Locus 6337

Sequence ID	2R_DroMel_CAF1
Location	19,856,418 – 19,856,522
Length	104
Max. P	0.999738

overview

Window 9

Location	19,856,418 – 19,856,522
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	73.72
Mean single sequence MFE	-36.30
Consensus MFE	-27.03
Energy contribution	-26.39
Covariance contribution	-0.64
Combinations/Pair	1.44
Mean z-score	-3.55
Structure conservation index	0.74
SVM decision value	3.98
SVM RNA-class probability	0.999738
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19856418 104 + 20766785
UUAGGAUGCUAUGAUCCACUGGGCUUCGCCUUCUGGCUUUUACUUGCCACUAGC--------------GUAAAGUACAGGCUAGUUAACGAAGUUCCAU-AGACCA-CACCAAAAUGAAU
...((...(((((.......((((((((....(((((((.(((((..(......--------------)..))))).)))))))....)))))))))))-)).)).-............. ( -27.61)
>DroSec_CAF1 98403 104 + 1
UUAGGACGCUAUGGUCCACUGGGCUUCGCAAUCUGGCCUUUACUUUCCAAUAGC--------------GUAAAGUAGAGGCUAGUUAACGAAGUUCCAU-AGACCA-CACCAAAAUAAUU
...........(((((...(((((((((....((((((((((((((.(......--------------).))))))))))))))....))))).)))).-.)))))-............. ( -37.40)
>DroSim_CAF1 75276 104 + 1
UUAGGAUGCUAUGGUCCACGGAGCUUCGCACUCUGGCUUUUACUUUCCAAUAGC--------------GCUUAUUGGAGGCUAGUUAACGAAGUUCCAU-AGACCA-CACCAAAAUGAUU
...((.((...(((((...(((((((((....((((((.......((((((((.--------------..))))))))))))))....)))))))))..-.)))))-))))......... ( -35.61)
>DroEre_CAF1 100290 119 + 1
CUGGGAUGCUGUGGUCCACUGGGCUUUGUAUUCUGGCUCUUACUUUCCAAACGCAUAGAACGGCGAUUGUAGAGUAACUGCCAGCUUGCGAAGUUCCAUUAGAACA-CUCCGAAGUGAUU
(((((((......))))..(((((((((((..(((((..(((((((.(((.(((........))).))).)))))))..)))))..))))))).)))).)))..((-((....))))... ( -41.40)
>DroYak_CAF1 98256 115 + 1
CUAGGAUGCUAUGGUCCACCGGGCUUUGUAUUCUGGCGCUUACUUUACAAAAGUUAA-----AUGAUUGUAGAGUAACUGCUAGCUUACAAAGUUCAAAUGGAACCCCUCCAAAAUGACU
...(((.(....((((((..((((((((((..((((((.(((((((((((.......-----....))))))))))).))))))..))))))))))...))).)))).)))......... ( -39.50)
>consensus
UUAGGAUGCUAUGGUCCACUGGGCUUCGCAUUCUGGCUUUUACUUUCCAAUAGC______________GUAAAGUAAAGGCUAGUUAACGAAGUUCCAU_AGACCA_CACCAAAAUGAUU
...((((......))))...((((((((....(((((((((((((..........................)))))))))))))....))))))))........................ (-27.03 = -26.39 +  -0.64)

alignment

secondary structure

dotplot

Window 0

Location	19,856,418 – 19,856,522
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	73.72
Mean single sequence MFE	-34.32
Consensus MFE	-13.01
Energy contribution	-13.93
Covariance contribution	0.92
Combinations/Pair	1.24
Mean z-score	-2.75
Structure conservation index	0.38
SVM decision value	3.20
SVM RNA-class probability	0.998715
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19856418 104 - 20766785
AUUCAUUUUGGUG-UGGUCU-AUGGAACUUCGUUAACUAGCCUGUACUUUAC--------------GCUAGUGGCAAGUAAAAGCCAGAAGGCGAAGCCCAGUGGAUCAUAGCAUCCUAA
........((.((-((((((-((((..(((((((.((((((.((.....)).--------------))))))(((........)))....))))))).))).))))))))).))...... ( -34.70)
>DroSec_CAF1 98403 104 - 1
AAUUAUUUUGGUG-UGGUCU-AUGGAACUUCGUUAACUAGCCUCUACUUUAC--------------GCUAUUGGAAAGUAAAGGCCAGAUUGCGAAGCCCAGUGGACCAUAGCGUCCUAA
.........(.((-((((((-((((..((((((...((.((((.((((((.(--------------(....)).)))))).)))).))...)))))).))).))))))))).)....... ( -37.30)
>DroSim_CAF1 75276 104 - 1
AAUCAUUUUGGUG-UGGUCU-AUGGAACUUCGUUAACUAGCCUCCAAUAAGC--------------GCUAUUGGAAAGUAAAAGCCAGAGUGCGAAGCUCCGUGGACCAUAGCAUCCUAA
........((.((-((((((-(((((.((((((...((.((.(((((((...--------------..)))))))........)).))...)))))).))))))))))))).))...... ( -38.90)
>DroEre_CAF1 100290 119 - 1
AAUCACUUCGGAG-UGUUCUAAUGGAACUUCGCAAGCUGGCAGUUACUCUACAAUCGCCGUUCUAUGCGUUUGGAAAGUAAGAGCCAGAAUACAAAGCCCAGUGGACCACAGCAUCCCAG
.....(....).(-((.((((.(((..(((.(....(((((..(((((...(((.(((........))).)))...)))))..)))))....).))).))).)))).))).......... ( -31.00)
>DroYak_CAF1 98256 115 - 1
AGUCAUUUUGGAGGGGUUCCAUUUGAACUUUGUAAGCUAGCAGUUACUCUACAAUCAU-----UUAACUUUUGUAAAGUAAGCGCCAGAAUACAAAGCCCGGUGGACCAUAGCAUCCUAG
.........(((..(((.((((..(..(((((((..((.((..(((((.(((((....-----.......))))).)))))..)).))..))))))).)..)))))))......)))... ( -29.70)
>consensus
AAUCAUUUUGGUG_UGGUCU_AUGGAACUUCGUUAACUAGCCUCUACUCUAC______________GCUAUUGGAAAGUAAAAGCCAGAAUGCGAAGCCCAGUGGACCAUAGCAUCCUAA
.........((...((((((..(((..((((((...((.((...((((............................))))...)).))...)))))).)))..))))))......))... (-13.01 = -13.93 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:40 2006