -22.50)
>consensus
ACUUAUUUUUAGCCGAUCUACAUUGCAUUCGGCGGCACCCAGCCACCGAAUUUACAAAUAAUGC__CGGAUUACAGGGCAAACACCUUGAAAUUCUA_CACUGCAUUUCAUAUGAUAACA
...............(((((((.(((((((((.(((.....))).))))).................(((((.(((((......))))).)))))......))))...)))).))).... (-15.93 = -17.67 +   1.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:23 2006