Locus 7134

Sequence ID	3R_DroMel_CAF1
Location	18,791,563 – 18,791,687
Length	124
Max. P	0.549731

overview

Window 1

Location	18,791,563 – 18,791,653
Length	90
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	82.22
Mean single sequence MFE	-21.22
Consensus MFE	-14.17
Energy contribution	-14.70
Covariance contribution	0.53
Combinations/Pair	1.06
Mean z-score	-1.47
Structure conservation index	0.67
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18791563 90 - 27905053
CCCCCCUACAACUCCUUCUUGCCAAUCUUAUCGCUUGGCUAACGAACUAACGCCAUUAGCCAACGUGGCCGGUGCGACAACCAGUG----GCUA
....................((((......((((((((((((((......))...)))))))).))))..(((......)))..))----)).. ( -21.80)
>DroSec_CAF1 16848 90 - 1
CCCCGCAACUCCUUCUCCUUGCCAAUCUUAUCGCUUGGCUAACGAACUAACGCCAUUAGCCAACGCGGCCGGUGCGACAACCAGUG----GCUA
....................((((......((((((((((((((......))...)))))))).))))..(((......)))..))----)).. ( -23.70)
>DroSim_CAF1 19211 90 - 1
CCCCACAACUCCUUCUUCUUGCCAAUCUUAUCGCUUGGCUAACGAACUAACGCCAUUAGCCAACGCGGCCGGUGCGACAACCAGUG----GCUA
....................((((......((((((((((((((......))...)))))))).))))..(((......)))..))----)).. ( -23.70)
>DroEre_CAF1 16416 87 - 1
CCGCAAAACUCCU---UCUCGCCAAUCUUAUCGCUUGGCUAACGAACUAACGCCAUUAGCCAACGCGGCCGGUGCGACAACCAGUG----GCUA
.............---....((((......((((((((((((((......))...)))))))).))))..(((......)))..))----)).. ( -24.00)
>DroWil_CAF1 17158 68 - 1
-------------------UGGCAAUCUUAUCGCUUGGCUAACGAAGUAACGCCAUUAGGCAACGCGU---UUGCGACAACAAACA----ACAA
-------------------..((.........((((.(....).))))...(((....)))...))((---(((......))))).----.... ( -13.40)
>DroYak_CAF1 18576 91 - 1
CCGCACAACUCCU---UCUUGCCAAUCUUAUCGCUUGGCUAACGAACUAACGCCAUUAGCCAACGCGGCCGGUGCGACAACCAGUGACCAGCUA
...(((.......---..............((((((((((((((......))...)))))))).))))..(((......))).)))........ ( -20.70)
>consensus
CCCCACAACUCCU___UCUUGCCAAUCUUAUCGCUUGGCUAACGAACUAACGCCAUUAGCCAACGCGGCCGGUGCGACAACCAGUG____GCUA
....................((.........(((((((((((((......))...)))))))).)))...(((......)))........)).. (-14.17 = -14.70 +   0.53)

alignment

secondary structure

dotplot

Window 2

Location	18,791,592 – 18,791,687
Length	95
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	79.33
Mean single sequence MFE	-30.72
Consensus MFE	-17.54
Energy contribution	-18.10
Covariance contribution	0.56
Combinations/Pair	1.17
Mean z-score	-1.68
Structure conservation index	0.57
SVM decision value	0.03
SVM RNA-class probability	0.549731
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18791592 95 + 27905053
GGCUAAUGGCGUUAGUUCGUUAGCCAAGCGAUAAGAUUGGCAAGAAGGAGUUGUAGGGG-----------G---GGAGUUGUGCUCGCAAUCACCAAUGUUUGUAGCAG
((((((((((....).)))))))))..((.(((((((((((((.......)))..((..-----------(---.(((.....))).)..)).))))).))))).)).. ( -26.10)
>DroPse_CAF1 23980 109 + 1
GGCUAAUGGCGUUAGUUCGUUAGCCAAGCGAUAAGAUUGCCAGCCGAAAGGGGGUCCGGUUCAAAGAACAGGGAGGGCAAGGCAUCCCCAUCUCCCAAUCUGGCGGCAG
((((((((((....).)))))))))............((((.(((((..(((((....((((...)))).((((..((...)).))))...)))))..)).))))))). ( -40.20)
>DroSec_CAF1 16877 95 + 1
GGCUAAUGGCGUUAGUUCGUUAGCCAAGCGAUAAGAUUGGCAAGGAGAAGGAGUUGCGG-----------G---GGACGACUGCUCGCAAUCACCAAUGUUUGUAGCAG
.((((..((((((..(((.((.(((((.(.....).))))))).)))..((.(((((((-----------(---.(.....).))))))))..))))))))..)))).. ( -29.50)
>DroSim_CAF1 19240 95 + 1
GGCUAAUGGCGUUAGUUCGUUAGCCAAGCGAUAAGAUUGGCAAGAAGAAGGAGUUGUGG-----------G---GGACGACUGCUCGCAAUCACCAAUGUUUGUAGCAG
((((((((((....).)))))))))..((.((((((((((...((.....((((.((.(-----------.---...).)).))))....)).))))).))))).)).. ( -30.30)
>DroEre_CAF1 16445 89 + 1
GGCUAAUGGCGUUAGUUCGUUAGCCAAGCGAUAAGAUUGGCGAGA---AGGAGUUUUGC-----------G---GG---ACUGCUCACAAUCACCAAUGUUUGUGGCAG
((((((((((....).)))))))))..((.((((((((((.((..---..((((.....-----------.---..---...))))....)).))))).))))).)).. ( -30.60)
>DroYak_CAF1 18609 90 + 1
GGCUAAUGGCGUUAGUUCGUUAGCCAAGCGAUAAGAUUGGCAAGA---AGGAGUUGUGC-----------G---GGA--ACCGCUCACAAUCACCAAUGUUUGUAGCAG
((((((((((....).)))))))))..((.((((((((((.....---..((((.((..-----------.---...--)).)))).......))))).))))).)).. ( -27.64)
>consensus
GGCUAAUGGCGUUAGUUCGUUAGCCAAGCGAUAAGAUUGGCAAGAAGAAGGAGUUGUGG___________G___GGAC_ACUGCUCGCAAUCACCAAUGUUUGUAGCAG
((((((((((....).)))))))))..((.(......).)).......................................(((((.((((.((....)).))))))))) (-17.54 = -18.10 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:15 2006