Locus 6372

Sequence ID	3L_DroMel_CAF1
Location	17,060,002 – 17,060,098
Length	96
Max. P	0.990546

overview

Window 8

Location	17,060,002 – 17,060,098
Length	96
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	75.73
Mean single sequence MFE	-24.07
Consensus MFE	-14.77
Energy contribution	-15.27
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.55
Structure conservation index	0.61
SVM decision value	2.22
SVM RNA-class probability	0.990546
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17060002 96 + 23771897
--UCUCCUGCC-UGACUGCCUGCUUAUGGGCCAUUGAUUAAGCUUAAUCAAUGCGCUUAAGGCAACUC-------GCAACUCCUGUGCACUGUAAUUAAAAUGCAG
--....((((.-....(((((.....((((((((((((((....))))))))).))))))))))....-------(((.(....))))..............)))) ( -25.80)
>DroVir_CAF1 13513 76 + 1
--UGUU-------------CUGCUUAUG-GCCAUUGAUUAAGUUUAAUCAAUGGGCUAAAGGCA--------------ACUUCUGUGCAUUGUAAUUAAAGUGCAG
--....-------------.(((((.((-(((((((((((....)))))))).))))).)))))--------------.......((((((........)))))). ( -25.40)
>DroPse_CAF1 18398 106 + 1
CGUGUCCUGCCAUUUCUGCCUGCUUAUGGGCCAUUGAUUAAGUUUAAUCAAUGCGCUUACGGCAACUCUUGCAACGCAACUCCUGUGCACAGUAAUUAAAAUGCAG
......((((.((((.(((.(((...((((((((((((((....))))))))).))))).(....)....)))..)))....(((....)))......)))))))) ( -25.00)
>DroGri_CAF1 18064 76 + 1
--GAUC-------------AUGCUUAUG-GCCAUUGAUUAAAUUUAAUCAAUGGGCUUAAGGCA--------------ACUCCUGUGCAUUGUAAUUAAAGUGCAG
--....-------------.(((((..(-.((((((((((....)))))))))).)...)))))--------------.......((((((........)))))). ( -24.40)
>DroMoj_CAF1 19683 80 + 1
--UGUU---------CGCGCUGCUUAUG-GCCAUUGAUUAAGUUUAAUCAAUGAGCUUAAGGCA--------------ACUUCUGUGCAUUGUAAUUAAAGUGCAG
--....---------.(((((.((((.(-(((((((((((....))))))))).)))))))(((--------------.(....))))...........))))).. ( -23.50)
>DroAna_CAF1 18323 96 + 1
--CCUCUUGCC-UGACUGCCUGCUUAUGGGCCAUUGAUUAAACUUAAUCAAUACGCUUAAGGCAACUC-------UCAACUCCUGUGCACUGUAAUUAAAAUGCAG
--....(((((-(....((((......)))).((((((((....)))))))).......))))))...-------..............(((((.......))))) ( -20.30)
>consensus
__UGUC_________CUGCCUGCUUAUG_GCCAUUGAUUAAGUUUAAUCAAUGCGCUUAAGGCA______________ACUCCUGUGCACUGUAAUUAAAAUGCAG
....................(((((....(((((((((((....))))))))).))...))))).....................((((.(........).)))). (-14.77 = -15.27 +   0.50)

alignment

secondary structure

dotplot

Window 9

Location	17,060,002 – 17,060,098
Length	96
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	75.73
Mean single sequence MFE	-21.62
Consensus MFE	-13.97
Energy contribution	-14.00
Covariance contribution	0.03
Combinations/Pair	1.06
Mean z-score	-1.80
Structure conservation index	0.65
SVM decision value	1.29
SVM RNA-class probability	0.938204
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17060002 96 - 23771897
CUGCAUUUUAAUUACAGUGCACAGGAGUUGC-------GAGUUGCCUUAAGCGCAUUGAUUAAGCUUAAUCAAUGGCCCAUAAGCAGGCAGUCA-GGCAGGAGA--
((((..............(((.......)))-------((.((((((......(((((((((....)))))))))((......)))))))))).-.))))....-- ( -25.10)
>DroVir_CAF1 13513 76 - 1
CUGCACUUUAAUUACAAUGCACAGAAGU--------------UGCCUUUAGCCCAUUGAUUAAACUUAAUCAAUGGC-CAUAAGCAG-------------AACA--
((((..............(((.......--------------))).....(.((((((((((....)))))))))).-)....))))-------------....-- ( -18.00)
>DroPse_CAF1 18398 106 - 1
CUGCAUUUUAAUUACUGUGCACAGGAGUUGCGUUGCAAGAGUUGCCGUAAGCGCAUUGAUUAAACUUAAUCAAUGGCCCAUAAGCAGGCAGAAAUGGCAGGACACG
.((((...(((((.(((....))).)))))...))))....(((((((.....(((((((((....)))))))))(((........)))....)))))))...... ( -29.10)
>DroGri_CAF1 18064 76 - 1
CUGCACUUUAAUUACAAUGCACAGGAGU--------------UGCCUUAAGCCCAUUGAUUAAAUUUAAUCAAUGGC-CAUAAGCAU-------------GAUC--
................((((..(((...--------------..)))...(.((((((((((....)))))))))).-)....))))-------------....-- ( -16.80)
>DroMoj_CAF1 19683 80 - 1
CUGCACUUUAAUUACAAUGCACAGAAGU--------------UGCCUUAAGCUCAUUGAUUAAACUUAAUCAAUGGC-CAUAAGCAGCGCG---------AACA--
.((((............)))).....((--------------(((.(((.((.(((((((((....)))))))))))-..))))))))...---------....-- ( -18.70)
>DroAna_CAF1 18323 96 - 1
CUGCAUUUUAAUUACAGUGCACAGGAGUUGA-------GAGUUGCCUUAAGCGUAUUGAUUAAGUUUAAUCAAUGGCCCAUAAGCAGGCAGUCA-GGCAAGAGG--
.((((((........))))))..........-------...((((((...((.(((((((((....)))))))))(((........))).)).)-)))))....-- ( -22.00)
>consensus
CUGCACUUUAAUUACAAUGCACAGGAGU______________UGCCUUAAGCGCAUUGAUUAAACUUAAUCAAUGGC_CAUAAGCAGGCAG_________GACA__
((((..............(((.....................))).....((.(((((((((....)))))))))))......))))................... (-13.97 = -14.00 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:48 2006