Locus 6499

Sequence ID	3L_DroMel_CAF1
Location	17,261,542 – 17,261,662
Length	120
Max. P	0.998181

overview

Window 3

Location	17,261,542 – 17,261,662
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.99
Mean single sequence MFE	-36.96
Consensus MFE	-31.26
Energy contribution	-33.10
Covariance contribution	1.84
Combinations/Pair	1.03
Mean z-score	-1.60
Structure conservation index	0.85
SVM decision value	0.93
SVM RNA-class probability	0.884583
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17261542 120 + 23771897
AACAGUCCCGGGCACUGUUGUUGUAAUUAUGUUGCCGGCUGUAAAACAAACUGCCAACAACGUCGACGAACAAGAGCCUCCAAGAAGACGAAGGAGAGCAACGCCAGUUGCGCCAGGACA
....((((..(((.((.(((((((....((((((..(((.((.......)).)))..))))))..)).))))).)).((((...........)))).(((((....)))))))).)))). ( -39.40)
>DroSec_CAF1 145110 120 + 1
AACAGUCCCGGGCACUGUUGUUGUAAUUAUGUUGCCGGCUGUAAAACAAACUGCCAACAACGUCGACGAACAAGAGCCUCCAAGAAGACGAAGGAGAGCAACGCCAGUUGCGCCAGGACA
....((((..(((.((.(((((((....((((((..(((.((.......)).)))..))))))..)).))))).)).((((...........)))).(((((....)))))))).)))). ( -39.40)
>DroSim_CAF1 140011 120 + 1
AACAGUCCCGGGCACUGUUGUUGUAAUUAUGUUGCCGGCUGUAAAACAAACUGCCAACAACGUCGACGAACAAGAGCCUCCAAGAAGACGAAGGAGAGCAACGCCAGUUGCGCCAGGACA
....((((..(((.((.(((((((....((((((..(((.((.......)).)))..))))))..)).))))).)).((((...........)))).(((((....)))))))).)))). ( -39.40)
>DroEre_CAF1 148228 118 + 1
AAGAGUCCCGGGCACUGUUGUUGUAAUUAUGUUGCCGGCUGUAAAACAAACUGCCAACAACGAGGACGAACAGGAGCCUCCAAGAAGACGAAGGAGAUG--CUGCCGUUGCGCCAGUACA
....((.(.((((.(((((((((((((...))))).(((.((.......)).))))))))).))((((..(((.(..((((...........)))).).--))).)))))).)).).)). ( -28.50)
>DroYak_CAF1 152510 118 + 1
AACAGUCCCGGGCGCUGUUGUUGUAAUUAUGUUGCCGGCUGUAAAACAAACUGCCAACAAGGACGACGAACAAGAGCCUCCAAGAAGACGAAGGAGCGC--CUGCCGUUGCGCCAGGACA
....((((..((((((((((((((.....(((((.(((.((.....))..))).)))))...))))).))))((.((((((...........)))).))--))......))))).)))). ( -38.10)
>consensus
AACAGUCCCGGGCACUGUUGUUGUAAUUAUGUUGCCGGCUGUAAAACAAACUGCCAACAACGUCGACGAACAAGAGCCUCCAAGAAGACGAAGGAGAGCAACGCCAGUUGCGCCAGGACA
....((((..(((.((.(((((((....((((((..(((.((.......)).)))..))))))..)).))))).)).((((...........)))).(((((....)))))))).)))). (-31.26 = -33.10 +   1.84)

alignment

secondary structure

dotplot

Window 4

Location	17,261,542 – 17,261,662
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.99
Mean single sequence MFE	-43.06
Consensus MFE	-36.80
Energy contribution	-37.24
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.53
Structure conservation index	0.85
SVM decision value	3.03
SVM RNA-class probability	0.998181
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17261542 120 - 23771897
UGUCCUGGCGCAACUGGCGUUGCUCUCCUUCGUCUUCUUGGAGGCUCUUGUUCGUCGACGUUGUUGGCAGUUUGUUUUACAGCCGGCAACAUAAUUACAACAACAGUGCCCGGGACUGUU
.(((((((.(((.(((..((((....((((((......))))))...............(((((((((.((.......)).))))))))).......))))..))))))))))))).... ( -45.00)
>DroSec_CAF1 145110 120 - 1
UGUCCUGGCGCAACUGGCGUUGCUCUCCUUCGUCUUCUUGGAGGCUCUUGUUCGUCGACGUUGUUGGCAGUUUGUUUUACAGCCGGCAACAUAAUUACAACAACAGUGCCCGGGACUGUU
.(((((((.(((.(((..((((....((((((......))))))...............(((((((((.((.......)).))))))))).......))))..))))))))))))).... ( -45.00)
>DroSim_CAF1 140011 120 - 1
UGUCCUGGCGCAACUGGCGUUGCUCUCCUUCGUCUUCUUGGAGGCUCUUGUUCGUCGACGUUGUUGGCAGUUUGUUUUACAGCCGGCAACAUAAUUACAACAACAGUGCCCGGGACUGUU
.(((((((.(((.(((..((((....((((((......))))))...............(((((((((.((.......)).))))))))).......))))..))))))))))))).... ( -45.00)
>DroEre_CAF1 148228 118 - 1
UGUACUGGCGCAACGGCAG--CAUCUCCUUCGUCUUCUUGGAGGCUCCUGUUCGUCCUCGUUGUUGGCAGUUUGUUUUACAGCCGGCAACAUAAUUACAACAACAGUGCCCGGGACUCUU
.(((((((((.(((((.((--(..((((...........))))))).))))))))....(((((((((.((.......)).))))))))).............))))))........... ( -37.10)
>DroYak_CAF1 152510 118 - 1
UGUCCUGGCGCAACGGCAG--GCGCUCCUUCGUCUUCUUGGAGGCUCUUGUUCGUCGUCCUUGUUGGCAGUUUGUUUUACAGCCGGCAACAUAAUUACAACAACAGCGCCCGGGACUGUU
.((((((((((.(((((..--(((..((((((......))))))....)))..)))))..((((((((.((.......)).))))))))................))).))))))).... ( -43.20)
>consensus
UGUCCUGGCGCAACUGGCGUUGCUCUCCUUCGUCUUCUUGGAGGCUCUUGUUCGUCGACGUUGUUGGCAGUUUGUUUUACAGCCGGCAACAUAAUUACAACAACAGUGCCCGGGACUGUU
.(((((((.((.............((((...........))))(((.(((((.((....(((((((((.((.......)).)))))))))......))))))).)))))))))))).... (-36.80 = -37.24 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:33 2006