Locus 4273

Sequence ID	X_DroMel_CAF1
Location	11,238,792 – 11,238,883
Length	91
Max. P	0.843574

overview

Window 5

Location	11,238,792 – 11,238,883
Length	91
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	86.57
Mean single sequence MFE	-21.25
Consensus MFE	-17.00
Energy contribution	-17.28
Covariance contribution	0.28
Combinations/Pair	1.12
Mean z-score	-1.85
Structure conservation index	0.80
SVM decision value	0.76
SVM RNA-class probability	0.843574
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11238792 91 + 22224390
GAGCAUAUAUUAAUAUUUUUAGCUCGCCUGCU-UAGGCUCCCUAGGCGUA-UACUUGACUUGACCCACUC-CCAGGGUUAAUUGGCAAUUUUUC
((((.................))))(((.(((-((((...)))))))...-........(((((((....-...)))))))..)))........ ( -25.93)
>DroSec_CAF1 25739 92 + 1
GAGCAUAUAUUAAUAUUUUUAGCCCGCCUGCUUUAGGCUCCCUAGGCGUA-UACUUGACUUGACCCACUC-CCAGGGUUAAUUGGCAAUUUUUC
.....................((((((((((.....)).....)))))..-........(((((((....-...)))))))..)))........ ( -19.80)
>DroEre_CAF1 25454 90 + 1
GAGCAU--AUUAAUAUUUUUAGCCCGCCUGCU-UAGGCUCCCUAGGCGAACCACUUGACUUGACCCACUC-CCAGGGUUAAUUGGCAAUUUUUC
......--.................(((((((-((((...))))))))...........(((((((....-...)))))))..)))........ ( -22.00)
>DroYak_CAF1 17634 89 + 1
GAGCAU--AUUAAUAUUUUUAGCCCGCCUGCU-UAGGCUCCCUAGGCGUA-CACUUGACUUGACCCACUC-CCAGGGUUAAUUGGCAAUUUUUC
......--.................(((.(((-((((...)))))))...-........(((((((....-...)))))))..)))........ ( -21.90)
>DroAna_CAF1 20231 79 + 1
GCGCUU--AUUAAUACUUUUAACCUGCCUGCC-CGAGCUCCCCAGGC------------CUGACCCACUCCCCAGGGUUAAUUGGCAAUUUUUC
..(((.--((((((........((((...((.-...))....))))(------------(((..........)))))))))).)))........ ( -16.60)
>consensus
GAGCAU__AUUAAUAUUUUUAGCCCGCCUGCU_UAGGCUCCCUAGGCGUA_CACUUGACUUGACCCACUC_CCAGGGUUAAUUGGCAAUUUUUC
.....................(((((((((............))))))...........(((((((........)))))))..)))........ (-17.00 = -17.28 +   0.28)

alignment

secondary structure

dotplot

Window 6

Location	11,238,792 – 11,238,883
Length	91
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	86.57
Mean single sequence MFE	-24.53
Consensus MFE	-16.21
Energy contribution	-16.33
Covariance contribution	0.12
Combinations/Pair	1.19
Mean z-score	-1.85
Structure conservation index	0.66
SVM decision value	-0.04
SVM RNA-class probability	0.510775
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11238792 91 - 22224390
GAAAAAUUGCCAAUUAACCCUGG-GAGUGGGUCAAGUCAAGUA-UACGCCUAGGGAGCCUA-AGCAGGCGAGCUAAAAAUAUUAAUAUAUGCUC
........(((......((((((-(.(((...(.......)..-))).))))))).((...-.)).)))((((.................)))) ( -23.93)
>DroSec_CAF1 25739 92 - 1
GAAAAAUUGCCAAUUAACCCUGG-GAGUGGGUCAAGUCAAGUA-UACGCCUAGGGAGCCUAAAGCAGGCGGGCUAAAAAUAUUAAUAUAUGCUC
........(((......((((((-(.(((...(.......)..-))).))))))).((((.....)))).)))..................... ( -24.80)
>DroEre_CAF1 25454 90 - 1
GAAAAAUUGCCAAUUAACCCUGG-GAGUGGGUCAAGUCAAGUGGUUCGCCUAGGGAGCCUA-AGCAGGCGGGCUAAAAAUAUUAAU--AUGCUC
........(((......((((((-(...(..(((.......)))..).))))))).((((.-...)))).))).............--...... ( -26.60)
>DroYak_CAF1 17634 89 - 1
GAAAAAUUGCCAAUUAACCCUGG-GAGUGGGUCAAGUCAAGUG-UACGCCUAGGGAGCCUA-AGCAGGCGGGCUAAAAAUAUUAAU--AUGCUC
........(((......((((((-(.(((.(.(.......)).-))).))))))).((((.-...)))).))).............--...... ( -25.10)
>DroAna_CAF1 20231 79 - 1
GAAAAAUUGCCAAUUAACCCUGGGGAGUGGGUCAG------------GCCUGGGGAGCUCG-GGCAGGCAGGUUAAAAGUAUUAAU--AAGCGC
......(((((.....((((........))))...------------(((((((...))))-))).)))))...............--...... ( -22.20)
>consensus
GAAAAAUUGCCAAUUAACCCUGG_GAGUGGGUCAAGUCAAGUA_UACGCCUAGGGAGCCUA_AGCAGGCGGGCUAAAAAUAUUAAU__AUGCUC
........(((......((((((...(((.................))))))))).((((.....)))).)))..................... (-16.21 = -16.33 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:55 2006