Locus 1266

Sequence ID	X_DroMel_CAF1
Location	3,773,034 – 3,773,137
Length	103
Max. P	0.678171

overview

Window 2

Location	3,773,034 – 3,773,137
Length	103
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	77.73
Mean single sequence MFE	-27.02
Consensus MFE	-13.24
Energy contribution	-13.64
Covariance contribution	0.40
Combinations/Pair	1.11
Mean z-score	-1.84
Structure conservation index	0.49
SVM decision value	0.05
SVM RNA-class probability	0.556478
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3773034 103 + 22224390
--------CCUCGCCGUAUUCUCAACUUGUUCACCACACUUGUGUUUUAUUCGCAAUGUCCUGCCCACCAGGAACAGGACAAUCGAGAGCGAAAUCGGUAGUGGAAGCGAA
--------..((((.((.......)).......((((..(((((.......)))))(((((((.((....))..)))))))(((((........))))).))))..)))). ( -27.50)
>DroSec_CAF1 26271 109 + 1
CAGCUUCCACUCGCCGUAUUCUCCACUCGUUCUCCACACUCG--UUUCAUUCGCAAUGUCCUGCCCACCAAGACCAAGACAUUCGAGAGCGAAAUCGGUAGUGGAAGCGCA
..(((((((((.((((.(((......((((((((.((....)--).......(.((((((.((..(.....)..)).)))))))))))))))))))))))))))))))... ( -35.60)
>DroSim_CAF1 24082 103 + 1
------CCACUCGCCGUAUUCUCCACUCGUUCUCCACACUCG--UUUCAUUCGCAAUGUCCUGCCCACCAAGACCAAGACAUUCGAGAGCGAAAUCGGUAGUGGAAGCGCA
------(((((.((((.(((......((((((((.((....)--).......(.((((((.((..(.....)..)).)))))))))))))))))))))))))))....... ( -26.00)
>DroEre_CAF1 27215 96 + 1
------CC-CUCACAUUUUUCUACAUUUU-U-----CACUUG--UUUCAUUCGCAAUGUCCUGCCCACUAAGGACAGGACAUCCGACAGCGAAAUCGGUAGUGGAAGCGCA
------..-.................(((-(-----((((..--.....(((((.((((((((.((.....)).))))))))......)))))......)))))))).... ( -24.72)
>DroYak_CAF1 28186 96 + 1
------CC-UCUACAAUUUUCUACAUUUU-U-----CACUUG--UUUUAUUCGCAAUAUCCUGCCCACCAAGGUUAGGACAUCCGACUGCGAUGUCGGCAGUGGAAGCGCA
------..-........(((((((.....-.-----......--..............(((((.((.....)).)))))...(((((......)))))..))))))).... ( -21.30)
>consensus
______CC_CUCGCCGUAUUCUCCACUUGUUC_CCACACUUG__UUUCAUUCGCAAUGUCCUGCCCACCAAGAACAGGACAUUCGAGAGCGAAAUCGGUAGUGGAAGCGCA
.................................................(((((.((((((((..(.....)..))))))))((((........))))..)))))...... (-13.24 = -13.64 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	3,773,034 – 3,773,137
Length	103
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	77.73
Mean single sequence MFE	-33.47
Consensus MFE	-19.72
Energy contribution	-19.28
Covariance contribution	-0.44
Combinations/Pair	1.24
Mean z-score	-1.77
Structure conservation index	0.59
SVM decision value	0.30
SVM RNA-class probability	0.678171
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3773034 103 - 22224390
UUCGCUUCCACUACCGAUUUCGCUCUCGAUUGUCCUGUUCCUGGUGGGCAGGACAUUGCGAAUAAAACACAAGUGUGGUGAACAAGUUGAGAAUACGGCGAGG--------
((((((........(((((((((..(((..((((((((.((....))))))))))...)))......(((....))))))))...)))).......)))))).-------- ( -31.16)
>DroSec_CAF1 26271 109 - 1
UGCGCUUCCACUACCGAUUUCGCUCUCGAAUGUCUUGGUCUUGGUGGGCAGGACAUUGCGAAUGAAA--CGAGUGUGGAGAACGAGUGGAGAAUACGGCGAGUGGAAGCUG
...(((((((((.(((.((((((((((((((((((((.((.....)).))))))))).)))......--.....((.....))))))))))....)))..))))))))).. ( -43.90)
>DroSim_CAF1 24082 103 - 1
UGCGCUUCCACUACCGAUUUCGCUCUCGAAUGUCUUGGUCUUGGUGGGCAGGACAUUGCGAAUGAAA--CGAGUGUGGAGAACGAGUGGAGAAUACGGCGAGUGG------
..((((((((((.....((((((.(((((((((((((.((.....)).)))))))))..........--)))).))))))....))))))......)))).....------ ( -34.20)
>DroEre_CAF1 27215 96 - 1
UGCGCUUCCACUACCGAUUUCGCUGUCGGAUGUCCUGUCCUUAGUGGGCAGGACAUUGCGAAUGAAA--CAAGUG-----A-AAAAUGUAGAAAAAUGUGAG-GG------
....((((((((((...(((((((.(((((((((((((((.....)))))))))))).)))......--..))))-----)-))...)))).....)).)))-).------ ( -35.00)
>DroYak_CAF1 28186 96 - 1
UGCGCUUCCACUGCCGACAUCGCAGUCGGAUGUCCUAACCUUGGUGGGCAGGAUAUUGCGAAUAAAA--CAAGUG-----A-AAAAUGUAGAAAAUUGUAGA-GG------
..(((.((((((((.(....)))))).)))((((((..((.....))..))))))..))).......--......-----.-....................-..------ ( -23.10)
>consensus
UGCGCUUCCACUACCGAUUUCGCUCUCGAAUGUCCUGGUCUUGGUGGGCAGGACAUUGCGAAUGAAA__CAAGUGUGG_GAACAAGUGGAGAAUACGGCGAG_GG______
........((((......(((((.....(((((((((.(((....))))))))))))))))).........)))).................................... (-19.72 = -19.28 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:22 2006