Locus 5857

Sequence ID	2R_DroMel_CAF1
Location	18,518,242 – 18,518,396
Length	154
Max. P	0.999838

overview

Window 5

Location	18,518,242 – 18,518,341
Length	99
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	93.60
Mean single sequence MFE	-31.20
Consensus MFE	-24.98
Energy contribution	-25.18
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.84
Structure conservation index	0.80
SVM decision value	0.85
SVM RNA-class probability	0.865516
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18518242 99 - 20766785
CGUCUUUUGCAACUUUGCAACGUACGACUGCGCGUUGUUUGCAAUAAUAAAGAUGACAAAUUUCUCGUCAUUUGUAAUUUCAAUGCGAGAAGCCGGAGC------------
((((((((((((....((((((..(....)..))))))))))).....))))))).....((((((((...(((......))).)))))))).......------------ ( -25.90)
>DroSec_CAF1 17244 111 - 1
CGUCUUUUGCAACUUUGCAACGUACGACUGCGCGUUGUUUGCAAUAAUAAAGAUGACAAAUUUCUCGUCAUUUGUAAUUUCAAUGCGAGAAGCCGGAGCUUUGGAGCCGCG
((((((((((((....((((((..(....)..))))))))))).....)))))))......(((((((...(((......))).)))))))((.((..(....)..)))). ( -30.20)
>DroSim_CAF1 15661 111 - 1
CGUCUUUUGCAACUUUGCAACGUACGACUGCGCGUUGUUUGCAAUAAUAAAGAUGACAAAUUUCUCGUCAUUUGUAAUUUCAAUGCGAGAAGCCGGAGCUUUGGAGCCGCG
((((((((((((....((((((..(....)..))))))))))).....)))))))......(((((((...(((......))).)))))))((.((..(....)..)))). ( -30.20)
>DroEre_CAF1 20485 111 - 1
CGUCUUUUGCAACUUUGCAACGUACGACUGCGCGUUGUUUGCAAUAAUAAAGAUGACAAAUUUCUCGUCAUUUGUAAUUUCAAUGCGAGAAGCCGGAGCUUUGGAGCUCCG
((((((((((((....((((((..(....)..))))))))))).....))))))).....((((((((...(((......))).)))))))).(((((((....))))))) ( -36.80)
>DroYak_CAF1 23179 111 - 1
CGUCUUUUGCAACUUUGCAACGUACGACCGCGCGUUGUUUGCAAUAAUAAAGAUGACAAAUUUCUCGUCAUUUGUAAUUUCAAUGCGCGAAGCCGGAGCUUUGCAGCUUUG
(((.(.(((((....))))).).)))..(((((((((.(((((........((((((.........)))))))))))...)))))))))....(((((((....))))))) ( -32.90)
>consensus
CGUCUUUUGCAACUUUGCAACGUACGACUGCGCGUUGUUUGCAAUAAUAAAGAUGACAAAUUUCUCGUCAUUUGUAAUUUCAAUGCGAGAAGCCGGAGCUUUGGAGCCGCG
((((((((((((....((((((..(....)..))))))))))).....))))))).....((((((((...(((......))).))))))))................... (-24.98 = -25.18 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	18,518,301 – 18,518,396
Length	95
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	98.75
Mean single sequence MFE	-35.14
Consensus MFE	-34.64
Energy contribution	-34.64
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.88
Structure conservation index	0.99
SVM decision value	4.21
SVM RNA-class probability	0.999838
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18518301 95 + 20766785
AAACAACGCGCAGUCGUACGUUGCAAAGUUGCAAAAGACGACAAACGACGACAAUGCUCCCCUGGACAAUUGCAAUUGGCGGGGAGUGCGUG--CCG
......(((((.(((((...(((((....)))))...))))).............(((((((....((((....))))..))))))))))))--... ( -35.00)
>DroSec_CAF1 17315 95 + 1
AAACAACGCGCAGUCGUACGUUGCAAAGUUGCAAAAGACGACAAACGACGACAAUGCUCCCCUGGACAAUUGCAAUUGGCGGGGAGUGCGUG--CCG
