Locus 4194

Sequence ID	2R_DroMel_CAF1
Location	13,799,414 – 13,799,548
Length	134
Max. P	0.900271

overview

Window 5

Location	13,799,414 – 13,799,508
Length	94
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	66.33
Mean single sequence MFE	-23.04
Consensus MFE	-12.40
Energy contribution	-12.60
Covariance contribution	0.20
Combinations/Pair	1.17
Mean z-score	-1.65
Structure conservation index	0.54
SVM decision value	1.01
SVM RNA-class probability	0.900271
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13799414 94 + 20766785
AUUUAUUUCUGCUUUCAAAAGCCUA---AAACUGAAUUCUGUAUGCUUUACUUACCGAACUUCUGGUCUCGGUGAAGUUGCUCAGGUCAGGAGUGAG
..((((((..((((....))))...---...((((..((((...((...(((((((((((.....)).)))))).))).)).)))))))))))))). ( -22.40)
>DroSec_CAF1 100189 94 + 1
AUUCAUUUCGGCUUUUAAAAGAAAA---CAACUCAGUCCUGUAUGUUUUACUUACCGAACUUCUGGUCUCGGUGAAGUUGCUCAGGUCAGGAGUGAG
.....((((...........)))).---...((((.(((((..((....(((((((((((.....)).)))))).)))....))...))))).)))) ( -25.70)
>DroSim_CAF1 104062 94 + 1
AUUCAUUUCGUCUUUCAAAAGAAGA---CAACUCAAUCCUGUAUGUUUUACUUACCGAACUUCUGGUCUCGGUGAAGUUGCUCAGGUCAGGAGUGAG
.........((((((.....)))))---)..((((.(((((..((....(((((((((((.....)).)))))).)))....))...))))).)))) ( -28.70)
>DroEre_CAF1 100622 72 + 1
AU----------------------A---CAAUUCAAUUCUGUCUGCUUUACUUACCGAACUUCUGGUCUCGGUAAAGUUGCUCAGGUCGGGAGUGAG
..----------------------.---....(((.(((((((((....(((((((((((.....)).))))).))))....)))).))))).))). ( -20.20)
>DroWil_CAF1 123564 82 + 1
----AG--------UUAAAGGGAAUCGCCAACCGAG---AGUAGAGAAUACAUACCGAACUUCUGGUUUCGGUGAAAUUGCUCAGAUCGGGCGUUAA
----..--------...........((((.((((((---(.(((((..............))))).)))))))((......))......)))).... ( -18.94)
>DroAna_CAF1 108994 71 + 1
------------------AGGACUA---GGAAG-GAUUAGAGAUG----UCUUACCGAACUUCUGGUCUCGGUAAAGUUGCUGAGGUCCGGUGUCAG
------------------..(((..---((.((-(((.......)----)))).))......((((((((((((....)))))))).)))).))).. ( -22.30)
>consensus
AU__AU________U_AAAAGAAAA___CAACUCAAUUCUGUAUGCUUUACUUACCGAACUUCUGGUCUCGGUGAAGUUGCUCAGGUCAGGAGUGAG
..........................................................(((((((..((.(((......))).))..)))))))... (-12.40 = -12.60 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	13,799,433 – 13,799,548
Length	115
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	76.63
Mean single sequence MFE	-31.18
Consensus MFE	-25.34
Energy contribution	-25.45
Covariance contribution	0.11
Combinations/Pair	1.22
Mean z-score	-0.88
Structure conservation index	0.81
SVM decision value	0.37
SVM RNA-class probability	0.709802
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13799433 115 - 20766785
AACUCCAAAGGGACGCGGAAAGCGCGGACGCAGUGCAGGUCUCACUCCUGACCUGAGCAACUUCACCGAGACCAGAAGUUCGGUAAGUAAAGCAUACAGAAUUCAGUUUUAGGCU
....((....(..((((.....))))..)((.((.((((((........)))))).)).((((.((((((........))))))))))...))..................)).. ( -32.70)
>DroVir_CAF1 122566 93 - 1
AACUCCAAAGGGACGCGGCAAGCGCGGACGCAGCGCUGGCUUAACGCCCGAUCUGAGCAACUUUACCGAAACCAGAAGCUCGGUGAGUCGA----------------------CU
.((((....(((.((.(((.(((((.......))))).)))...)))))...((((((..((...........))..)))))).))))...----------------------.. ( -29.10)
>DroEre_CAF1 100624 110 - 1
AACUCCAAAGGGACGCGGCAAGCGCGGACGCAGUGCAGGUCUCACUCCCGACCUGAGCAACUUUACCGAGACCAGAAGUUCGGUAAGUAAAGCAGACAGAAUUGAAUUGU-----
.....(((..(..((((.....))))..)((.((.((((((........)))))).)).((((.((((((........))))))))))...))........)))......----- ( -31.40)
>DroYak_CAF1 104796 108 - 1
AACUCCAAAGGGACGCGGCAAGCGCGGACGCAGUGCAGGUCUCACUCCCGACCUGAGCAACUUCACCGAAACCAGAAGUUCGGUAAGUAAAACAAACAGGAUUUAA--GA-----
...(((....(..((((.....))))..)...((.((((((........)))))).)).((((.((((((........))))))))))..........))).....--..----- ( -31.40)
>DroMoj_CAF1 136453 90 - 1
UACUCCAAAGGGACGCGGCAAGCGCGGACGCAGCGCAGGUCUGACGCCCGAUCUGAGCAACUUUACCGAAACCAGAAGCUCGGUGAGUAC-------------------------
(((((....(((.((((((..((((.......))))..).))).)))))...((((((..((...........))..)))))).))))).------------------------- ( -29.80)
>DroAna_CAF1 108995 110 - 1
AACUCCAAAGGGACGCGGCAAGCGCGGACGCAGUGCAGGUCUGACACCGGACCUCAGCAACUUUACCGAGACCAGAAGUUCGGUAAGA----CAUCUCUAAUC-CUUCCUAGUCC
..........(((((((.....)))(((.((..((.(((((((....)))))))))))...(((((((((........))))))))).----.........))-)......)))) ( -32.70)
>consensus
AACUCCAAAGGGACGCGGCAAGCGCGGACGCAGUGCAGGUCUCACUCCCGACCUGAGCAACUUUACCGAAACCAGAAGUUCGGUAAGUAAA_CA_ACAGAAUU_A____U_____
..........(..((((.....))))..)...((.((((((........)))))).)).((((.((((((........))))))))))........................... (-25.34 = -25.45 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:03 2006