Locus 539

Sequence ID	3L_DroMel_CAF1
Location	1,570,164 – 1,570,335
Length	171
Max. P	0.988959

overview

Window 9

Location	1,570,164 – 1,570,273
Length	109
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	92.14
Mean single sequence MFE	-28.32
Consensus MFE	-25.42
Energy contribution	-25.22
Covariance contribution	-0.20
Combinations/Pair	1.11
Mean z-score	-1.64
Structure conservation index	0.90
SVM decision value	1.65
SVM RNA-class probability	0.969663
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1570164 109 - 23771897
CAAAAUCAUUAAAGCAUUCAGCAAUCUUUCUGCGAAACGCUCGCGAGCACAGCUCAAAGCACACUGAGCCAAAGAUCCAUUCUGAGCGAGCGGGCAGCAGCCACA-AAAG
.............((.....)).......((((....(((((((.......(((((........)))))...(((.....)))..)))))))....)))).....-.... ( -29.00)
>DroSec_CAF1 14618 109 - 1
CAAAAUCAUUAAAGCAUUCAGCAAUAUAUCUGCGAAACGCUCGCGAGCACAGCUCAAAGCACACUGAGCCAAAAAGCCAUUCUGAGCGAGCGGGCAGCAGCCACA-AAAG
.............((.....)).......((((....(((((((((((...)))).........((.((......))))......)))))))....)))).....-.... ( -27.60)
>DroSim_CAF1 14871 109 - 1
CAAAAUCAUUCAAGCAUUCAGCAAUAUUUCUGCGAAACGCUCGCGAGCACAGCUCAAAGCACACUGAGCCAAAGAUCCAUUCUGAGCGAGCGGGCAGCAGCCACA-AAAG
.............((.....)).......((((....(((((((.......(((((........)))))...(((.....)))..)))))))....)))).....-.... ( -29.00)
>DroEre_CAF1 20827 109 - 1
UAAAAUCAUUUAGGCACUCAACAAUAUUUCUGCGAACCGCUCGCGAGCACAGCUCAAAGCACACUGAGCCAAAGAUCCGUUCUGAGUGAGCGGGCAGCAGCUUCA-AGAG
.............................((((...((((((((.......(((((........)))))...(((.....)))..))))))))...)))).....-.... ( -29.50)
>DroYak_CAF1 15168 110 - 1
CAAAAUCAUUAAAGCAUUCAGCAAUAUUUCUGCGAUACGCUCGCGAGCACAGCUCAAAGCACACUGAGUCAAAGAUCCAUUCUGGGUGAGCGGGCAGCAGCCCCAAAGAG
.....((......((.....((.........((((.....))))((((...))))...)).((((.((.............)).)))).))((((....))))....)). ( -26.52)
>consensus
CAAAAUCAUUAAAGCAUUCAGCAAUAUUUCUGCGAAACGCUCGCGAGCACAGCUCAAAGCACACUGAGCCAAAGAUCCAUUCUGAGCGAGCGGGCAGCAGCCACA_AAAG
.............................((((....(((((((.......(((((........)))))...(((.....)))..)))))))....)))).......... (-25.42 = -25.22 +  -0.20)

