Locus 5608

Sequence ID	2L_DroMel_CAF1
Location	15,886,304 – 15,886,544
Length	240
Max. P	0.945887

overview

Window 6

Location	15,886,304 – 15,886,424
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.83
Mean single sequence MFE	-32.00
Consensus MFE	-24.82
Energy contribution	-26.46
Covariance contribution	1.64
Combinations/Pair	1.09
Mean z-score	-2.26
Structure conservation index	0.78
SVM decision value	1.36
SVM RNA-class probability	0.945887
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15886304 120 + 22407834
UUUUUCUAUGAUUAUUGUUUUUUCCGGUGGUGCCAAACUACGACGAUUCAACCUUUGAACGUUAAUUAAUACGGCCUUAUUGACGUACUUUUGGACGCCAUCGGCCUCCACUUUCAGUAU
............(((((......((((((((((((((.(((((((.((((.....)))))))...((((((......))))))))))..))))).)))))))))..........))))). ( -29.09)
>DroSec_CAF1 59746 120 + 1
UUUUUCUAUGAAAAGUGAUUUUUCCGGUGGUGCCAAACUACGUCGUUUCAACCUUUGAACAUUAAUUAAUACGGCUUUGUUGACGUACUUUUGGACGCCAUCGGCCUCCACUUUUAGUAU
......(((.(((((((......((((((((((((((.(((((((...(((((.((((.......))))...))..))).)))))))..))))).)))))))))....))))))).))). ( -35.60)
>DroSim_CAF1 59942 120 + 1
UUUUUCUAUGAAAAGUGAUUUUUCCGGUGGUGCCAAACUACGUCGUUUCAACCUUUGAACAUCAAUUAAUACGGCUUUGUUGACGUACUUUUGGACGCCAUCGGCCUCCACUUUUAGUAU
......(((.(((((((......((((((((((((((.(((((((...(((((.((((.......))))...))..))).)))))))..))))).)))))))))....))))))).))). ( -35.60)
>DroEre_CAF1 49306 120 + 1
UUCUUCUAUGACAAGUGUCUUCUCCGGCGGCGCCAGACUUCGUCGCUUCCGCCUUUGAACGGUAAUUAAUACGGCUUUGUUGACGUACUUUGGGACGCCUUCGGCCUCCACUUUCAGUAU
........(((.(((((......((((.(((((((((...(((((.....(((.((((.......))))...))).....)))))...)))))..)))).))))....)))))))).... ( -30.50)
>DroYak_CAF1 37664 120 + 1
UUCUUCCACGAUAAGUGAUUUUUCCGGCGGUGCCAGACUACGUCGCGUCAACCUUUGAACGUUAAUUAAUACGGCUUUGUUGACGUACUUUGUUACGCCAUCGGCCUCCACUUUCAGUAU
.......((...(((((......(((..((((...(((...((.((((((((.......(((........))).....))))))))))...))).))))..)))....)))))...)).. ( -29.20)
>consensus
UUUUUCUAUGAAAAGUGAUUUUUCCGGUGGUGCCAAACUACGUCGCUUCAACCUUUGAACGUUAAUUAAUACGGCUUUGUUGACGUACUUUUGGACGCCAUCGGCCUCCACUUUCAGUAU
......(((...(((((......((((((((((((((.(((((((......((.((((.......))))...))......)))))))..))))).)))))))))....)))))...))). (-24.82 = -26.46 +   1.64)

