Locus 5686

Sequence ID	X_DroMel_CAF1
Location	14,704,989 – 14,705,116
Length	127
Max. P	0.985323

overview

Window 3

Location	14,704,989 – 14,705,079
Length	90
Sequences	4
Columns	97
Reading direction	reverse
Mean pairwise identity	87.88
Mean single sequence MFE	-12.78
Consensus MFE	-8.31
Energy contribution	-8.12
Covariance contribution	-0.19
Combinations/Pair	1.06
Mean z-score	-1.91
Structure conservation index	0.65
SVM decision value	0.06
SVM RNA-class probability	0.563445
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14704989 90 - 22224390
AGUCAGCGGUUU--GAAAAUCCGACCUAAAUAAUC-CAUAUAUGC----AUACAUAUAUGUACAUAUUUCUCAAACAUCAUCAAAUUCAACCAAUCC
.......((((.--(.....).)))).........-((((((((.----...))))))))..................................... ( -10.20)
>DroSec_CAF1 23919 90 - 1
AGUCAGCGGUUU--GAAAAUCCGGCCUAAAUAAUC-CAUAUAUGC----AUACAUAUAUGUACAUAUUUUGAAAACAUCAUCAAAUUCAACCAAUCC
.......((((.--(((..................-((((((((.----...)))))))).......(((((........))))))))))))..... ( -13.80)
>DroEre_CAF1 24294 90 - 1
AGUCAGCGGUUU--GAAAAUCCGAGCUAAAUAAUCAUAUAUAUGC----AUACAUAUAUGUGCAUAUUUCUUAAACAUCGUCAAAUUCAA-CAAUCC
.....(((((((--(......))))).(((((..((((((((((.----...))))))))))..))))).........))).........-...... ( -14.20)
>DroYak_CAF1 22087 96 - 1
AGUCAGCGGCUUAUAAAAAUCCGACCUAAAUAAUC-CAUAUAUGCCUAUAUACAUAUAUGUACGUAUUUCUUAAACGACGUCAAAUUCAAUCAAUCC
.(((..(((.((.....)).)))....(((((...-((((((((........))))))))....))))).......))).................. ( -12.90)
>consensus
AGUCAGCGGUUU__GAAAAUCCGACCUAAAUAAUC_CAUAUAUGC____AUACAUAUAUGUACAUAUUUCUUAAACAUCAUCAAAUUCAACCAAUCC
......(((...........)))....(((((....((((((((........))))))))....)))))............................ ( -8.31 =  -8.12 +  -0.19)

alignment

secondary structure

dotplot

Window 4

Location	14,705,024 – 14,705,116
Length	92
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	79.60
Mean single sequence MFE	-30.00
Consensus MFE	-19.06
Energy contribution	-20.98
Covariance contribution	1.92
Combinations/Pair	1.10
Mean z-score	-2.57
Structure conservation index	0.64
SVM decision value	2.00
SVM RNA-class probability	0.985323
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14705024 92 + 22224390
U-------ACAUAUAUGUAU-----GCAUAUAUG-GAUUAU--UUAGGUCGGAUUUUC--AAACCGCUGACUGCGUCUGCGCGGCUGCGUUGCACGUAGUCAACUGAAC
.-------.((((((((...-----.))))))))-.....(--(((((.(((......--...))))((((((((((.((((....)))).).))))))))).))))). ( -31.10)
>DroGri_CAF1 18399 102 + 1
AAAAAAAAACAGCUAUUUAUUUUGAUCGUAUAUC-GAUUAUCGUUAA-UCGGUCU-----GUGCGGAGCACUGCGUCCGUGCGGUUGCGUUGCACGCUUUCAACUGAAC
.........(((.........((((..((..(((-(((((....)))-)))))..-----((((((.((((((((....))))).))).))))))))..)))))))... ( -26.80)
>DroSec_CAF1 23954 92 + 1
U-------ACAUAUAUGUAU-----GCAUAUAUG-GAUUAU--UUAGGCCGGAUUUUC--AAACCGCUGACUGCGUCUGCGCGGCUGCGUUGCACGUAGUCAACUGAAC
.-------.((((((((...-----.))))))))-.....(--((((((.((......--...))))((((((((((.((((....)))).).))))))))).))))). ( -31.10)
>DroEre_CAF1 24328 93 + 1
C-------ACAUAUAUGUAU-----GCAUAUAUAUGAUUAU--UUAGCUCGGAUUUUC--AAACCGCUGACUGCGUCUGCGCGGCUGCGUUGCACGUAGUCAACUGAAC
.-------.(((((((((..-----..)))))))))....(--((((..(((......--...))).((((((((((.((((....)))).).))))))))).))))). ( -28.10)
>DroYak_CAF1 22122 98 + 1
U-------ACAUAUAUGUAUAUAG-GCAUAUAUG-GAUUAU--UUAGGUCGGAUUUUUAUAAGCCGCUGACUGCGUCUGCGCGGCUGCGUUGCACGUAGUCAACUGAAC
.-------.(((((((((......-)))))))))-.....(--(((((.(((.(((....)))))))((((((((((.((((....)))).).))))))))).))))). ( -32.90)
>consensus
U_______ACAUAUAUGUAU_____GCAUAUAUG_GAUUAU__UUAGGUCGGAUUUUC__AAACCGCUGACUGCGUCUGCGCGGCUGCGUUGCACGUAGUCAACUGAAC
.........(((((((((.......))))))))).........((((..(((...........))).((((((((((..(((....)))..).))))))))).)))).. (-19.06 = -20.98 +   1.92)

