Locus 4134

Sequence ID	X_DroMel_CAF1
Location	10,864,902 – 10,864,997
Length	95
Max. P	0.994018

overview

Window 4

Location	10,864,902 – 10,864,997
Length	95
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	72.21
Mean single sequence MFE	-35.44
Consensus MFE	-17.03
Energy contribution	-17.75
Covariance contribution	0.72
Combinations/Pair	1.25
Mean z-score	-2.39
Structure conservation index	0.48
SVM decision value	2.44
SVM RNA-class probability	0.994018
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10864902 95 + 22224390
--AC---CACAGCCCACUGAAACCGGCGAAGAUGAGCAACGUUUGCUUCCAA-----------AGCAGCGGAAACGGAUGCAGAACGGAUGUGG------AAGUGGGCCAGGU-GG--UU
--((---(((.(((((((....((.((........)).(((((((.(((...-----------.(((.((....))..))).))))))))))))------.)))))))...))-))--). ( -36.60)
>DroSec_CAF1 18616 98 + 1
--ACCACCACAGCCCACUGAAACCGGCGAAGAUGAGCAACGUUUGCUUCCAA-----------AGCAGCGGAAACGGAUGCAGAACGGAUGUGG------AAGUGGGCCAGGU-GG--UU
--((((((...(((((((....((.((........)).(((((((.(((...-----------.(((.((....))..))).))))))))))))------.)))))))..)))-))--). ( -39.20)
>DroSim_CAF1 20152 97 + 1
--AC-ACGUCAGCCCAUUGAAACCAGAAUGGAUGAUCAAAGUCUGCUUCCAA-----------AGCAGCGGAAACGGAUGCAGAACGGAUGUGG------AAGUGGGCCAGGU-GG--UU
--.(-((((((..(((((........))))).))))....(((..(((((..-----------.(((.((....))..)))...((....))))------)))..)))...))-).--.. ( -31.50)
>DroYak_CAF1 18758 106 + 1
--ACACACACAGCCCACUGAAAGCGGCGAGGAUGAGCAGAGUUUGCUUCGAA-----------AGCAGCGGAAACGGAUGCAGAACGGAUGUGGAAAUGGAAGUGGGCCAGGU-GGGGUU
--...(((...(((((((.....(.((((((.(((((...)))))))))...-----------.(((.((....))..))).........)).).......)))))))...))-)..... ( -32.20)
>DroAna_CAF1 16639 104 + 1
UGUC-ACAUCCAACCACU--AACCAGAG-----GGAGAACCUCCACCUCCAGCUACAGCAACCGGAAGCGGAAGCGGAUGCUGAGCGGAAGUGG------CAGCGGGCCAGAAAGG--GU
((((-((.(((.......--.....(((-----(..(.....)..))))..(((.(((((.((....((....)))).))))))))))).))))------))....(((......)--)) ( -37.70)
>consensus
__AC_ACCACAGCCCACUGAAACCGGCGAAGAUGAGCAACGUUUGCUUCCAA___________AGCAGCGGAAACGGAUGCAGAACGGAUGUGG______AAGUGGGCCAGGU_GG__UU
...........(((((((.......((........)).(((((((.(((...............(((.((....))..))).)))))))))).........)))))))............ (-17.03 = -17.75 +   0.72)

alignment

secondary structure

dotplot

Window 5

Location	10,864,902 – 10,864,997
Length	95
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	72.21
Mean single sequence MFE	-31.78
Consensus MFE	-15.35
Energy contribution	-15.19
Covariance contribution	-0.16
Combinations/Pair	1.35
Mean z-score	-2.02
Structure conservation index	0.48
SVM decision value	1.26
SVM RNA-class probability	0.937470
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10864902 95 - 22224390
AA--CC-ACCUGGCCCACUU------CCACAUCCGUUCUGCAUCCGUUUCCGCUGCU-----------UUGGAAGCAAACGUUGCUCAUCUUCGCCGGUUUCAGUGGGCUGUG---GU--
.(--((-((..((((((((.------((.....((((.(((.((((...........-----------.)))).)))))))..((........)).))....)))))))))))---))-- ( -31.60)
>DroSec_CAF1 18616 98 - 1
AA--CC-ACCUGGCCCACUU------CCACAUCCGUUCUGCAUCCGUUUCCGCUGCU-----------UUGGAAGCAAACGUUGCUCAUCUUCGCCGGUUUCAGUGGGCUGUGGUGGU--
.(--((-((((((((((((.------((.....((((.(((.((((...........-----------.)))).)))))))..((........)).))....))))))))).))))))-- ( -36.20)
>DroSim_CAF1 20152 97 - 1
AA--CC-ACCUGGCCCACUU------CCACAUCCGUUCUGCAUCCGUUUCCGCUGCU-----------UUGGAAGCAGACUUUGAUCAUCCAUUCUGGUUUCAAUGGGCUGACGU-GU--
..--.(-((..((((((...------..........(((((.((((...........-----------.)))).)))))..((((....((.....))..))))))))))...))-).-- ( -25.60)
>DroYak_CAF1 18758 106 - 1
AACCCC-ACCUGGCCCACUUCCAUUUCCACAUCCGUUCUGCAUCCGUUUCCGCUGCU-----------UUCGAAGCAAACUCUGCUCAUCCUCGCCGCUUUCAGUGGGCUGUGUGUGU--
.....(-((.(((((((((..............((....(((..((....)).))).-----------..)).((((.....))))................))))))))).)))...-- ( -23.10)
>DroAna_CAF1 16639 104 - 1
AC--CCUUUCUGGCCCGCUG------CCACUUCCGCUCAGCAUCCGCUUCCGCUUCCGGUUGCUGUAGCUGGAGGUGGAGGUUCUCC-----CUCUGGUU--AGUGGUUGGAUGU-GACA
..--....((..(((.((((------((((((((((((((((.(((..........))).))))).))).))))))(((((.....)-----)))))).)--))))))..))...-.... ( -42.40)
>consensus
AA__CC_ACCUGGCCCACUU______CCACAUCCGUUCUGCAUCCGUUUCCGCUGCU___________UUGGAAGCAAACGUUGCUCAUCCUCGCCGGUUUCAGUGGGCUGUGGU_GU__
...........((((((((...............((...))....(((((((.................)))))))..........................)))))))).......... (-15.35 = -15.19 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:13 2006