alignment

secondary structure

dotplot

Window 0

Location	1,570,195 – 1,570,297
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-22.03
Consensus MFE	-21.37
Energy contribution	-21.41
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-1.56
Structure conservation index	0.97
SVM decision value	2.14
SVM RNA-class probability	0.988959
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1570195 102 - 23771897
CGACAGUGACGCGUUGAAUAAAUACAAAAUCAUUAAAGCAUUCAGCAAUCUUUCUGCGAAACGCUCGCGAGCACAGCUCAAAGCACACUGAGCCAAAGAUCC
...(((((..(((((((((....................))))))).........((((.....))))((((...))))...)).)))))............ ( -21.85)
>DroSec_CAF1 14649 102 - 1
CGACAGUGACGCGUUGAAUAAAUACAAAAUCAUUAAAGCAUUCAGCAAUAUAUCUGCGAAACGCUCGCGAGCACAGCUCAAAGCACACUGAGCCAAAAAGCC
...(((((..(((((((((....................))))))).........((((.....))))((((...))))...)).)))))............ ( -21.85)
>DroSim_CAF1 14902 102 - 1
CGACAGUGACGCGUUGAAUAAAUACAAAAUCAUUCAAGCAUUCAGCAAUAUUUCUGCGAAACGCUCGCGAGCACAGCUCAAAGCACACUGAGCCAAAGAUCC
...(((((..((.((((((............)))))))).....((.........((((.....))))((((...))))...)).)))))............ ( -23.40)
>DroEre_CAF1 20858 102 - 1
CGACAGUGACGCGUUGAAUAAAUAUAAAAUCAUUUAGGCACUCAACAAUAUUUCUGCGAACCGCUCGCGAGCACAGCUCAAAGCACACUGAGCCAAAGAUCC
...(((((..(((((((.(((((........))))).....))))).........((((.....))))((((...))))...)).)))))............ ( -21.40)
>DroYak_CAF1 15200 102 - 1
CGACAGUGACGCGUUGAAUAAAUACAAAAUCAUUAAAGCAUUCAGCAAUAUUUCUGCGAUACGCUCGCGAGCACAGCUCAAAGCACACUGAGUCAAAGAUCC
...(((((..(((((((((....................))))))).........((((.....))))((((...))))...)).)))))............ ( -21.65)
>consensus
CGACAGUGACGCGUUGAAUAAAUACAAAAUCAUUAAAGCAUUCAGCAAUAUUUCUGCGAAACGCUCGCGAGCACAGCUCAAAGCACACUGAGCCAAAGAUCC
...(((((..(((((((((....................))))))).........((((.....))))((((...))))...)).)))))............ (-21.37 = -21.41 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	1,570,233 – 1,570,335
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	93.53
Mean single sequence MFE	-23.16
Consensus MFE	-19.22
Energy contribution	-19.66
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.66
Structure conservation index	0.83
SVM decision value	0.88
SVM RNA-class probability	0.873409
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1570233 102 - 23771897
CCUAAUUUACGAUCUAUUCGGUUUUAUGACAACGCGCGCGACAGUGACGCGUUGAAUAAAUACAAAAUCAUUAAAGCAUUCAGCAAUCUUUCUGCGAAACGC
.........(((.....)))(((((((((((((((((((....))).))))))).............))).)))))).(((.(((.......)))))).... ( -22.21)
>DroSec_CAF1 14687 102 - 1
CCUAAUUUACGAUCUAUUUGGUUUUAUCGCAACGCGCGCGACAGUGACGCGUUGAAUAAAUACAAAAUCAUUAAAGCAUUCAGCAAUAUAUCUGCGAAACGC
..........(((...((((..(((((..((((((((((....))).))))))).)))))..)))))))......((.((..(((.......)))..)).)) ( -22.60)
>DroSim_CAF1 14940 102 - 1
CCUAAUUUACGAUCUAUUUGGUUUUAUGGCAACGCGCGCGACAGUGACGCGUUGAAUAAAUACAAAAUCAUUCAAGCAUUCAGCAAUAUUUCUGCGAAACGC
..........(((...((((..(((((..((((((((((....))).))))))).)))))..)))))))......((.((..(((.......)))..)).)) ( -23.80)
>DroEre_CAF1 20896 102 - 1
CCUAAUUUACGAUCUUUUUGAUUUUACGUCAACGCGCGCGACAGUGACGCGUUGAAUAAAUAUAAAAUCAUUUAGGCACUCAACAAUAUUUCUGCGAACCGC
..........(.(((...((((((((..(((((((((((....))).)))))))).......))))))))...))))................(((...))) ( -22.70)
>DroYak_CAF1 15238 102 - 1
CCUAAUUUACGAUCUAUUUGGUUUUAUGGCAACGCGCGCGACAGUGACGCGUUGAAUAAAUACAAAAUCAUUAAAGCAUUCAGCAAUAUUUCUGCGAUACGC
.........(((((..((((..(((((..((((((((((....))).))))))).)))))..))))................(((.......)))))).)). ( -24.50)
>consensus
CCUAAUUUACGAUCUAUUUGGUUUUAUGGCAACGCGCGCGACAGUGACGCGUUGAAUAAAUACAAAAUCAUUAAAGCAUUCAGCAAUAUUUCUGCGAAACGC
..........(((...((((..(((((..((((((((((....))).))))))).)))))..)))))))......((.....(((.......))).....)) (-19.22 = -19.66 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:46 2006