Locus 1433

Sequence ID	2R_DroMel_CAF1
Location	5,500,497 – 5,500,648
Length	151
Max. P	0.999776

overview

Window 9

Location	5,500,497 – 5,500,608
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	96.40
Mean single sequence MFE	-24.58
Consensus MFE	-22.94
Energy contribution	-23.18
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.53
Structure conservation index	0.93
SVM decision value	4.05
SVM RNA-class probability	0.999776
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5500497 111 + 20766785
AUAAAACUGAAAGUAAAGCUAAAUAAAACGCUGCCAUAAUUGGCAUCGUUAAUGCCAAAACCAUGAAUACUAAAAAGUUUUUACGAGCAUAAGCUGCGAUUGAGCAGUUAU
....(((((..(((..((((......((((.(((((....))))).)))).((((......(.((((.(((....))).)))).).)))).))))...)))...))))).. ( -24.50)
>DroSec_CAF1 25188 111 + 1
AUAAAACUGAAAGUAAAGCUGAAUAAAACGCUGCCAUAAUUGGCAUCGUUAAUGCCAAAACCAUGAAUACUAAAAAGUUUAUACGAGCUUAAGCUCCGAUUGAGCAGUUAU
....((((.......(((((......((((.(((((....))))).))))............((((((........))))))...)))))..((((.....)))))))).. ( -24.00)
>DroSim_CAF1 2329 111 + 1
AUAAAACUGAAAGUAAAGCUGAAUAAAACGCUGCCAUAAUUGGCAUCGUUAAUGCCAAAACCAUGAAUACUAAAAAGUUUUUACGAGCUUAAGCUGCGAUUGAGCAGUUAU
...............(((((......((((.(((((....))))).)))).............((((.(((....))).))))..))))).((((((......)))))).. ( -25.50)
>DroEre_CAF1 2217 111 + 1
AUAAAACUGAAAGUAAAGCUAAAUAAAACGCUGCCAUAAUUGGCAUCGUUAAUGCCAAAACCAUGAAUACUAAAAAGUUUUUACGAGCUUAAGCUGCAAUUGGGCAGUAAC
...............(((((......((((.(((((....))))).)))).............((((.(((....))).))))..)))))..(((((......)))))... ( -24.10)
>DroYak_CAF1 1883 111 + 1
AUAAAACUGAAAGUAAAGCUGAAUAAAACGCUGCCAUAAUUGGCGUCGUUAAUGCCAAAACCAUGAAUACUAAAAAGUUUUUACGAGCUUAAGCUGCGAUUGAGCAGUUAC
...............(((((......((((.(((((....))))).)))).............((((.(((....))).))))..))))).((((((......)))))).. ( -24.80)
>consensus
AUAAAACUGAAAGUAAAGCUGAAUAAAACGCUGCCAUAAUUGGCAUCGUUAAUGCCAAAACCAUGAAUACUAAAAAGUUUUUACGAGCUUAAGCUGCGAUUGAGCAGUUAU
....(((((..(((..((((......((((.(((((....))))).))))........................((((((....)))))).))))...)))...))))).. (-22.94 = -23.18 +   0.24)

