Locus 3015

Sequence ID	X_DroMel_CAF1
Location	8,058,344 – 8,058,442
Length	98
Max. P	0.890781

overview

Window 6

Location	8,058,344 – 8,058,442
Length	98
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	89.57
Mean single sequence MFE	-26.30
Consensus MFE	-18.37
Energy contribution	-18.77
Covariance contribution	0.40
Combinations/Pair	1.10
Mean z-score	-2.04
Structure conservation index	0.70
SVM decision value	0.12
SVM RNA-class probability	0.593177
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8058344 98 + 22224390
AAAAAAUUCACGGCACGCGCAUGCGCAGCAUUUUUUCUACUGCUGUCCGCAUGUUGUUCUUUUCGUUCGAGUUUGCU----------GUACUGUUCUGUGCCUUUUCA
...........(((((..((((((((((((..........)))))..))))))).((....(((....)))...)).----------..........)))))...... ( -24.20)
>DroSec_CAF1 40318 98 + 1
AAAAAAUUCUCGGCACGCGCAUGCGCAGCAUUUUUUCUACUGCUGUCCGCAUGUUGUUCUUUUCGUUCGAGUUUGCU----------GUACUGUUCUGUGCCUUUUCA
...........(((((..((((((((((((..........)))))..))))))).((....(((....)))...)).----------..........)))))...... ( -24.20)
>DroSim_CAF1 15990 98 + 1
AAAAAAUUCUCGGCACGCGCAUGCGCAGCAUUUUUUCUACUGCUGUCCGCAUGUUGUUCUUUUCGUUCGAGUUUGCU----------GUACUGUUCUGUGCCUUUUCA
...........(((((..((((((((((((..........)))))..))))))).((....(((....)))...)).----------..........)))))...... ( -24.20)
>DroEre_CAF1 28187 94 + 1
AAAAAAUUCUCGGCACGCGCAUGCGCAGCAUUUUUUCUACUGCGGUCAGCACGUUGUUCCUUU----CGAGUUUGCU----------GUGCUGUGCUGUGCCUUUUCA
...........((((((((((.((((((((..(((...((.(((.......))).))......----.)))..))))----------))))))))).)))))...... ( -34.40)
>DroYak_CAF1 34180 104 + 1
AAAAAAUUCUCGGCACGCGCAUGCGCAGCAUUUUUUCUACUGUUGUCCGCACGUUGUUCUUUU----CGAGUUUGCUAUGCUGUACUGUGCUGUGCUUUGCCUUUUCA
...........((((.(((((.((((((.........(((.((.((..((.((..(....)..----)).))..))...)).))))))))))))))..))))...... ( -24.50)
>consensus
AAAAAAUUCUCGGCACGCGCAUGCGCAGCAUUUUUUCUACUGCUGUCCGCAUGUUGUUCUUUUCGUUCGAGUUUGCU__________GUACUGUUCUGUGCCUUUUCA
...........(((((..((((((((((((..........))))))..)))))).((............((....))............))......)))))...... (-18.37 = -18.77 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	8,058,344 – 8,058,442
Length	98
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	89.57
Mean single sequence MFE	-25.00
Consensus MFE	-19.28
Energy contribution	-19.20
Covariance contribution	-0.08
Combinations/Pair	1.11
Mean z-score	-2.04
Structure conservation index	0.77
SVM decision value	0.96
SVM RNA-class probability	0.890781
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8058344 98 - 22224390
UGAAAAGGCACAGAACAGUAC----------AGCAAACUCGAACGAAAAGAACAACAUGCGGACAGCAGUAGAAAAAAUGCUGCGCAUGCGCGUGCCGUGAAUUUUUU
......(((((..........----------.......((....)).........((((((..(((((..........)))))))))))...)))))........... ( -23.00)
>DroSec_CAF1 40318 98 - 1
UGAAAAGGCACAGAACAGUAC----------AGCAAACUCGAACGAAAAGAACAACAUGCGGACAGCAGUAGAAAAAAUGCUGCGCAUGCGCGUGCCGAGAAUUUUUU
......(((((..........----------.......((....)).........((((((..(((((..........)))))))))))...)))))........... ( -23.00)
>DroSim_CAF1 15990 98 - 1
UGAAAAGGCACAGAACAGUAC----------AGCAAACUCGAACGAAAAGAACAACAUGCGGACAGCAGUAGAAAAAAUGCUGCGCAUGCGCGUGCCGAGAAUUUUUU
......(((((..........----------.......((....)).........((((((..(((((..........)))))))))))...)))))........... ( -23.00)
>DroEre_CAF1 28187 94 - 1
UGAAAAGGCACAGCACAGCAC----------AGCAAACUCG----AAAGGAACAACGUGCUGACCGCAGUAGAAAAAAUGCUGCGCAUGCGCGUGCCGAGAAUUUUUU
......(((((.(((((((((----------.......((.----...))......))))))..(((((((.......)))))))..)))..)))))........... ( -33.52)
>DroYak_CAF1 34180 104 - 1
UGAAAAGGCAAAGCACAGCACAGUACAGCAUAGCAAACUCG----AAAAGAACAACGUGCGGACAACAGUAGAAAAAAUGCUGCGCAUGCGCGUGCCGAGAAUUUUUU
......(((...((...((........))...)).......----.........(((((((.....(((((.......)))))....))))))))))........... ( -22.50)
>consensus
UGAAAAGGCACAGAACAGUAC__________AGCAAACUCGAACGAAAAGAACAACAUGCGGACAGCAGUAGAAAAAAUGCUGCGCAUGCGCGUGCCGAGAAUUUUUU
......(((((......((.............)).....................(((((.....((((((.......)))))))))))...)))))........... (-19.28 = -19.20 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:58 2006