Locus 4376

Sequence ID	2L_DroMel_CAF1
Location	12,606,655 – 12,606,745
Length	90
Max. P	0.937761

overview

Window 2

Location	12,606,655 – 12,606,745
Length	90
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.24
Mean single sequence MFE	-24.88
Consensus MFE	-16.36
Energy contribution	-16.78
Covariance contribution	0.42
Combinations/Pair	1.12
Mean z-score	-2.58
Structure conservation index	0.66
SVM decision value	1.26
SVM RNA-class probability	0.937761
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12606655 90 + 22407834
---------------------------AAGUAAAUUGCA---AUAAUUGUACUAAUUGUUAUUGCAAUUAUUGCUGGCAAUUACCAUGACUAAUGUGGGGCAAAAUGUUUGUGCAUAUUG
---------------------------.(((((((((((---(((((.((....)).)))))))))))..))))).((.....((((.......)))).((((.....))))))...... ( -19.40)
>DroPse_CAF1 232506 101 + 1
AC------------ACACAUAC-AGCCAGGUAAAUUGCA---AUAAUUGUACUAAUUGUUAUUGCAAUUAUUGUUGGCAAUUACCAUGACUAAUGUGGGGCAAAAUGUUUGUGAAUG---
..------------.((((.((-((((((...(((((((---(((((.((....)).))))))))))))....))))).....((((.......)))).......))).))))....--- ( -28.10)
>DroWil_CAF1 266347 102 + 1
CA------------AAACA------UCACGUCAAUUGCAAAAAUAAUUGUACUAAUUGUUUAUGCAAUUAUUGUUGGUAAUUACCAUGACUAAUGUGGGGCAAAAUGUUUAUGAAUAAUA
..------------(((((------(...(((((((((...((((((((((.(((....)))))))))))))....)))))).((((.......)))))))...)))))).......... ( -22.00)
>DroYak_CAF1 177703 113 + 1
AC----AUACUUACAUAUAUACGAGCCAAGUAAAUUGCA---AUAAUUGUACUAAUUGUUAUUGCAAUUAUUGCUGGCAAUUACCAUGACUAAUGUGGGGCAAAAUGUUUGUGCAUAUUG
..----.(((..((((........((((.((((((((((---(((((.((....)).)))))))))))..)))))))).....((((.......))))......))))..)))....... ( -27.30)
>DroAna_CAF1 172462 115 + 1
ACGAAAAAAUCC--ACAAACAUAAGCUACGUAAAUUGCA---AUAAUUGUACUAAUUGUUAUUGCAAUUAUUGCUGGCAAUUACCAUGACUAAUGUGGGGCAAAAUGUUUAUGAAUAAUA
...........(--(.((((((..((((.((((((((((---(((((.((....)).)))))))))))..)))))))).....((((.......))))......)))))).))....... ( -25.40)
>DroPer_CAF1 226017 101 + 1
AC------------ACACAUAC-UGCUAGGUAAAUUGCA---AUAAUUGUACUAAUUGUUAUUGCAAUUAUUGCUGGCAAUUACCAUGACUAAUGUGGGGCAAAAUGUUUGUGAAUG---
..------------.((((.((-((((((...(((((((---(((((.((....)).))))))))))))....))))))....((((.......))))........)).))))....--- ( -27.10)
>consensus
AC____________ACACAUAC_AGCCAAGUAAAUUGCA___AUAAUUGUACUAAUUGUUAUUGCAAUUAUUGCUGGCAAUUACCAUGACUAAUGUGGGGCAAAAUGUUUGUGAAUA_U_
........................(((.....((((((....(((((((((.((.....)).))))))))).....)))))).((((.......)))))))................... (-16.36 = -16.78 +   0.42)

alignment

secondary structure

dotplot

Window 3

Location	12,606,655 – 12,606,745
Length	90
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.24
Mean single sequence MFE	-21.62
Consensus MFE	-9.11
Energy contribution	-8.75
Covariance contribution	-0.36
Combinations/Pair	1.12
Mean z-score	-2.67
Structure conservation index	0.42
SVM decision value	0.20
SVM RNA-class probability	0.632681
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12606655 90 - 22407834
CAAUAUGCACAAACAUUUUGCCCCACAUUAGUCAUGGUAAUUGCCAGCAAUAAUUGCAAUAACAAUUAGUACAAUUAU---UGCAAUUUACUU---------------------------
(((.(((......))).)))..............((((....))))((((((((((...((.....))...)))))))---))).........--------------------------- ( -14.30)
>DroPse_CAF1 232506 101 - 1
---CAUUCACAAACAUUUUGCCCCACAUUAGUCAUGGUAAUUGCCAACAAUAAUUGCAAUAACAAUUAGUACAAUUAU---UGCAAUUUACCUGGCU-GUAUGUGU------------GU
---....................(((((((((((.((((((((....))))(((((((((((............))))---))))))))))))))))-).))))).------------.. ( -24.10)
>DroWil_CAF1 266347 102 - 1
UAUUAUUCAUAAACAUUUUGCCCCACAUUAGUCAUGGUAAUUACCAACAAUAAUUGCAUAAACAAUUAGUACAAUUAUUUUUGCAAUUGACGUGA------UGUUU------------UG
........................(((((((((.((((....)))).....(((((((.(((.((((.....)))).))).)))))))))).)))------)))..------------.. ( -17.80)
>DroYak_CAF1 177703 113 - 1
CAAUAUGCACAAACAUUUUGCCCCACAUUAGUCAUGGUAAUUGCCAGCAAUAAUUGCAAUAACAAUUAGUACAAUUAU---UGCAAUUUACUUGGCUCGUAUAUAUGUAAGUAU----GU
..((((((.........(((((..((....))...)))))..(((((....(((((((((((............))))---)))))))...)))))..))))))..........----.. ( -23.30)
>DroAna_CAF1 172462 115 - 1
UAUUAUUCAUAAACAUUUUGCCCCACAUUAGUCAUGGUAAUUGCCAGCAAUAAUUGCAAUAACAAUUAGUACAAUUAU---UGCAAUUUACGUAGCUUAUGUUUGU--GGAUUUUUUCGU
....((((((((((((...((..(..........((((....))))((((((((((...((.....))...)))))))---))).......)..))..))))))))--))))........ ( -28.10)
>DroPer_CAF1 226017 101 - 1
---CAUUCACAAACAUUUUGCCCCACAUUAGUCAUGGUAAUUGCCAGCAAUAAUUGCAAUAACAAUUAGUACAAUUAU---UGCAAUUUACCUAGCA-GUAUGUGU------------GU
---.....(((.((((.((((.............((((....))))((((((((((...((.....))...)))))))---)))..........)))-).)))).)------------)) ( -22.10)
>consensus
_A_UAUUCACAAACAUUUUGCCCCACAUUAGUCAUGGUAAUUGCCAGCAAUAAUUGCAAUAACAAUUAGUACAAUUAU___UGCAAUUUACCUGGCU_GUAUGUGU____________GU
.................((((.........((..((((....))))))..((((((......))))))..............)))).................................. ( -9.11 =  -8.75 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:20 2006