Locus 848

Sequence ID	X_DroMel_CAF1
Location	2,411,880 – 2,411,973
Length	93
Max. P	0.990469

overview

Window 8

Location	2,411,880 – 2,411,973
Length	93
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	77.96
Mean single sequence MFE	-17.04
Consensus MFE	-11.52
Energy contribution	-11.80
Covariance contribution	0.28
Combinations/Pair	1.13
Mean z-score	-1.44
Structure conservation index	0.68
SVM decision value	-0.02
SVM RNA-class probability	0.523585
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2411880 93 + 22224390
-CCUGUGGCCAACUUAAACGUUCUUGUAAUCAAAUUGUGCCACUUGCGGCACA--GCCGU--------CGCCAUCUCGACCACAUCUGUCCACUUCAC---CAU---UUU
-...((((.((.......................(((((((......))))))--)..((--------((......))))......)).)))).....---...---... ( -19.60)
>DroSim_CAF1 20233 93 + 1
-CCUGUGGCCAACUUAAACGUUCUUGUAAUCAAAUUGUGCCACUUGCGGCACA--GCCGU--------CCCCAUCUCGACCACAUCUGUCCACUUCAC---CAC---UUU
-...((((.((.......................(((((((......))))))--)..((--------(........)))......)).)))).....---...---... ( -17.40)
>DroEre_CAF1 57898 92 + 1
-CCUGUGGCCAACUUAAACGUUCUUGUAAUCAAAUUGUGCCACUUGCGGCACA--GCCA---------ACCCAUCUCGACCACAUCUGUCCACUUCAC---CAG---UUU
-.(((((((........(((....)))........((((((......))))))--))))---------.........(((.......)))........---)))---... ( -17.00)
>DroYak_CAF1 58025 105 + 1
UCCUGUGGCCAACUUAAACGUUCUUGUAAUCAAAUUGUGCCACUUGCGGCACA--GCCAUGUUCACAGUCCCAUCUCGACCACAUCUGUUCACUUCGCCAUCAG---UUU
..(((((((...............(((...((..(((((((......))))))--)...))...)))(((.......)))................)))).)))---... ( -20.40)
>DroAna_CAF1 63386 79 + 1
-CCUGCGGCCAACUUAAACGUUCUUGUAAUCAAAUUGUGCCACUUGCGGCCCACAACUCU---------------------------GACCUUUCCAC---CACCAGACU
-..((.((((.......(((...(((....)))..)))((.....))))))))....(((---------------------------(..........---...)))).. ( -10.82)
>consensus
_CCUGUGGCCAACUUAAACGUUCUUGUAAUCAAAUUGUGCCACUUGCGGCACA__GCCAU________CCCCAUCUCGACCACAUCUGUCCACUUCAC___CAC___UUU
....((((.((......(((....)))........((((((......)))))).................................)).))))................. (-11.52 = -11.80 +   0.28)

alignment

secondary structure

dotplot

Window 9

Location	2,411,880 – 2,411,973
Length	93
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	77.96
Mean single sequence MFE	-29.22
Consensus MFE	-17.32
Energy contribution	-17.24
Covariance contribution	-0.08
Combinations/Pair	1.16
Mean z-score	-2.56
Structure conservation index	0.59
SVM decision value	2.21
SVM RNA-class probability	0.990469
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2411880 93 - 22224390
AAA---AUG---GUGAAGUGGACAGAUGUGGUCGAGAUGGCG--------ACGGC--UGUGCCGCAAGUGGCACAAUUUGAUUACAAGAACGUUUAAGUUGGCCACAGG-
...---...---.....((((((((.(((.(((.....))).--------))).)--))).))))..(((((.((((((((..((......)))))))))))))))...- ( -32.20)
>DroSim_CAF1 20233 93 - 1
AAA---GUG---GUGAAGUGGACAGAUGUGGUCGAGAUGGGG--------ACGGC--UGUGCCGCAAGUGGCACAAUUUGAUUACAAGAACGUUUAAGUUGGCCACAGG-
...---(((---((.((.(((((...((((((((((.((...--------.))..--(((((((....))))))).)))))))))).....)))))..)).)))))...- ( -33.50)
>DroEre_CAF1 57898 92 - 1
AAA---CUG---GUGAAGUGGACAGAUGUGGUCGAGAUGGGU---------UGGC--UGUGCCGCAAGUGGCACAAUUUGAUUACAAGAACGUUUAAGUUGGCCACAGG-
...---.((---((.((.(((((...((((((((((...((.---------...)--)((((((....))))))..)))))))))).....)))))..)).))))....- ( -26.20)
>DroYak_CAF1 58025 105 - 1
AAA---CUGAUGGCGAAGUGAACAGAUGUGGUCGAGAUGGGACUGUGAACAUGGC--UGUGCCGCAAGUGGCACAAUUUGAUUACAAGAACGUUUAAGUUGGCCACAGGA
...---(((.((((.((.(((((...((((((((((...((.((((....)))))--)((((((....))))))..)))))))))).....)))))..)).))))))).. ( -34.20)
>DroAna_CAF1 63386 79 - 1
AGUCUGGUG---GUGGAAAGGUC---------------------------AGAGUUGUGGGCCGCAAGUGGCACAAUUUGAUUACAAGAACGUUUAAGUUGGCCGCAGG-
...(((.((---((.....((((---------------------------(((.((((..((((....))))))))))))))).....(((......))).))))))).- ( -20.00)
>consensus
AAA___CUG___GUGAAGUGGACAGAUGUGGUCGAGAUGGGG________ACGGC__UGUGCCGCAAGUGGCACAAUUUGAUUACAAGAACGUUUAAGUUGGCCACAGG_
...................................................((((.....))))...(((((.((((((((..((......))))))))))))))).... (-17.32 = -17.24 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:14 2006