Locus 3647

Sequence ID	X_DroMel_CAF1
Location	9,780,419 – 9,780,544
Length	125
Max. P	0.993230

overview

Window 1

Location	9,780,419 – 9,780,519
Length	100
Sequences	4
Columns	105
Reading direction	reverse
Mean pairwise identity	71.34
Mean single sequence MFE	-26.60
Consensus MFE	-19.65
Energy contribution	-20.02
Covariance contribution	0.38
Combinations/Pair	1.14
Mean z-score	-1.69
Structure conservation index	0.74
SVM decision value	1.79
SVM RNA-class probability	0.977240
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9780419 100 - 22224390
CAGAUGCCAUAUCCUUUGUGGCGAUACUCUAGGGUAUCGAUCGAGCAUAUUGGCACGCCAAGCUGCAAG-GACACAUAAGAUCUUUUGGGAAAUUAAGUAC----
((((.((((((.....))))))((((((....))))))((((..(((..((((....))))..)))..(-....)....)))).)))).............---- ( -27.90)
>DroSec_CAF1 76736 101 - 1
CAGAUGCCAUAUCCUUUGUGGCGAUACUCUAGGGUAUCGAUCGAGUAUAUUGGCAAGCCAA--UGCAAA-AGCACUUAAAACCGUUGGGAGAAUUAGUUUA-AUA
..(((((((((.....))))))((((((....)))))).)))((((..(((((....))))--)((...-.))))))....((....))............-... ( -25.50)
>DroEre_CAF1 75042 96 - 1
CGGAUGCCAUAUCCUUUGUGGCGAUACCACAGGGUAUCGAUCGAGCGUAUC---GAGCCAC--UGCACA-GGCAGUUAAAA--GUCAGGAAAAUA-AAUAAAUAA
.((..((((((.....))))))((((((....))))))..((((.....))---)).))((--(((...-.))))).....--............-......... ( -26.90)
>DroYak_CAF1 67512 93 - 1
CAGAUGCCAUAUCCUUUGUGGCGAUACCACAGGGUAUCGAUCAAGCAUAUUGGCAAGGCAC--UGCAAAAGGUUUUCGAAA--GCUUGGAAAAAG--------AG
.....((((((.....))))))((((((....))))))..((((((...((.(.(((((.(--(.....)))))))).)).--))))))......--------.. ( -26.10)
>consensus
CAGAUGCCAUAUCCUUUGUGGCGAUACCACAGGGUAUCGAUCGAGCAUAUUGGCAAGCCAA__UGCAAA_GGCACUUAAAA__GUUUGGAAAAUU_A_UAA__AA
..(((((((((.....))))))((((((....)))))).)))..(((...(((....)))...)))....................................... (-19.65 = -20.02 +   0.38)