alignment

secondary structure

dotplot

Window 5

Location	14,705,024 – 14,705,116
Length	92
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	79.60
Mean single sequence MFE	-25.52
Consensus MFE	-13.86
Energy contribution	-15.94
Covariance contribution	2.08
Combinations/Pair	1.05
Mean z-score	-2.03
Structure conservation index	0.54
SVM decision value	0.46
SVM RNA-class probability	0.746638
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14705024 92 - 22224390
GUUCAGUUGACUACGUGCAACGCAGCCGCGCAGACGCAGUCAGCGGUUU--GAAAAUCCGACCUAA--AUAAUC-CAUAUAUGC-----AUACAUAUAUGU-------A
.....(((((((.(((.(..(((....)))..)))).)))))))((((.--(.....).))))...--......-((((((((.-----...)))))))).-------. ( -26.70)
>DroGri_CAF1 18399 102 - 1
GUUCAGUUGAAAGCGUGCAACGCAACCGCACGGACGCAGUGCUCCGCAC-----AGACCGA-UUAACGAUAAUC-GAUAUACGAUCAAAAUAAAUAGCUGUUUUUUUUU
...((((((...(((.(((..((..((....))..))..)))..)))..-----....(((-(((....)))))-)..................))))))......... ( -22.10)
>DroSec_CAF1 23954 92 - 1
GUUCAGUUGACUACGUGCAACGCAGCCGCGCAGACGCAGUCAGCGGUUU--GAAAAUCCGGCCUAA--AUAAUC-CAUAUAUGC-----AUACAUAUAUGU-------A
.....(((((((.(((.(..(((....)))..)))).)))))))(((..--(.....)..)))...--......-((((((((.-----...)))))))).-------. ( -26.50)
>DroEre_CAF1 24328 93 - 1
GUUCAGUUGACUACGUGCAACGCAGCCGCGCAGACGCAGUCAGCGGUUU--GAAAAUCCGAGCUAA--AUAAUCAUAUAUAUGC-----AUACAUAUAUGU-------G
((((.(((((((.(((.(..(((....)))..)))).)))))))((..(--....).))))))...--.....((((((((((.-----...)))))))))-------) ( -29.30)
>DroYak_CAF1 22122 98 - 1
GUUCAGUUGACUACGUGCAACGCAGCCGCGCAGACGCAGUCAGCGGCUUAUAAAAAUCCGACCUAA--AUAAUC-CAUAUAUGC-CUAUAUACAUAUAUGU-------A
.....(((((((.(((.(..(((....)))..)))).)))))))......................--......-((((((((.-.......)))))))).-------. ( -23.00)
>consensus
GUUCAGUUGACUACGUGCAACGCAGCCGCGCAGACGCAGUCAGCGGUUU__GAAAAUCCGACCUAA__AUAAUC_CAUAUAUGC_____AUACAUAUAUGU_______A
.....(((((((.(((.(..(((....)))..)))).)))))))...............................((((((((.........))))))))......... (-13.86 = -15.94 +   2.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:03 2006