Locus 5915

Sequence ID	2R_DroMel_CAF1
Location	18,657,691 – 18,657,820
Length	129
Max. P	0.868402

overview

Window 3

Location	18,657,691 – 18,657,794
Length	103
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	84.88
Mean single sequence MFE	-33.28
Consensus MFE	-22.98
Energy contribution	-24.87
Covariance contribution	1.89
Combinations/Pair	1.10
Mean z-score	-3.09
Structure conservation index	0.69
SVM decision value	0.37
SVM RNA-class probability	0.709600
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18657691 103 - 20766785
GAAAUUAAGUCAAUGUCCUGCGGGGUCAGUUGCGUUUUGGAUAAAUGUAAUUAACCUUUAGGAUCGCGAGCAUUGAGUUGGGUAUCCCAACUUAAACAACGGA-----
.........((...((((((.(((((.((((((((((.....)))))))))).)))))))))))...))...((((((((((...))))))))))........----- ( -31.70)
>DroSec_CAF1 21228 103 - 1
GAAAUUAAGUCAAUGUCCUGCGGGGUCAGUUGCGUUUUGGAUAAAUGUAAUUAACCUUCAGGAUCGCGAGCAUUGAGUUGGGUAGCCCAACUUAAACAACGCA-----
..............((((((.(((((.((((((((((.....)))))))))).))))))))))).(((....((((((((((...))))))))))....))).----- ( -37.60)
>DroEre_CAF1 21208 103 - 1
GAAAUUAAGUCAAUGUCCUGCGGGUUCAGUUGCGUUUUGGAUAAAUGUAAUUAACCUUCAGGAUCGCCAGCAUUGAGUUGGGUAGCCCAACUUAAACAGCGGA-----
..............((((((.(((((.((((((((((.....))))))))))))))).))))))(((.....((((((((((...))))))))))...)))..----- ( -36.80)
>DroWil_CAF1 32262 100 - 1
GAAAUUAAGUCAAUGUCCUGCGGGGUCAGUUGCGUU-UGGAUAAAUGUAAUUAACCUACAGGAUA---AGCAUUGAGUUGGGUCCU----UUUAAUAAUCAAGGACAA
....((((.(((((((((((..((((.(((((((((-(....)))))))))).)))).))))...---.))))))).))))(((((----(.........)))))).. ( -33.30)
>DroYak_CAF1 21653 103 - 1
GAAAUUAAGCCAAUGUCCUGCGGGGUCAGUUGCGUUUUGGAUAAAUGUAAUUAACCUUCAGGAUCGCGCGAGUUGAGUUGGGUAGUCCAACUUAAACAACGGA-----
........((....((((((.(((((.((((((((((.....)))))))))).))))))))))).)).((..(((((((((.....)))))))))....))..----- ( -33.60)
>DroAna_CAF1 21844 95 - 1
GAAAUUAAGUCAAUGUCCUGCGG-GUCAGUUGCGUUUUGGAUAAAUGUAAUUAACCUUAAGGAUCGACGGCAUUGAGUUGGGUCGCC-------AGGGACGGA-----
....((((.((((((((((..((-((.((((((((((.....)))))))))).))))..))).......))))))).))))(((...-------...)))...----- ( -26.71)
>consensus
GAAAUUAAGUCAAUGUCCUGCGGGGUCAGUUGCGUUUUGGAUAAAUGUAAUUAACCUUCAGGAUCGCGAGCAUUGAGUUGGGUAGCCCAACUUAAACAACGGA_____
..............((((((.(((...((((((((((.....))))))))))..))).))))))........((((((((((...))))))))))............. (-22.98 = -24.87 +   1.89)

alignment

secondary structure

dotplot

Window 4

Location	18,657,714 – 18,657,820
Length	106
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	80.55
Mean single sequence MFE	-26.39
Consensus MFE	-20.29
Energy contribution	-20.54
Covariance contribution	0.25
Combinations/Pair	1.08
Mean z-score	-1.85
Structure conservation index	0.77
SVM decision value	0.86
SVM RNA-class probability	0.868402
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18657714 106 - 20766785
GACGAUGAAGA-ACAAC-AAACGCCACGGAAAUUAAGUCAAUGUCCUGCGGGGUCAGUUGCGUUUUGGAUAAAUGUAAUUAACCUUUAGGAUCGCGAGCAUUGAGUUG
...........-.((((-.....(....)........(((((((((((.(((((.((((((((((.....)))))))))).)))))))))).(....))))))))))) ( -24.90)
>DroVir_CAF1 43340 103 - 1
GGAGGGGUGGAAAAAAA-AAACGCUGGGGAAAUUAAGUCAAUGUCCUGCGGGGUCAGUUGCGUU-UGGAUAAAUGUAAUUAACCUUCAGGAUA---AGCAUUGAGUUG
.....((((........-...))))........(((.(((((((((((.(((((.(((((((((-(....)))))))))).)))))))))...---.))))))).))) ( -28.60)
>DroGri_CAF1 42643 103 - 1
AAACAAAAUAAAAGAAA-AAACGCUGGGGAAAUUAAGUCAAUGUCCUGCGGGGUCAGUUGCGUU-UGGAUAAAUGUAAUUAACCUUCAGGAUA---AGCAUUGAGUUG
.................-...............(((.(((((((((((.(((((.(((((((((-(....)))))))))).)))))))))...---.))))))).))) ( -26.20)
>DroWil_CAF1 32286 101 - 1
UGCGGGAAAA---AAACAGAACGCCAGGGAAAUUAAGUCAAUGUCCUGCGGGGUCAGUUGCGUU-UGGAUAAAUGUAAUUAACCUACAGGAUA---AGCAUUGAGUUG
.(((......---........))).........(((.(((((((((((..((((.(((((((((-(....)))))))))).)))).))))...---.))))))).))) ( -27.74)
>DroAna_CAF1 21860 99 - 1
AA----A-AGG-AAAAC--AGCGCCAGGGAAAUUAAGUCAAUGUCCUGCGG-GUCAGUUGCGUUUUGGAUAAAUGUAAUUAACCUUAAGGAUCGACGGCAUUGAGUUG
..----.-...-....(--((.(((((.....))..(((...(((((..((-((.((((((((((.....)))))))))).))))..))))).)))))).)))..... ( -25.40)
>DroPer_CAF1 24949 101 - 1
GAGGGUA-GG-----GA-AAACGGCAUGGAAAUUAAGUCAAUGUCCUGCGGGUUCCAUUGCGUUGUGGAUAAAUGUAAUUAACCUUCAGGAUCAGAAUCAUUGAGUUG
((((((.-((-----((-...(.(((.(((.(((.....))).)))))).).))))((((((((.......))))))))..))))))..................... ( -25.50)
>consensus
GAAGGGAAAGA_AAAAA_AAACGCCAGGGAAAUUAAGUCAAUGUCCUGCGGGGUCAGUUGCGUU_UGGAUAAAUGUAAUUAACCUUCAGGAUA___AGCAUUGAGUUG
.................................(((.(((((((((((.(((...(((((((((.......)))))))))..))).))))).......)))))).))) (-20.29 = -20.54 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:00 2006