Locus 5985

Sequence ID	2L_DroMel_CAF1
Location	16,868,213 – 16,868,303
Length	90
Max. P	0.957645

overview

Window 7

Location	16,868,213 – 16,868,303
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	92.61
Mean single sequence MFE	-21.16
Consensus MFE	-18.06
Energy contribution	-18.26
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.76
Structure conservation index	0.85
SVM decision value	1.48
SVM RNA-class probability	0.957645
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16868213 90 + 22407834
UUUUUUCUCGCGCCAGGAAAUUGGCAACUAAGCCAAGCCAAGCCAAGUCCAAGGCAUUGUGUCCUUCCUUUUCCUCUUGACUGGCUGCAU
.........(((((((..(((((((......)))))((((((((........))).))).))..............))..))))).)).. ( -24.50)
>DroSec_CAF1 7630 86 + 1
U--UUUCU--CGCCAGGAAAUUGGCAACUAAGCCAAGCCAAGCCAAGUCCAAGGCAUUGUGUCCUUCCUUUUCCUCUUGACUGGCUGCAU
.--.....--.((..((...(((((......))))).)).(((((.(((..(((.(..(........)..).)))...)))))))))).. ( -22.30)
>DroSim_CAF1 10100 83 + 1
UUUUUUCU--CGCCAGGAAAUUGGCAACUAAGCCA-----AGCCAAGUCCAAAGCAUUGUGUCCUUCCUUUUCCUCUUGACUGGCUGCAU
........--.(((((....(((((......))))-----)..((((...((((.............))))....)))).)))))..... ( -17.62)
>DroEre_CAF1 39886 80 + 1
U---UUCU--CGCCAGGAAAUUGGCAACUAAGCCA-----AGCCAAGUCCAAGGCAUUGUGUCCUUCCUUUUCCUCUUGACUGGCUGCAU
.---....--.(((((..(((((((......))))-----)(((........))).....................))..)))))..... ( -20.70)
>DroYak_CAF1 2993 80 + 1
U---UUCU--CGCCAGGAAAUUGGCAACUAAGCCA-----AGCCAAGUCCAAGGCAUUGUGUCCUUUCUUUUCCUCUUGACUGGCUGCAU
.---....--.(((((..(((((((......))))-----)(((........))).....................))..)))))..... ( -20.70)
>consensus
U__UUUCU__CGCCAGGAAAUUGGCAACUAAGCCA_____AGCCAAGUCCAAGGCAUUGUGUCCUUCCUUUUCCUCUUGACUGGCUGCAU
...........(((((..((.((((......))))......(((........))).....................))..)))))..... (-18.06 = -18.26 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	16,868,213 – 16,868,303
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	92.61
Mean single sequence MFE	-24.12
Consensus MFE	-21.32
Energy contribution	-21.16
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.60
Structure conservation index	0.88
SVM decision value	1.40
SVM RNA-class probability	0.950441
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16868213 90 - 22407834
AUGCAGCCAGUCAAGAGGAAAAGGAAGGACACAAUGCCUUGGACUUGGCUUGGCUUGGCUUAGUUGCCAAUUUCCUGGCGCGAGAAAAAA
.((((((((((((((.....(((.((((.(.....)))))...)))..)))))).))))).....((((......)))))))........ ( -27.20)
>DroSec_CAF1 7630 86 - 1
AUGCAGCCAGUCAAGAGGAAAAGGAAGGACACAAUGCCUUGGACUUGGCUUGGCUUGGCUUAGUUGCCAAUUUCCUGGCG--AGAAA--A
....(((((((((((.....(((.((((.(.....)))))...)))..)))))).)))))...((((((......)))))--)....--. ( -25.90)
>DroSim_CAF1 10100 83 - 1
AUGCAGCCAGUCAAGAGGAAAAGGAAGGACACAAUGCUUUGGACUUGGCU-----UGGCUUAGUUGCCAAUUUCCUGGCG--AGAAAAAA
....(((((((((((....((((.(.........).))))...)))))).-----)))))...((((((......)))))--)....... ( -21.80)
>DroEre_CAF1 39886 80 - 1
AUGCAGCCAGUCAAGAGGAAAAGGAAGGACACAAUGCCUUGGACUUGGCU-----UGGCUUAGUUGCCAAUUUCCUGGCG--AGAA---A
....(((((((((((.....((((..(....)....))))...)))))).-----)))))...((((((......)))))--)...---. ( -23.60)
>DroYak_CAF1 2993 80 - 1
AUGCAGCCAGUCAAGAGGAAAAGAAAGGACACAAUGCCUUGGACUUGGCU-----UGGCUUAGUUGCCAAUUUCCUGGCG--AGAA---A
....(((((((((((.........((((.(.....)))))...)))))).-----)))))...((((((......)))))--)...---. ( -22.10)
>consensus
AUGCAGCCAGUCAAGAGGAAAAGGAAGGACACAAUGCCUUGGACUUGGCU_____UGGCUUAGUUGCCAAUUUCCUGGCG__AGAAA__A
.....(((((..((..((......((((.(.....))))).((((.((((......)))).)))).))..))..)))))........... (-21.32 = -21.16 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:11 2006