Locus 6133

Sequence ID	2R_DroMel_CAF1
Location	19,303,027 – 19,303,177
Length	150
Max. P	0.947100

overview

Window 8

Location	19,303,027 – 19,303,118
Length	91
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	81.60
Mean single sequence MFE	-23.45
Consensus MFE	-11.92
Energy contribution	-11.96
Covariance contribution	0.04
Combinations/Pair	1.19
Mean z-score	-2.05
Structure conservation index	0.51
SVM decision value	-0.00
SVM RNA-class probability	0.531902
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19303027 91 - 20766785
AUCAGCGCAAGUGCUUGUUGUUGUUUUUGCAGU-------UUGUGGCAAAGUUGCAUGUUGUAACAACGGCUGGAAAAAAUCAUAACAAUUGCA---AGAG
....((....)).(((((.((((((.......(-------((.((((...(((((.....)))))....)))).))).......)))))).)))---)).. ( -23.44)
>DroSec_CAF1 52851 93 - 1
AUCAGCGCAAGUGCUUGUUGUUGUUUUUGCAGU-------UUGUGGCAAAGUUGCAUGUUGUAACAGCGGCUG-AAAAAAUCAUAACAAUUGCAACAAGAG
....((....)).((((((((((((.((((((.-------.((..((...))..))..)))))).))))..((-(.....)))........)))))))).. ( -23.40)
>DroEre_CAF1 45787 87 - 1
AUCAGCGCAAGUGCUUGUU---GUUUUUGUAGC-------UUGUGGCAAAGUUGCAUGUUGUAACAACGGCUG-CAAAAAUCAUAACAAUUGCA---AGAG
......((((.((.((((.---(((((((((((-------(((..((...))..)).((((...)))))))))-))))))).)))))).)))).---.... ( -26.60)
>DroYak_CAF1 46804 94 - 1
AUCAGCGCAAGUGCUUGUU---GUUUUUGCAGUUUGUUGUUUGUGGCAAAGUUGCAUGUUGUAACAACGGCUG-AAAAAAUCAUAACAAUUGCA---AGAG
......((((.((.((((.---((((((.(((((.((((((.(..(((........)))..))))))))))))-.)))))).)))))).)))).---.... ( -24.80)
>DroAna_CAF1 50771 76 - 1
AUCAGUGUAAGCUGUUGCU---GUUGUUGUUGU-------UUUUU-----GUUGCAUGUUGUAACAACAGCUG-AAAAAAUUAUAACA---------AGAG
..((((....))))...((---.(((((((.((-------(((((-----...((.(((((...)))))))..-))))))).))))))---------).)) ( -19.00)
>consensus
AUCAGCGCAAGUGCUUGUU___GUUUUUGCAGU_______UUGUGGCAAAGUUGCAUGUUGUAACAACGGCUG_AAAAAAUCAUAACAAUUGCA___AGAG
..(((((((((.((........)).)))))....................(((((.....)))))....))))............................ (-11.92 = -11.96 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	19,303,085 – 19,303,177
Length	92
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	73.75
Mean single sequence MFE	-37.30
Consensus MFE	-19.40
Energy contribution	-20.18
Covariance contribution	0.78
Combinations/Pair	1.23
Mean z-score	-2.06
Structure conservation index	0.52
SVM decision value	1.37
SVM RNA-class probability	0.947100
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19303085 92 + 20766785
----ACUGCAAAAACAACAACAAGCACUUGCGCUGAUUGCGUGCUGCGUCGGCGU------------CGCAGUCGACUGCGCUGCCGCAGUUGGCGUUGCGGUCGAAG-
----(((((((...((((.....(((...((((.....))))..)))(.(((((.------------(((((....))))).)))))).))))...))))))).....- ( -39.40)
>DroSec_CAF1 52911 74 + 1
----ACUGCAAAAACAACAACAAGCACUUGCGCUGAUUGCGUGCUGCGUCGGCGU------------CGCAGUC------------------GGCGAUGCGGUCGAAG-
----((((((.............((....))(((((((((((((((...))))).------------)))))))------------------)))..)))))).....- ( -30.80)
>DroEre_CAF1 45844 89 + 1
----GCUACAAAAAC---AACAAGCACUUGCGCUGAUUGCGUGCUGCGCCGGCGU------------CGCAGUCGACUGCGCUGCCGCAGUCGGCGCUGCGGUCGAAG-
----...........---.....(((...((((((((((((.((.((((((((..------------....))))...)))).)))))))))))))))))........- ( -40.40)
>DroYak_CAF1 46864 93 + 1
ACAAACUGCAAAAAC---AACAAGCACUUGCGCUGAUUGCGUGCUGCGUCGGCGU------------CGCAGUCGACUGCGCAGUCGGCGGCGGCGUUGCGGUCGAAG-
....(((((((....---...........((((.....))))(((((((((((..------------(((((....)))))..)))))).))))).))))))).....- ( -39.10)
>DroAna_CAF1 50817 102 + 1
----ACAACAACAAC---AGCAACAGCUUACACUGAUUGCGUGCUGCGUCGGCGUAGGAGUCUCAGUCGCAGUCGCCGUCGCCGUUGACGUAGCAGUUGCGGUCGAAGC
----.(.((..((((---.(((((((......))).)))).(((((((((((((..((.(.(((....).)).).))..))))...)))))))))))))..)).).... ( -36.80)
>consensus
____ACUGCAAAAAC___AACAAGCACUUGCGCUGAUUGCGUGCUGCGUCGGCGU____________CGCAGUCGACUGCGCUGCCGCAGUCGGCGUUGCGGUCGAAG_
.....(.((....................((((((((.((.....))))))))))............((((((((.(((((....))))).))))..)))))).).... (-19.40 = -20.18 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:33 2006