alignment

secondary structure

dotplot

Window 0

Location	5,500,497 – 5,500,608
Length	111
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	96.40
Mean single sequence MFE	-22.80
Consensus MFE	-20.00
Energy contribution	-21.00
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.31
Structure conservation index	0.88
SVM decision value	0.18
SVM RNA-class probability	0.621763
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5500497 111 - 20766785
AUAACUGCUCAAUCGCAGCUUAUGCUCGUAAAAACUUUUUAGUAUUCAUGGUUUUGGCAUUAACGAUGCCAAUUAUGGCAGCGUUUUAUUUAGCUUUACUUUCAGUUUUAU
((((((((......)))).)))).......((((((....((((.(((((((..(((((((...)))))))))))))).(((..........))).))))...)))))).. ( -23.10)
>DroSec_CAF1 25188 111 - 1
AUAACUGCUCAAUCGGAGCUUAAGCUCGUAUAAACUUUUUAGUAUUCAUGGUUUUGGCAUUAACGAUGCCAAUUAUGGCAGCGUUUUAUUCAGCUUUACUUUCAGUUUUAU
..(((((........((((....)))).............((((.(((((((..(((((((...)))))))))))))).(((..........))).))))..))))).... ( -22.00)
>DroSim_CAF1 2329 111 - 1
AUAACUGCUCAAUCGCAGCUUAAGCUCGUAAAAACUUUUUAGUAUUCAUGGUUUUGGCAUUAACGAUGCCAAUUAUGGCAGCGUUUUAUUCAGCUUUACUUUCAGUUUUAU
..(((((.......((.(((.((((.(((.((.(((....))).)).))))))).)))...((((.(((((....))))).)))).......))........))))).... ( -23.16)
>DroEre_CAF1 2217 111 - 1
GUUACUGCCCAAUUGCAGCUUAAGCUCGUAAAAACUUUUUAGUAUUCAUGGUUUUGGCAUUAACGAUGCCAAUUAUGGCAGCGUUUUAUUUAGCUUUACUUUCAGUUUUAU
...((((.......((.(((.((((.(((.((.(((....))).)).))))))).)))...((((.(((((....))))).)))).......))........))))..... ( -22.96)
>DroYak_CAF1 1883 111 - 1
GUAACUGCUCAAUCGCAGCUUAAGCUCGUAAAAACUUUUUAGUAUUCAUGGUUUUGGCAUUAACGACGCCAAUUAUGGCAGCGUUUUAUUCAGCUUUACUUUCAGUUUUAU
((((..(((.((((((.(((.((((.(((.((.(((....))).)).))))))).))).........((((....)))).)))....))).))).))))............ ( -22.80)
>consensus
AUAACUGCUCAAUCGCAGCUUAAGCUCGUAAAAACUUUUUAGUAUUCAUGGUUUUGGCAUUAACGAUGCCAAUUAUGGCAGCGUUUUAUUCAGCUUUACUUUCAGUUUUAU
..(((((.......((.(((.((((.(((.((.(((....))).)).))))))).)))...((((.(((((....))))).)))).......))........))))).... (-20.00 = -21.00 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	5,500,537 – 5,500,648
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	88.62
Mean single sequence MFE	-31.14
Consensus MFE	-25.64
Energy contribution	-27.96
Covariance contribution	2.32
Combinations/Pair	1.09
Mean z-score	-2.12
Structure conservation index	0.82
SVM decision value	1.66
SVM RNA-class probability	0.970440
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5500537 111 + 20766785
UGGCAUCGUUAAUGCCAAAACCAUGAAUACUAAAAAGUUUUUACGAGCAUAAGCUGCGAUUGAGCAGUUAUUGUAGGGACAGGUUGAUGGCCGAGUGUUCUAGGGAAAUGA
((((((.....))))))...((..(((((((.....((((((((((.....((((((......)))))).)))))))))).(((.....))).)))))))...))...... ( -36.40)
>DroSec_CAF1 25228 103 + 1
UGGCAUCGUUAAUGCCAAAACCAUGAAUACUAAAAAGUUUAUACGAGCUUAAGCUCCGAUUGAGCAGUUAUUGUAGGGACAGGUUGAUGGCCGAGUGUUUUU--------A
((((((.....)))))).......(((((((.....(((..(((((......((((.....)))).....)))))..))).(((.....))).)))))))..--------. ( -25.80)
>DroSim_CAF1 2369 111 + 1
UGGCAUCGUUAAUGCCAAAACCAUGAAUACUAAAAAGUUUUUACGAGCUUAAGCUGCGAUUGAGCAGUUAUUGUAGGGACAGGUUGAUGGCCGAGUGUUCUAUGGAAAAGA
((((((.....))))))...(((((((((((.....((((((((((.....((((((......)))))).)))))))))).(((.....))).))))))).))))...... ( -38.40)
>DroEre_CAF1 2257 108 + 1
UGGCAUCGUUAAUGCCAAAACCAUGAAUACUAAAAAGUUUUUACGAGCUUAAGCUGCAAUUGGGCAGUAACUAUAGCGACAGGUUGAUGGCCGACGGUUCUAGGGC---AU
(((.((((((...((((.((((.((((.(((....))).))))...(((...(((((......)))))......)))....))))..)))).)))))).)))....---.. ( -27.80)
>DroYak_CAF1 1923 111 + 1
UGGCGUCGUUAAUGCCAAAACCAUGAAUACUAAAAAGUUUUUACGAGCUUAAGCUGCGAUUGAGCAGUUACUACAGGGGCAGGUUGAUGGCCGACUGUUCUAGGGAAAUAU
((((((.....))))))...((.((.........((((((....)))))).((((((......))))))....))(((((((.(((.....)))))))))).))....... ( -27.30)
>consensus
UGGCAUCGUUAAUGCCAAAACCAUGAAUACUAAAAAGUUUUUACGAGCUUAAGCUGCGAUUGAGCAGUUAUUGUAGGGACAGGUUGAUGGCCGAGUGUUCUAGGGAAA_AA
((((((.....))))))...((..(((((((.....((((((((((.....((((((......)))))).)))))))))).(((.....))).)))))))...))...... (-25.64 = -27.96 +   2.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:45 2006