alignment

secondary structure

dotplot

Window 7

Location	15,886,304 – 15,886,424
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.83
Mean single sequence MFE	-30.84
Consensus MFE	-23.21
Energy contribution	-24.21
Covariance contribution	1.00
Combinations/Pair	1.17
Mean z-score	-1.77
Structure conservation index	0.75
SVM decision value	0.37
SVM RNA-class probability	0.709719
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15886304 120 - 22407834
AUACUGAAAGUGGAGGCCGAUGGCGUCCAAAAGUACGUCAAUAAGGCCGUAUUAAUUAACGUUCAAAGGUUGAAUCGUCGUAGUUUGGCACCACCGGAAAAAACAAUAAUCAUAGAAAAA
...(((...((((.((((..((((((.(....).))))))....))))((...((((((((((((.....)))).)))..)))))..)).)))))))....................... ( -27.40)
>DroSec_CAF1 59746 120 - 1
AUACUAAAAGUGGAGGCCGAUGGCGUCCAAAAGUACGUCAACAAAGCCGUAUUAAUUAAUGUUCAAAGGUUGAAACGACGUAGUUUGGCACCACCGGAAAAAUCACUUUUCAUAGAAAAA
...((((((((((...(((.(((.(.(((((..((((((.....((((...................)))).....)))))).)))))).))).))).....)))))))...)))..... ( -32.31)
>DroSim_CAF1 59942 120 - 1
AUACUAAAAGUGGAGGCCGAUGGCGUCCAAAAGUACGUCAACAAAGCCGUAUUAAUUGAUGUUCAAAGGUUGAAACGACGUAGUUUGGCACCACCGGAAAAAUCACUUUUCAUAGAAAAA
...((((((((((...(((.(((.(.(((((..((((((.....((((...................)))).....)))))).)))))).))).))).....)))))))...)))..... ( -32.31)
>DroEre_CAF1 49306 120 - 1
AUACUGAAAGUGGAGGCCGAAGGCGUCCCAAAGUACGUCAACAAAGCCGUAUUAAUUACCGUUCAAAGGCGGAAGCGACGAAGUCUGGCGCCGCCGGAGAAGACACUUGUCAUAGAAGAA
.((((....(.(((.(((...))).))))..))))((((.....(((.(((.....))).))).....((....))))))...((((((...))))))...(((....)))......... ( -32.90)
>DroYak_CAF1 37664 120 - 1
AUACUGAAAGUGGAGGCCGAUGGCGUAACAAAGUACGUCAACAAAGCCGUAUUAAUUAACGUUCAAAGGUUGACGCGACGUAGUCUGGCACCGCCGGAAAAAUCACUUAUCGUGGAAGAA
...(((...(((..((((..((((((.....((((((.(......).)))))).....))).)))..))))..)))....)))((((((...))))))....((((.....))))..... ( -29.30)
>consensus
AUACUGAAAGUGGAGGCCGAUGGCGUCCAAAAGUACGUCAACAAAGCCGUAUUAAUUAACGUUCAAAGGUUGAAACGACGUAGUUUGGCACCACCGGAAAAAUCACUUAUCAUAGAAAAA
...(((.(((((....(((.(((.(((..(((.((((((.....((((...................)))).....)))))).)))))).))).)))......)))))....)))..... (-23.21 = -24.21 +   1.00)

alignment

secondary structure

dotplot

Window 8

Location	15,886,424 – 15,886,544
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.83
Mean single sequence MFE	-41.72
Consensus MFE	-30.94
Energy contribution	-31.58
Covariance contribution	0.64
Combinations/Pair	1.22
Mean z-score	-1.82
Structure conservation index	0.74
SVM decision value	0.38
SVM RNA-class probability	0.712338
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15886424 120 + 22407834
UUGAUGGAGUCUGUCACCGGCAUAUUUCGAAAUGGCGGUGAUUUUCAGAGUAGUCAGGCCCACUUUCUUUGGGCGGAUCAUGAAUGAAAUGCCACGUCCUGUAUUCGCGGGAAUCCAUAA
...(((((....(((((((.(((........))).)))))))(((((..((.(((..(((((.......))))).))).))...))))).......((((((....)))))).))))).. ( -40.00)
>DroSec_CAF1 59866 120 + 1
UUGAUGGAGUCUGUCACCGGCAUAUGACGAGAUGGCGGUGAUUUUCAGAGUGGUCAGACCCAUUUUCUUUGGGCGGAUCAUGAAUGAAAUGCCACGUCCCGUAUUUGCGGGAAUCCAUAA
...(((((....(((((((.(((........))).)))))))(((((..((((((.(.((((.......))))).))))))...))))).......((((((....)))))).))))).. ( -45.30)
>DroSim_CAF1 60062 120 + 1
UUGAUGGAGUCUGUCACCGGCAUAUGACGAAAUGGCGGUGAUUUUCAGAGUGGUCAGACCCACUUUCUUUGGGCGGAUCAUGAAUGAAAUGCCACGUCCCGUAUUUGCGGGAAUCCAUAA
...(((((....(((((((.(((........))).)))))))(((((..((((((.(.((((.......))))).))))))...))))).......((((((....)))))).))))).. ( -44.30)
>DroEre_CAF1 49426 120 + 1
UUGAUGGAGUCUGUCGCCGGCAUUUGGCGAGAUGGCGGAGAUCUUUAGGGUGGUCAGACCUACUUUCCUCGGGCGGAUCAUGAAGGAGAUGCUUCGUCCGGUACUGGCGGGUAUCCAUAA
...((((((((((((((((.(((((....))))).)((....))....))))).))))).((((..(((((((((((.(((.......))).)))))))))....))..))))))))).. ( -40.80)
>DroYak_CAF1 37784 120 + 1
UUGAUUUAGUCUGUCACCGGCAAAUGGCGAGAUGGCGGUGAUCUUCAGAGCGGUCAGACCAACUUUCUUCGGGCGGAUCAUGAACGAUAUGCUACGUCCGGUAUUUGCCGGUAUCCAUAU
..(((.......)))(((((((((((.((.((((..(((((((((((((..((.....))..((.((....)).)).)).)))).))).)))).)))))).)))))))))))........ ( -38.20)
>consensus
UUGAUGGAGUCUGUCACCGGCAUAUGACGAGAUGGCGGUGAUUUUCAGAGUGGUCAGACCCACUUUCUUUGGGCGGAUCAUGAAUGAAAUGCCACGUCCCGUAUUUGCGGGAAUCCAUAA
...((((((...(((((((.(((........))).)))))))...)(((((((......)))))))...((((((..((......))..)))).))((((((....)))))).))))).. (-30.94 = -31.58 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:33 2006