Locus 2828

Sequence ID	2L_DroMel_CAF1
Location	8,092,219 – 8,092,314
Length	95
Max. P	0.998409

overview

Window 4

Location	8,092,219 – 8,092,314
Length	95
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	74.05
Mean single sequence MFE	-17.00
Consensus MFE	-4.94
Energy contribution	-5.74
Covariance contribution	0.80
Combinations/Pair	1.10
Mean z-score	-2.57
Structure conservation index	0.29
SVM decision value	2.69
SVM RNA-class probability	0.996370
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8092219 95 + 22407834
CCCAAGUCUGAGAAUAUUCCAUAGGUCUUGUCACAU----ACAUAUGU----ACAUAUGU----AUGUACACUGUACC-------AUGUACUCCUCCUUAUUUCUCUUUUGUUU
..((((...(((((........(((...(((.((((----((((((..----..))))))----)))))))..((((.-------..)))).)))......))))).))))... ( -20.54)
>DroSec_CAF1 48376 96 + 1
--CAAGCCUGAGAAUAUUCCAUAGGUCUUGUCACAU----AUAUGUUUGC-UACAUACAU----AUGUACACUGUACC-------AUGUACUCCUCCUUAUUUCUCUUUUGUUU
--((((...(((((........(((...(((.((((----((((((....-.)))))..)----)))))))..((((.-------..)))).)))......))))).))))... ( -14.24)
>DroSim_CAF1 49592 86 + 1
-----------------UCCAUAGGUCUUGUCACAU----AUAUGUGUACAUACAUACAUAUGUAUGUACACUGUACC-------AUGUACUCCUCCUUAUUUCUCUUUUGUUU
-----------------.....(((....((.((((----.(((((((((((((((....)))))))))))).)))..-------))))))....)))................ ( -21.30)
>DroEre_CAF1 48800 89 + 1
CCCAAGCUUGAGAAUAUUCC-UAGGUCUUGUCACAUACGUAUAUGU------------GU----AUGUACACUGUACU-------ACGUACUCCACCUUUU-UCUCUUUUGUUU
...((((..(((((......-.((((...((.((.((.(((((.((------------((----....))))))))))-------).))))...))))..)-))))....)))) ( -16.70)
>DroYak_CAF1 49539 94 + 1
CCCAAGCUUGAACACAUUCCAUAGGUCUUGUCACAU----AUAUGU------------GU----AUGUACACUGUACCAUGUACCAUGUACUCCUCCUUUUGUCUCUUUUGUUU
..((((...((((((((...(((.((......)).)----))))))------------))----..(((((..((((...))))..)))))...........))...))))... ( -12.20)
>consensus
CCCAAGCCUGAGAAUAUUCCAUAGGUCUUGUCACAU____AUAUGU_U____ACAUA_GU____AUGUACACUGUACC_______AUGUACUCCUCCUUAUUUCUCUUUUGUUU
......................(((...(((.((((......((((((......))))))....)))))))..((((..........))))....)))................ ( -4.94 =  -5.74 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	8,092,219 – 8,092,314
Length	95
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	74.05
Mean single sequence MFE	-21.16
Consensus MFE	-8.16
Energy contribution	-7.68
Covariance contribution	-0.48
Combinations/Pair	1.21
Mean z-score	-2.72
Structure conservation index	0.39
SVM decision value	3.09
SVM RNA-class probability	0.998409
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8092219 95 - 22407834
AAACAAAAGAGAAAUAAGGAGGAGUACAU-------GGUACAGUGUACAU----ACAUAUGU----ACAUAUGU----AUGUGACAAGACCUAUGGAAUAUUCUCAGACUUGGG
..................(((((...(((-------(((....(((((((----((((((..----..))))))----)))).)))..))).))).....)))))......... ( -23.90)
>DroSec_CAF1 48376 96 - 1
AAACAAAAGAGAAAUAAGGAGGAGUACAU-------GGUACAGUGUACAU----AUGUAUGUA-GCAAACAUAU----AUGUGACAAGACCUAUGGAAUAUUCUCAGGCUUG--
..................(((((...(((-------(((....(((.(((----((((((((.-....))))))----))))))))..))).))).....))))).......-- ( -24.50)
>DroSim_CAF1 49592 86 - 1
AAACAAAAGAGAAAUAAGGAGGAGUACAU-------GGUACAGUGUACAUACAUAUGUAUGUAUGUACACAUAU----AUGUGACAAGACCUAUGGA-----------------
................(((.....(((((-------(.....((((((((((((....))))))))))))...)----)))))......))).....----------------- ( -22.50)
>DroEre_CAF1 48800 89 - 1
AAACAAAAGAGA-AAAAGGUGGAGUACGU-------AGUACAGUGUACAU----AC------------ACAUAUACGUAUGUGACAAGACCUA-GGAAUAUUCUCAAGCUUGGG
........((((-(....((.(.((((((-------(.....((((....----))------------))...))))))).).))....(...-.)....)))))......... ( -16.50)
>DroYak_CAF1 49539 94 - 1
AAACAAAAGAGACAAAAGGAGGAGUACAUGGUACAUGGUACAGUGUACAU----AC------------ACAUAU----AUGUGACAAGACCUAUGGAAUGUGUUCAAGCUUGGG
........((((((.....(((.((((((.((((...)))).))))))..----.(------------(((...----.))))......)))......))).)))......... ( -18.40)
>consensus
AAACAAAAGAGAAAUAAGGAGGAGUACAU_______GGUACAGUGUACAU____AC_UAUGU____A_ACAUAU____AUGUGACAAGACCUAUGGAAUAUUCUCAAGCUUGGG
................(((....((((((.............)))))).....................(((((....)))))......)))...................... ( -8.16 =  -7.68 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:16 2006