Locus 6298

Sequence ID	3L_DroMel_CAF1
Location	16,781,506 – 16,781,598
Length	92
Max. P	0.725750

overview

Window 3

Location	16,781,506 – 16,781,598
Length	92
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	81.93
Mean single sequence MFE	-19.97
Consensus MFE	-14.76
Energy contribution	-14.09
Covariance contribution	-0.66
Combinations/Pair	1.24
Mean z-score	-1.47
Structure conservation index	0.74
SVM decision value	0.19
SVM RNA-class probability	0.624988
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16781506 92 + 23771897
UUGUUGUUGCGACCAUUCUUUUUUCCUAUUUCAUUUUUUUGGUGGUGCCUGGCACCGGAUCGCAUCUUUUAGCAUAAAUUAU--UUGCGGCUAG
.......(((((((................(((......))).(((((...))))))).))))).....((((...((....--))...)))). ( -19.50)
>DroPse_CAF1 30798 74 + 1
-UGUUG--GAGAUCGUU-----------------UUUUUCGGUGGUGCCUGGCACCGCAUCGCAUCUUUUAGCAUAAAUUAUACUCUCGACUAG
-.((((--(((......-----------------.......(((((((...)))))))...((........))..........))).))))... ( -19.30)
>DroSim_CAF1 32778 92 + 1
UUGUUGUUGCGACCAUUCUUUUUUCCUAUUUCAUUUUUUUGGUGGUGCCUGGCACCGGAUCGCAUCUUUUAGCAUAAAUUAU--UUGCGGCUAG
.......(((((((................(((......))).(((((...))))))).))))).....((((...((....--))...)))). ( -19.50)
>DroEre_CAF1 30597 92 + 1
UUGUUGUUGCGACCAUUCUUUUUUGCCAUUUAAUUUUUUUGGUGGUGCCUGGCACCGGAUCGCAUCUUUUAGCAUAAAUUAU--UUGCGGCUAG
.......(((((((..........((((...........))))(((((...))))))).))))).....((((...((....--))...)))). ( -22.70)
>DroYak_CAF1 30603 92 + 1
UUGUUGUUGCGACCAUUCUUUUUUCCUAUUUCAUUUUUUUGGUGGUGCCUGGCACCGGAUCGCAUCUUUUAGCAUAAAUUAU--UUGCGGCUAG
.......(((((((................(((......))).(((((...))))))).))))).....((((...((....--))...)))). ( -19.50)
>DroPer_CAF1 31153 74 + 1
-UGUUG--GAGAUCGUU-----------------UUUUUCGGUGGUGCCUGGCACCGCAUCGCAUCUUUUAGCAUAAAUUAUACUCUCGACUAG
-.((((--(((......-----------------.......(((((((...)))))))...((........))..........))).))))... ( -19.30)
>consensus
UUGUUGUUGCGACCAUUCUUUUUUCCUAUUUCAUUUUUUUGGUGGUGCCUGGCACCGGAUCGCAUCUUUUAGCAUAAAUUAU__UUGCGGCUAG
.....((((((((((........................))))(((((...))))).....((........))............))))))... (-14.76 = -14.09 +  -0.66)

alignment

secondary structure

dotplot

Window 4

Location	16,781,506 – 16,781,598
Length	92
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	81.93
Mean single sequence MFE	-16.80
Consensus MFE	-12.66
Energy contribution	-12.00
Covariance contribution	-0.66
Combinations/Pair	1.17
Mean z-score	-1.68
Structure conservation index	0.75
SVM decision value	0.41
SVM RNA-class probability	0.725750
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16781506 92 - 23771897
CUAGCCGCAA--AUAAUUUAUGCUAAAAGAUGCGAUCCGGUGCCAGGCACCACCAAAAAAAUGAAAUAGGAAAAAAGAAUGGUCGCAACAACAA
.((((.....--.........))))...(.(((((((.(((((...))))).((..............))..........))))))).)..... ( -18.18)
>DroPse_CAF1 30798 74 - 1
CUAGUCGAGAGUAUAAUUUAUGCUAAAAGAUGCGAUGCGGUGCCAGGCACCACCGAAAAA-----------------AACGAUCUC--CAACA-
......((((((((.((((........))))...))))(((((...))))).........-----------------.....))))--.....- ( -13.80)
>DroSim_CAF1 32778 92 - 1
CUAGCCGCAA--AUAAUUUAUGCUAAAAGAUGCGAUCCGGUGCCAGGCACCACCAAAAAAAUGAAAUAGGAAAAAAGAAUGGUCGCAACAACAA
.((((.....--.........))))...(.(((((((.(((((...))))).((..............))..........))))))).)..... ( -18.18)
>DroEre_CAF1 30597 92 - 1
CUAGCCGCAA--AUAAUUUAUGCUAAAAGAUGCGAUCCGGUGCCAGGCACCACCAAAAAAAUUAAAUGGCAAAAAAGAAUGGUCGCAACAACAA
.((((.....--.........))))...(.(((((((.(((((...))))).(((...........)))...........))))))).)..... ( -18.64)
>DroYak_CAF1 30603 92 - 1
CUAGCCGCAA--AUAAUUUAUGCUAAAAGAUGCGAUCCGGUGCCAGGCACCACCAAAAAAAUGAAAUAGGAAAAAAGAAUGGUCGCAACAACAA
.((((.....--.........))))...(.(((((((.(((((...))))).((..............))..........))))))).)..... ( -18.18)
>DroPer_CAF1 31153 74 - 1
CUAGUCGAGAGUAUAAUUUAUGCUAAAAGAUGCGAUGCGGUGCCAGGCACCACCGAAAAA-----------------AACGAUCUC--CAACA-
......((((((((.((((........))))...))))(((((...))))).........-----------------.....))))--.....- ( -13.80)
>consensus
CUAGCCGCAA__AUAAUUUAUGCUAAAAGAUGCGAUCCGGUGCCAGGCACCACCAAAAAAAUGAAAUAGGAAAAAAGAAUGGUCGCAACAACAA
...((((.............(((........)))....(((((...)))))............................))))........... (-12.66 = -12.00 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:03 2006