Locus 6055

Sequence ID	2R_DroMel_CAF1
Location	19,058,851 – 19,058,941
Length	90
Max. P	0.657203

overview

Window 2

Location	19,058,851 – 19,058,941
Length	90
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	84.09
Mean single sequence MFE	-28.70
Consensus MFE	-19.90
Energy contribution	-19.66
Covariance contribution	-0.24
Combinations/Pair	1.17
Mean z-score	-1.81
Structure conservation index	0.69
SVM decision value	0.26
SVM RNA-class probability	0.657203
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19058851 90 + 20766785
AGAACACCCUCUACAAAUUAAUCGAUGGCCACCAAUCGAUGAUU-------AGUGCUAUCGACGAGCGGCCAUCGCCGCUUGGCGGCAAGUGCAUAC
....(((................(((((((.(...((((((...-------.....))))))...).)))))))(((((...)))))..)))..... ( -29.90)
>DroSec_CAF1 1315 90 + 1
AGAACACCCUCUACAAAUUAAUCGAUGGCUACCAAUCGAUGAUU-------AGUGCUAUCGACGGGCGGCCAUCGCCGCUUGGCGGCAAGUGCAUAC
....(((................((((((..((..((((((...-------.....))))))..))..))))))(((((...)))))..)))..... ( -33.00)
>DroSim_CAF1 1169 90 + 1
AGAACACCCUCUACAAAUUAAUCGAUGGAUACCAAUCGAUGAUU-------UGUGCUAUCGACGGACGGCCAUCGCCGCUUGGCGGCAAGUGCAUAC
....(((.....((((((((.(((((((...)).))))))))))-------)))(((..((((((.((.....))))).)))..)))..)))..... ( -25.20)
>DroEre_CAF1 1358 92 + 1
GGAACACCCUCUACACAUUAAUCGAUAUCGCCCAGUCGAUG-----UCAGCCGUGCUAUCGAAGGCCGGUCAUCGCCGCUUGGCGGCAAGUGCAUAC
((.....))....(((.......(((((((......)))))-----)).((((.(((......)))))))....(((((...)))))..)))..... ( -27.30)
>DroYak_CAF1 1347 97 + 1
AGAACACCUUUAUUAAAUUAAUCGAUUUCACCCAAUCGAUGUUUAGUCGGCUGUGCUAUCGACGGCCGGCCAUCGUCGCUUGGCGGCAAGUGCAUAC
....(((......(((((..(((((((......))))))))))))(((((((((.......)))))))))....(((((...)))))..)))..... ( -28.10)
>consensus
AGAACACCCUCUACAAAUUAAUCGAUGGCUACCAAUCGAUGAUU_______AGUGCUAUCGACGGCCGGCCAUCGCCGCUUGGCGGCAAGUGCAUAC
....................((((((........))))))............(..((...((.((....)).))(((((...))))).))..).... (-19.90 = -19.66 +  -0.24)

alignment

secondary structure

dotplot

Window 3

Location	19,058,851 – 19,058,941
Length	90
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	84.09
Mean single sequence MFE	-31.04
Consensus MFE	-23.43
Energy contribution	-24.91
Covariance contribution	1.48
Combinations/Pair	1.15
Mean z-score	-1.61
Structure conservation index	0.75
SVM decision value	0.13
SVM RNA-class probability	0.596088
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19058851 90 - 20766785
GUAUGCACUUGCCGCCAAGCGGCGAUGGCCGCUCGUCGAUAGCACU-------AAUCAUCGAUUGGUGGCCAUCGAUUAAUUUGUAGAGGGUGUUCU
....(((((((((((...)))))((((((((((.((((((......-------....)))))).))))))))))..............))))))... ( -39.00)
>DroSec_CAF1 1315 90 - 1
GUAUGCACUUGCCGCCAAGCGGCGAUGGCCGCCCGUCGAUAGCACU-------AAUCAUCGAUUGGUAGCCAUCGAUUAAUUUGUAGAGGGUGUUCU
....(((((((((((...)))))((((((..((.((((((......-------....)))))).))..))))))..............))))))... ( -35.50)
>DroSim_CAF1 1169 90 - 1
GUAUGCACUUGCCGCCAAGCGGCGAUGGCCGUCCGUCGAUAGCACA-------AAUCAUCGAUUGGUAUCCAUCGAUUAAUUUGUAGAGGGUGUUCU
....(((((((((((...)))))(((((....)))))......(((-------(((.((((((.((...))))))))..))))))...))))))... ( -27.60)
>DroEre_CAF1 1358 92 - 1
GUAUGCACUUGCCGCCAAGCGGCGAUGACCGGCCUUCGAUAGCACGGCUGA-----CAUCGACUGGGCGAUAUCGAUUAAUGUGUAGAGGGUGUUCC
....(((((((((((...)))))((((..(((((...........))))).-----))))..(((.(((.((.....)).))).))).))))))... ( -27.70)
>DroYak_CAF1 1347 97 - 1
GUAUGCACUUGCCGCCAAGCGACGAUGGCCGGCCGUCGAUAGCACAGCCGACUAAACAUCGAUUGGGUGAAAUCGAUUAAUUUAAUAAAGGUGUUCU
....(((((((((((((........))).)))).((((((..(((..(((((........).)))))))..))))))...........))))))... ( -25.40)
>consensus
GUAUGCACUUGCCGCCAAGCGGCGAUGGCCGCCCGUCGAUAGCACA_______AAUCAUCGAUUGGUAGCCAUCGAUUAAUUUGUAGAGGGUGUUCU
....(((((((((((...)))))((((((.(((.((((((.................)))))).))).))))))..............))))))... (-23.43 = -24.91 +   1.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:25 2006