Locus 5126

Sequence ID	2L_DroMel_CAF1
Location	14,560,808 – 14,560,908
Length	100
Max. P	0.915437

overview

Window 3

Location	14,560,808 – 14,560,908
Length	100
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	78.65
Mean single sequence MFE	-24.47
Consensus MFE	-14.95
Energy contribution	-16.65
Covariance contribution	1.70
Combinations/Pair	1.18
Mean z-score	-1.64
Structure conservation index	0.61
SVM decision value	0.38
SVM RNA-class probability	0.710958
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14560808 100 + 22407834
------GCAUC-GCAUCGCAUCGAGAAAUUUGUGGCCCGAACAAAUUUCCCAAAGUCUGUGUUGAAAAAUUAAUGUGCA-CAACUGUCAGUGCAGUGACAGAGAUGCG
------.....-....(((((((.(((((((((.......))))))))).)....((((((((((....))))).((((-(........)))))...))))))))))) ( -28.60)
>DroVir_CAF1 34383 89 + 1
--------------GACACAUCGAAAAAUUUGUUGCUCC---AAUUCUC-UAAACUCUGUGCUGAAAAAUUAAUGUGCC-CAACUGUCAUUGCAAUGACAGAGAUGAA
--------------....((((.................---.......-........(..(............)..).-...(((((((....))))))).)))).. ( -13.80)
>DroSim_CAF1 79895 93 + 1
--------------AUCGCAUCGAGAAAUUUGUGGCCCGAACAAAUUUCCCAAAGUCUGUGUUGAAAAAUUAAUGUGCA-CAACUGUCAGUGCAGUGACAGAGAUGCG
--------------..(((((((.(((((((((.......))))))))).)....((((((((((....))))).((((-(........)))))...))))))))))) ( -28.60)
>DroYak_CAF1 83884 107 + 1
GCAUCAGCAUCAGCAUCGCAUCGAGAAAUUUGUGGCCCGAACAAAUUUCCCAAAGUCUGUGUUGAAAAAUUAAUGUGCA-CAACUGUCAGUGCAGUGACAGAGAUGCG
(((((.((((((((((.((...(.(((((((((.......))))))))).)...))..)))))))..........))).-...((((((......)))))).))))). ( -31.30)
>DroMoj_CAF1 41231 90 + 1
---------------UCACAUUGAGAAAUUUGUUGUUCC---AAUUUUCGUAAAUUCUGUGCUGAAAAAUGAAUGUGCCCCAACAGUCAUUGCAUUGACAGCGAUGUG
---------------.(((((((.((((.(((......)---)).)))).......((((.(.....(((((.(((......))).))))).....)))))))))))) ( -19.70)
>DroAna_CAF1 31181 88 + 1
-------------------AUCGAGAAAUUUGUGGCCCGAACAAAUUUUCCAAAGUCUGCGUUGAAAAAUUAAUGUGCA-CGACUGUCACUGCAGUGACAGAGAUGCG
-------------------...(..((((((((.......))))))))..).......(((((((....)))))))(((-...(((((((....)))))))...))). ( -24.80)
>consensus
______________AUCGCAUCGAGAAAUUUGUGGCCCGAACAAAUUUCCCAAAGUCUGUGUUGAAAAAUUAAUGUGCA_CAACUGUCAGUGCAGUGACAGAGAUGCG
................(((((((.(((((((((.......))))))))).)................................((((((......)))))).)))))) (-14.95 = -16.65 +   1.70)

alignment

secondary structure

dotplot

Window 4

Location	14,560,808 – 14,560,908
Length	100
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	78.65
Mean single sequence MFE	-25.36
Consensus MFE	-15.27
Energy contribution	-17.58
Covariance contribution	2.31
Combinations/Pair	1.17
Mean z-score	-2.17
Structure conservation index	0.60
SVM decision value	1.10
SVM RNA-class probability	0.915437
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14560808 100 - 22407834
CGCAUCUCUGUCACUGCACUGACAGUUG-UGCACAUUAAUUUUUCAACACAGACUUUGGGAAAUUUGUUCGGGCCACAAAUUUCUCGAUGCGAUGC-GAUGC------
((((((.((((((......))))))...-.(((..........((......))..(((((((((((((.......)))))))))))))))))))))-)....------ ( -29.60)
>DroVir_CAF1 34383 89 - 1
UUCAUCUCUGUCAUUGCAAUGACAGUUG-GGCACAUUAAUUUUUCAGCACAGAGUUUA-GAGAAUU---GGAGCAACAAAUUUUUCGAUGUGUC--------------
..((...(((((((....))))))).))-((((((((.....(((......)))....-(((((((---(......)))..)))))))))))))-------------- ( -19.60)
>DroSim_CAF1 79895 93 - 1
CGCAUCUCUGUCACUGCACUGACAGUUG-UGCACAUUAAUUUUUCAACACAGACUUUGGGAAAUUUGUUCGGGCCACAAAUUUCUCGAUGCGAU--------------
((((((.((((((......))))))(((-((................))))).....(((((((((((.......)))))))))))))))))..-------------- ( -27.89)
>DroYak_CAF1 83884 107 - 1
CGCAUCUCUGUCACUGCACUGACAGUUG-UGCACAUUAAUUUUUCAACACAGACUUUGGGAAAUUUGUUCGGGCCACAAAUUUCUCGAUGCGAUGCUGAUGCUGAUGC
.((((..((((((......))))))..)-))).(((((.....(((.((..(...(((((((((((((.......)))))))))))))..)..)).)))...))))). ( -31.60)
>DroMoj_CAF1 41231 90 - 1
CACAUCGCUGUCAAUGCAAUGACUGUUGGGGCACAUUCAUUUUUCAGCACAGAAUUUACGAAAAUU---GGAACAACAAAUUUCUCAAUGUGA---------------
(((((.((((..((((.((((..(((....)))))))))))...))))...........((((.((---(......))).))))...))))).--------------- ( -18.30)
>DroAna_CAF1 31181 88 - 1
CGCAUCUCUGUCACUGCAGUGACAGUCG-UGCACAUUAAUUUUUCAACGCAGACUUUGGAAAAUUUGUUCGGGCCACAAAUUUCUCGAU-------------------
.((((..(((((((....)))))))..)-)))(((..((((((((((........)))))))))))))(((((..........))))).------------------- ( -25.20)
>consensus
CGCAUCUCUGUCACUGCACUGACAGUUG_UGCACAUUAAUUUUUCAACACAGACUUUGGGAAAUUUGUUCGGGCCACAAAUUUCUCGAUGCGAU______________
((((((.((((((......))))))................................(((((((((((.......)))))))))))))))))................ (-15.27 = -17.58 +   2.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:40 2006