Locus 6340

Sequence ID	2R_DroMel_CAF1
Location	19,882,741 – 19,882,835
Length	94
Max. P	0.968373

overview

Window 4

Location	19,882,741 – 19,882,835
Length	94
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.22
Mean single sequence MFE	-28.02
Consensus MFE	-15.80
Energy contribution	-16.05
Covariance contribution	0.25
Combinations/Pair	1.05
Mean z-score	-1.50
Structure conservation index	0.56
SVM decision value	0.08
SVM RNA-class probability	0.575337
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19882741 94 + 20766785
--C--------CAGCUCAUUGAGAUGCGUGCCGGCAAACAGCCUGGCCAGCACUUAUACGCAAUUUCGCGCCAUAUUUGGUUCAAACAUAUUGGAUUU-----------UUUUGU-----
--(--------((((....((((.(((..((((((.....))).)))..)))))))...))......(.((((....)))).)........)))....-----------......----- ( -24.20)
>DroVir_CAF1 155593 94 + 1
AGUUGCGCUCUUGGCUCAUUGAAAUGCGUGCCGGCGUGCAACGCGGCCAGCACUUAUACGCAAUUUCGCGCCAUAUUUGGUGCAAGCAUAUUGC--------------------------
.(((((((.((.(((.(((....)))...))))).)))))))((.....((........))......((((((....))))))..)).......-------------------------- ( -30.80)
>DroGri_CAF1 156394 102 + 1
AGC--------UGGCUCAUUGAAAUGCGCGCCGGCGUGCAACGCGGCCAGCACUUAUACGCAAUUUCGCGCCAUAUUUGGUGCAAGCAUAUUGCUUUUUUCU-----UAUUUUUC-----
.((--------(((((....(...((((((....))))))...))))))))........(((((...((((((....))))))......)))))........-----........----- ( -34.50)
>DroWil_CAF1 257527 93 + 1
-----------AAGCUCAUUGAGAUGCGUGGCGGCUAACAGCCUGGCCAGCACUUAUACGCAAUUUCGCGCCAUAUUUGGAGCAAACAUAUUGGUUUU-----------UUUUUU-----
-----------..((((..((((.(((.(((((((.....)))..)))))))))))..(((......))).........))))...............-----------......----- ( -25.40)
>DroMoj_CAF1 205527 115 + 1
AGCGCUGCUCAUGGCUCAUUGAAAUGCGUGCCGGCGAGCAACGCGGCCAGCACUUAUACGCAAUUUCGCGCCAUAUUUGGUCCAAGCAUAUUGUUUUUCCCUCUUUAUAUUUUGU-----
.(((.(((((.((((.(((....)))...))))..))))).)))((((((....(((.(((......)))..))).)))))).((((.....))))...................----- ( -28.20)
>DroAna_CAF1 110812 99 + 1
--C--------CAUCUCAUUGAGAUGCGUGCCGGCAAACAGCCUGGCCAGCACUUAUACGCAAUUUCGCGCCAUAUUUGGUUCAAACAUAUUGGCUUU-----------UUUUUCGUACU
--.--------((((((...)))))).((((.(((.....))).(((((((........))......(.((((....)))).)........)))))..-----------......)))). ( -25.00)
>consensus
__C________UAGCUCAUUGAAAUGCGUGCCGGCGAACAACCCGGCCAGCACUUAUACGCAAUUUCGCGCCAUAUUUGGUGCAAACAUAUUGGUUUU___________UUUUUU_____
....................(((((((((((.(((..........))).))......)))).)))))(.((((....)))).)..................................... (-15.80 = -16.05 +   0.25)

alignment

secondary structure

dotplot

Window 5

Location	19,882,741 – 19,882,835
Length	94
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.22
Mean single sequence MFE	-29.30
Consensus MFE	-20.47
Energy contribution	-20.25
Covariance contribution	-0.22
Combinations/Pair	1.12
Mean z-score	-1.82
Structure conservation index	0.70
SVM decision value	1.62
SVM RNA-class probability	0.968373
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19882741 94 - 20766785
-----ACAAAA-----------AAAUCCAAUAUGUUUGAACCAAAUAUGGCGCGAAAUUGCGUAUAAGUGCUGGCCAGGCUGUUUGCCGGCACGCAUCUCAAUGAGCUG--------G--
-----......-----------....(((.((((((((...))))))))(((((....)))))....((((((((..........))))))))((.((.....))))))--------)-- ( -24.90)
>DroVir_CAF1 155593 94 - 1
--------------------------GCAAUAUGCUUGCACCAAAUAUGGCGCGAAAUUGCGUAUAAGUGCUGGCCGCGUUGCACGCCGGCACGCAUUUCAAUGAGCCAAGAGCGCAACU
--------------------------((.((((((((((.(((....))).))))....))))))..((((((((.((...))..)))))))))).......((.((.....)).))... ( -31.00)
>DroGri_CAF1 156394 102 - 1
-----GAAAAAUA-----AGAAAAAAGCAAUAUGCUUGCACCAAAUAUGGCGCGAAAUUGCGUAUAAGUGCUGGCCGCGUUGCACGCCGGCGCGCAUUUCAAUGAGCCA--------GCU
-----........-----...........((((((((((.(((....))).))))....))))))....(((((((((((((.....)))))))(((....))).))))--------)). ( -31.10)
>DroWil_CAF1 257527 93 - 1
-----AAAAAA-----------AAAACCAAUAUGUUUGCUCCAAAUAUGGCGCGAAAUUGCGUAUAAGUGCUGGCCAGGCUGUUAGCCGCCACGCAUCUCAAUGAGCUU-----------
-----......-----------...............((((........(((((....)))))....((((((((..(((.....))))))).))))......))))..----------- ( -24.20)
>DroMoj_CAF1 205527 115 - 1
-----ACAAAAUAUAAAGAGGGAAAAACAAUAUGCUUGGACCAAAUAUGGCGCGAAAUUGCGUAUAAGUGCUGGCCGCGUUGCUCGCCGGCACGCAUUUCAAUGAGCCAUGAGCAGCGCU
-----................................((.(((.((...(((((....)))))....))..)))))((((((((((..(((...(((....))).))).)))))))))). ( -33.00)
>DroAna_CAF1 110812 99 - 1
AGUACGAAAAA-----------AAAGCCAAUAUGUUUGAACCAAAUAUGGCGCGAAAUUGCGUAUAAGUGCUGGCCAGGCUGUUUGCCGGCACGCAUCUCAAUGAGAUG--------G--
.(((((.....-----------...((((...((((((...)))))))))).........)))))..((((((((..........)))))))).((((((...))))))--------.-- ( -31.63)
>consensus
_____AAAAAA___________AAAACCAAUAUGCUUGCACCAAAUAUGGCGCGAAAUUGCGUAUAAGUGCUGGCCACGCUGCUCGCCGGCACGCAUCUCAAUGAGCCA________G__
...............................((((..............(((((....)))))....((((((((..........))))))))))))....................... (-20.47 = -20.25 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:45 2006