Locus 2656

Sequence ID	2R_DroMel_CAF1
Location	9,377,441 – 9,377,534
Length	93
Max. P	0.962712

overview

Window 8

Location	9,377,441 – 9,377,534
Length	93
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	71.63
Mean single sequence MFE	-18.06
Consensus MFE	-11.44
Energy contribution	-11.40
Covariance contribution	-0.04
Combinations/Pair	1.17
Mean z-score	-1.54
Structure conservation index	0.63
SVM decision value	0.69
SVM RNA-class probability	0.824100
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9377441 93 + 20766785
AUUAAUUAUGCAGUUCAUGCCGGUUAUGGCUAUAUUUCAGUUGUAUCAUGCAUAAUAUAU----GUUUGUUUGUGAUAUAUCCUAAUGGCCAGCAUA
......(((((.((....))......(((((((........(((((((((.((((.....----..)))).))))))))).....)))))))))))) ( -19.42)
>DroSec_CAF1 2571 81 + 1
AUAAAAUAUGUAAUUUAUGCCGGUUAUGGCUAUAUUUGAG------------UAAUAUAU----GUUUGUUUGUGAUAGAUCCUAAUGGCCAGCAUA
...............(((((.((((((((...((((....------------.((((...----...))))...))))...))..)))))).))))) ( -13.40)
>DroSim_CAF1 2403 93 + 1
AUGAAAUAUGUGUUUCAUGCCGGUUAUGGCUAUAUUUGAGUUGUAUCAUCCAUAAUAUAU----GUUUGUUUGUGAUAUAUCCUAAUGGCCAGCAUA
(((((((....)))))))........(((((((....(.(.((((((((..((((.....----..))))..)))))))).))..)))))))..... ( -19.70)
>DroEre_CAF1 2599 73 + 1
GUGAAAU----AGUUCACGUAGGUUAUGGCUAUAUUU---------------UGAUAUAUG-----UUGUUUAUGAUAUAUCCAAAUGGCCAGCGUA
(((((..----..)))))((.((((((((.((((((.---------------.((((....-----.))))...)))))).)))..))))).))... ( -18.20)
>DroYak_CAF1 2606 77 + 1
GU---------CGUUAGUGCCGGUUAUGGCUAUAUUUG-------UCA----UGAUGCAUGUAUGUUUAUUUAUGAUAUAUGCUAAUCGCCAGCAUA
..---------.....((((.(((((((((.......)-------)))----))..((((((((...........)))))))).....))).)))). ( -19.60)
>consensus
AUGAAAUAUG_AGUUCAUGCCGGUUAUGGCUAUAUUUGAG_____UCA____UAAUAUAU____GUUUGUUUGUGAUAUAUCCUAAUGGCCAGCAUA
................((((.((((((((.((((((......................................)))))).))..)))))).)))). (-11.44 = -11.40 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	9,377,441 – 9,377,534
Length	93
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	71.63
Mean single sequence MFE	-13.14
Consensus MFE	-6.76
Energy contribution	-7.52
Covariance contribution	0.76
Combinations/Pair	1.13
Mean z-score	-2.06
Structure conservation index	0.51
SVM decision value	1.54
SVM RNA-class probability	0.962712
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9377441 93 - 20766785
UAUGCUGGCCAUUAGGAUAUAUCACAAACAAAC----AUAUAUUAUGCAUGAUACAACUGAAAUAUAGCCAUAACCGGCAUGAACUGCAUAAUUAAU
(((((.(..((((((....(((((.........----............)))))...))))......(((......))).))..).)))))...... ( -13.60)
>DroSec_CAF1 2571 81 - 1
UAUGCUGGCCAUUAGGAUCUAUCACAAACAAAC----AUAUAUUA------------CUCAAAUAUAGCCAUAACCGGCAUAAAUUACAUAUUUUAU
((((((((((....)).................----.((((((.------------....)))))).......))))))))............... ( -13.00)
>DroSim_CAF1 2403 93 - 1
UAUGCUGGCCAUUAGGAUAUAUCACAAACAAAC----AUAUAUUAUGGAUGAUACAACUCAAAUAUAGCCAUAACCGGCAUGAAACACAUAUUUCAU
((((((((((....)).................----.....((((((...(((.........)))..))))))))))))))............... ( -15.80)
>DroEre_CAF1 2599 73 - 1
UACGCUGGCCAUUUGGAUAUAUCAUAAACAA-----CAUAUAUCA---------------AAAUAUAGCCAUAACCUACGUGAACU----AUUUCAC
.....((((.((((.(((((((.........-----.))))))).---------------))))...))))........(((((..----..))))) ( -11.80)
>DroYak_CAF1 2606 77 - 1
UAUGCUGGCGAUUAGCAUAUAUCAUAAAUAAACAUACAUGCAUCA----UGA-------CAAAUAUAGCCAUAACCGGCACUAACG---------AC
(((((((.....)))))))..((.............((((...))----)).-------........(((......)))......)---------). ( -11.50)
>consensus
UAUGCUGGCCAUUAGGAUAUAUCACAAACAAAC____AUAUAUUA____UGA_____CUCAAAUAUAGCCAUAACCGGCAUGAACU_CAUAUUUCAU
((((((((......((.(((((........................................))))).))....))))))))............... ( -6.76 =  -7.52 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:30 2006