......(((((.(((((...(((((....)))))...))))).............(((((((....((((....))))..))))))))))))--... ( -35.00)
>DroSim_CAF1 15732 95 + 1
AAACAACGCGCAGUCGUACGUUGCAAAGUUGCAAAAGACGACAAACGACGACAAUGCUCCCCUGGACAAUUGCAAUUGGCGGGGAGUGCGUG--CCG
......(((((.(((((...(((((....)))))...))))).............(((((((....((((....))))..))))))))))))--... ( -35.00)
>DroEre_CAF1 20556 97 + 1
AAACAACGCGCAGUCGUACGUUGCAAAGUUGCAAAAGACGACAAACGACGACAAUGCUCCCCUGGACAAUUGCAAUUGGCGGGGAGUGCGUGCGCCG
.......((((.(((((...(((((....)))))...))))).....(((.....(((((((....((((....))))..))))))).))))))).. ( -35.90)
>DroYak_CAF1 23250 95 + 1
AAACAACGCGCGGUCGUACGUUGCAAAGUUGCAAAAGACGACAAACGACGACAAUGCUCCCCUGGACAAUUGCAAUUGGCGGGGAGUGCGUG--CCG
......(((((.(((((...(((((....)))))...))))).............(((((((....((((....))))..))))))))))))--... ( -34.80)
>consensus
AAACAACGCGCAGUCGUACGUUGCAAAGUUGCAAAAGACGACAAACGACGACAAUGCUCCCCUGGACAAUUGCAAUUGGCGGGGAGUGCGUG__CCG
......(((((.(((((...(((((....)))))...))))).............(((((((....((((....))))..))))))))))))..... (-34.64 = -34.64 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	18,518,301 – 18,518,396
Length	95
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	98.75
Mean single sequence MFE	-31.70
Consensus MFE	-29.50
Energy contribution	-29.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.93
SVM decision value	1.21
SVM RNA-class probability	0.930861
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18518301 95 - 20766785
CGG--CACGCACUCCCCGCCAAUUGCAAUUGUCCAGGGGAGCAUUGUCGUCGUUUGUCGUCUUUUGCAACUUUGCAACGUACGACUGCGCGUUGUUU
(((--(.((((((((((..((((....))))....)))))).......(((((....(((....((((....))))))).))))))))).))))... ( -31.40)
>DroSec_CAF1 17315 95 - 1
CGG--CACGCACUCCCCGCCAAUUGCAAUUGUCCAGGGGAGCAUUGUCGUCGUUUGUCGUCUUUUGCAACUUUGCAACGUACGACUGCGCGUUGUUU
(((--(.((((((((((..((((....))))....)))))).......(((((....(((....((((....))))))).))))))))).))))... ( -31.40)
>DroSim_CAF1 15732 95 - 1
CGG--CACGCACUCCCCGCCAAUUGCAAUUGUCCAGGGGAGCAUUGUCGUCGUUUGUCGUCUUUUGCAACUUUGCAACGUACGACUGCGCGUUGUUU
(((--(.((((((((((..((((....))))....)))))).......(((((....(((....((((....))))))).))))))))).))))... ( -31.40)
>DroEre_CAF1 20556 97 - 1
CGGCGCACGCACUCCCCGCCAAUUGCAAUUGUCCAGGGGAGCAUUGUCGUCGUUUGUCGUCUUUUGCAACUUUGCAACGUACGACUGCGCGUUGUUU
(((((((((((((((((..((((....))))....))))))...)).))).((..(((((.(.(((((....))))).).))))).))))))))... ( -33.50)
>DroYak_CAF1 23250 95 - 1
CGG--CACGCACUCCCCGCCAAUUGCAAUUGUCCAGGGGAGCAUUGUCGUCGUUUGUCGUCUUUUGCAACUUUGCAACGUACGACCGCGCGUUGUUU
(((--(.(((.((((((..((((....))))....)))))).......(((((....(((....((((....))))))).))))).))).))))... ( -30.80)
>consensus
CGG__CACGCACUCCCCGCCAAUUGCAAUUGUCCAGGGGAGCAUUGUCGUCGUUUGUCGUCUUUUGCAACUUUGCAACGUACGACUGCGCGUUGUUU
......((((.((((((..((((....))))....))))))....((.(((((....(((....((((....))))))).))))).))))))..... (-29.50 = -29.50 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:35 2006