Locus 7711

Sequence ID	2L_DroMel_CAF1
Location	21,810,611 – 21,810,740
Length	129
Max. P	0.996705

overview

Window 3

Location	21,810,611 – 21,810,727
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	93.09
Mean single sequence MFE	-30.64
Consensus MFE	-28.12
Energy contribution	-27.92
Covariance contribution	-0.19
Combinations/Pair	1.09
Mean z-score	-2.20
Structure conservation index	0.92
SVM decision value	2.74
SVM RNA-class probability	0.996705
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21810611 116 - 22407834
UAUGAGCUUCAUUAUAAAGUCGCCCAUUUUAUUGGGUCGCCCUCGAAUAAAUAAGGUUCAAUAAAGUUGUUACUUUAUAUUGACACUCGCAGGCGGCAAUCGCUCGUCACAUUCUG----
...(((..(((.((((((((.((..(((((((((..((................))..))))))))).)).)))))))).)))..)))...((((((....)).))))........---- ( -31.59)
>DroVir_CAF1 66146 117 - 1
UAUGUGCAUCAUUAUAAAGUUGCCCAUUUUAUUGGUUCGCCCUCGAAUAAAUAAGGAUCAAUAAAGUUGUUACUUUAUAUUGACACUUGCAGGCGGCAAUCGCUCGUCACUUUCGGU---
....(((((((.((((((((.((..(((((((((((((................))))))))))))).)).)))))))).)))....))))((((((....)).)))).........--- ( -31.59)
>DroPse_CAF1 72657 120 - 1
UAUGUGCAUCAUUAUAAAGUUGCCCAUUUUAUUGGAUCGCCCUCGAAUAAAUAAGGUUCAAUAAAGUUGUUACUUUAUAUUGACACUUGCAGGCGGCAAUCGCUCGUCACUUUCGGUUGU
....(((((((.((((((((.((..(((((((((((((................))))))))))))).)).)))))))).)))....))))((((((....)).))))............ ( -31.59)
>DroYak_CAF1 47022 116 - 1
UAUGAGAAUCAUUAUAAAGUCGCCCAUUUUAUUGGGUCGCCCUCGAAUAAAUAAGGUUCAAUAAAGUUGUUACUUUAUAUUGACACGCGCAGGCGGCAAUCGCUCGUCACAUUCGG----
.....((((((.((((((((.((..(((((((((..((................))..))))))))).)).)))))))).)))........((((((....)).))))...)))..---- ( -28.29)
>DroMoj_CAF1 69915 116 - 1
UAUGUGCAUCAUUAUAAAGUUGCCCAUUUUAUUGGUUUGCCCUCGAAUAAAUAAGGAUCAAUAAAGUUGUUACUUUAUAUUGACACUUGCAGGCGGCAAUCGCUCGUCACUCUCA-U---
....(((((((.((((((((.((..(((((((((((((................))))))))))))).)).)))))))).)))....))))((((((....)).)))).......-.--- ( -29.19)
>DroPer_CAF1 74606 120 - 1
UAUGUGCAUCAUUAUAAAGUUGCCCAUUUUAUUGGAUCGCCCUCGAAUAAAUAAGGUUCAAUAAAGUUGUUACUUUAUAUUGACACUUGCAGGCGGCAAUCGCUCGUCACUUUCGGUUGU
....(((((((.((((((((.((..(((((((((((((................))))))))))))).)).)))))))).)))....))))((((((....)).))))............ ( -31.59)
>consensus
UAUGUGCAUCAUUAUAAAGUUGCCCAUUUUAUUGGAUCGCCCUCGAAUAAAUAAGGUUCAAUAAAGUUGUUACUUUAUAUUGACACUUGCAGGCGGCAAUCGCUCGUCACUUUCGGU___
.....((((((.((((((((.((..(((((((((((((................))))))))))))).)).)))))))).)))....))).((((((....)).))))............ (-28.12 = -27.92 +  -0.19)

alignment

secondary structure

dotplot

Window 4

Location	21,810,647 – 21,810,740
Length	93
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.28
Mean single sequence MFE	-22.40
Consensus MFE	-18.17
Energy contribution	-17.39
Covariance contribution	-0.78
Combinations/Pair	1.19
Mean z-score	-1.49
Structure conservation index	0.81
SVM decision value	0.11
SVM RNA-class probability	0.587732
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21810647 93 - 22407834
---------------------------GCCAAGCGUUAUUUAUGAGCUUCAUUAUAAAGUCGCCCAUUUUAUUGGGUCGCCCUCGAAUAAAUAAGGUUCAAUAAAGUUGUUACUUUAUAU
---------------------------....(((.(((((((((((............((.(((((......))))).)).)))..)))))))).)))..(((((((....))))))).. ( -18.82)
>DroVir_CAF1 66183 92 - 1
----------------------------GGGCGCGUUAUUUAUGUGCAUCAUUAUAAAGUUGCCCAUUUUAUUGGUUCGCCCUCGAAUAAAUAAGGAUCAAUAAAGUUGUUACUUUAUAU
----------------------------..((((((.....)))))).....((((((((.((..(((((((((((((................))))))))))))).)).)))))))). ( -24.99)
>DroPse_CAF1 72697 100 - 1
-----------------GUC---GCAGCCACAGCGUUAUUUAUGUGCAUCAUUAUAAAGUUGCCCAUUUUAUUGGAUCGCCCUCGAAUAAAUAAGGUUCAAUAAAGUUGUUACUUUAUAU
-----------------...---...((.(((..........))))).....((((((((.((..(((((((((((((................))))))))))))).)).)))))))). ( -20.49)
>DroMoj_CAF1 69951 120 - 1
GCAAGGAGAGCGGAGGGGUAGAGGCAGAGGGCGCGUUAUUUAUGUGCAUCAUUAUAAAGUUGCCCAUUUUAUUGGUUUGCCCUCGAAUAAAUAAGGAUCAAUAAAGUUGUUACUUUAUAU
.....(((.(((((..(((((((((((...((((((.....))))))............)))))...))))))..))))).)))................(((((((....))))))).. ( -26.96)
>DroAna_CAF1 50884 93 - 1
---------------------------CCGGAGCGUUAUUUAUGCGCAUCAUUAUAAAGUUACCCAUUUUAUUGGGUCGCCCUCGAAUAAAUAAGGUUCAAUAAAGUUGUUACUUUAUAU
---------------------------...((((.((((((((.((............((.(((((......))))).))...)).)))))))).)))).(((((((....))))))).. ( -22.66)
>DroPer_CAF1 74646 100 - 1
-----------------GUC---GCAGCCACAGCGUUAUUUAUGUGCAUCAUUAUAAAGUUGCCCAUUUUAUUGGAUCGCCCUCGAAUAAAUAAGGUUCAAUAAAGUUGUUACUUUAUAU
-----------------...---...((.(((..........))))).....((((((((.((..(((((((((((((................))))))))))))).)).)))))))). ( -20.49)
>consensus
___________________________CCGGAGCGUUAUUUAUGUGCAUCAUUAUAAAGUUGCCCAUUUUAUUGGAUCGCCCUCGAAUAAAUAAGGUUCAAUAAAGUUGUUACUUUAUAU
................................((((.......)))).....((((((((.((..(((((((((((((................))))))))))))).)).)))))))). (-18.17 = -17.39 +  -0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:19 2006