alignment

secondary structure

dotplot

Window 2

Location	9,780,451 – 9,780,544
Length	93
Sequences	4
Columns	93
Reading direction	forward
Mean pairwise identity	87.32
Mean single sequence MFE	-30.30
Consensus MFE	-20.33
Energy contribution	-22.57
Covariance contribution	2.25
Combinations/Pair	1.00
Mean z-score	-1.84
Structure conservation index	0.67
SVM decision value	0.20
SVM RNA-class probability	0.629946
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9780451 93 + 22224390
UUGCAGCUUGGCGUGCCAAUAUGCUCGAUCGAUACCCUAGAGUAUCGCCACAAAGGAUAUGGCAUCUGCAUAUGGGCACGCUGAACAGAGGCA
.(((..((..(((((((.((((((..(((.(((((......)))))((((.........))))))).)))))).)))))))..)...)..))) ( -36.60)
>DroSec_CAF1 76771 91 + 1
UUGCA--UUGGCUUGCCAAUAUACUCGAUCGAUACCCUAGAGUAUCGCCACAAAGGAUAUGGCAUCUGCAUAUGGGCACGCUGAACAGAGGCA
.(((.--(..((.((((.((((.(..(((.(((((......)))))((((.........))))))).).)))).)))).))..)......))) ( -23.00)
>DroEre_CAF1 75075 88 + 1
GUGCA--GUGGCUC---GAUACGCUCGAUCGAUACCCUGUGGUAUCGCCACAAAGGAUAUGGCAUCCGCAUAUGGGAACGCUGAGCAGAGGCA
((((.--(((((((---((.....))))..((((((....)))))))))))...((((.....))))))))........(((.......))). ( -29.70)
>DroYak_CAF1 67539 91 + 1
UUGCA--GUGCCUUGCCAAUAUGCUUGAUCGAUACCCUGUGGUAUCGCCACAAAGGAUAUGGCAUCUGCAUAUGGCCACGCGGAACAGAGGCA
.....--.((((((((((.(((.(((...(((((((....))))))).....))).))))))).(((((..........)))))...)))))) ( -31.90)
>consensus
UUGCA__GUGGCUUGCCAAUAUGCUCGAUCGAUACCCUAGAGUAUCGCCACAAAGGAUAUGGCAUCUGCAUAUGGGCACGCUGAACAGAGGCA
.(((....((((.((((.((((((..(((.(((((......)))))((((.........))))))).)))))).)))).)))).......))) (-20.33 = -22.57 +   2.25)

alignment

secondary structure

dotplot

Window 3

Location	9,780,451 – 9,780,544
Length	93
Sequences	4
Columns	93
Reading direction	reverse
Mean pairwise identity	87.32
Mean single sequence MFE	-35.83
Consensus MFE	-28.73
Energy contribution	-28.98
Covariance contribution	0.25
Combinations/Pair	1.17
Mean z-score	-3.69
Structure conservation index	0.80
SVM decision value	2.38
SVM RNA-class probability	0.993230
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9780451 93 - 22224390
UGCCUCUGUUCAGCGUGCCCAUAUGCAGAUGCCAUAUCCUUUGUGGCGAUACUCUAGGGUAUCGAUCGAGCAUAUUGGCACGCCAAGCUGCAA
(((....(((..(((((((.((((((.(((((((((.....))))))((((((....)))))).)))..)))))).)))))))..))).))). ( -43.60)
>DroSec_CAF1 76771 91 - 1
UGCCUCUGUUCAGCGUGCCCAUAUGCAGAUGCCAUAUCCUUUGUGGCGAUACUCUAGGGUAUCGAUCGAGUAUAUUGGCAAGCCAA--UGCAA
......(((...((.((((.((((((.(((((((((.....))))))((((((....)))))).)))..)))))).)))).))...--.))). ( -33.40)
>DroEre_CAF1 75075 88 - 1
UGCCUCUGCUCAGCGUUCCCAUAUGCGGAUGCCAUAUCCUUUGUGGCGAUACCACAGGGUAUCGAUCGAGCGUAUC---GAGCCAC--UGCAC
(((....((((.(((((((((((...(((((...)))))..)))))(((((((....)))))))...))))))...---))))...--.))). ( -32.20)
>DroYak_CAF1 67539 91 - 1
UGCCUCUGUUCCGCGUGGCCAUAUGCAGAUGCCAUAUCCUUUGUGGCGAUACCACAGGGUAUCGAUCAAGCAUAUUGGCAAGGCAC--UGCAA
......(((...((.(.(((((((((....((((((.....))))))((((((....))))))......))))).)))).).))..--.))). ( -34.10)
>consensus
UGCCUCUGUUCAGCGUGCCCAUAUGCAGAUGCCAUAUCCUUUGUGGCGAUACCACAGGGUAUCGAUCGAGCAUAUUGGCAAGCCAA__UGCAA
......(((...((.((((.((((((.(((((((((.....))))))((((((....)))))).)))..)))))).)))).))......))). (-28.73 = -28.98 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:30 2006