Locus 1626

Sequence ID	3L_DroMel_CAF1
Location	4,752,757 – 4,752,904
Length	147
Max. P	0.992359

overview

Window 5

Location	4,752,757 – 4,752,864
Length	107
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.31
Mean single sequence MFE	-32.75
Consensus MFE	-24.23
Energy contribution	-24.47
Covariance contribution	0.25
Combinations/Pair	1.08
Mean z-score	-1.67
Structure conservation index	0.74
SVM decision value	0.32
SVM RNA-class probability	0.688286
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4752757 107 + 23771897
GUGGAAAAAUCCAUC------------AGCA-AAAUAUUUGGCAUAAUAAUAAGAGUGCAUGAUGCAUGCUGUCUAUGGCCACUGGUCAAUGGCCAAUGGCCAAGGGUCUGUUGCAAUUC
(((((....))))).------------.(((-(.......(((.........(((..(((((...)))))..))).((((((.((((.....)))).))))))...)))..))))..... ( -32.70)
>DroSec_CAF1 16133 118 + 1
GUGGAAAAAUCCAUCACUGGGUGGC-UAGCU-AAAUAUUUGGCAUAAUAAUAGGAGUGCAUGAUGCAUGCUGUCUAUGGCCAUUGGUCAAUGGCCAAUGGCCAAGGGUCUGUUGCAAUUC
(..(....((((.....((((..((-..(((-((....)))))............((((.....))))))..))))(((((((((((.....))))))))))).))))...)..)..... ( -42.40)
>DroSim_CAF1 13518 118 + 1
GUGGAAAAAUCCAUCACUGGGUGGC-UAGCA-AAAUAUUUGGCAUAAUAAUAGGAGUGCAUGAUGCAUGCUGUCUAUGGCCACUGGUCAAUGGCCAAUGACCAAGGGUCUGUUGCAAUUC
.(((....(((((....)))))..)-))(((-(....((((((((....(((((...(((((...)))))..)))))(((((........))))).))).)))))......))))..... ( -32.90)
>DroEre_CAF1 5442 106 + 1
GUGGACAAGUCCAUCACUGGGGGAUAUAGAAAAAAUAUUUGGCAUAAUAAUAAGAGUGCAUGAUGCAUGCUGUCUAUGGCCACUG--------------GCCAAGGGUCUGAUGCAAUUC
(((((....))))).......((((((.......)))))).((((.......(((..(((((...)))))..))).(((((...)--------------))))........))))..... ( -23.00)
>consensus
GUGGAAAAAUCCAUCACUGGGUGGC_UAGCA_AAAUAUUUGGCAUAAUAAUAAGAGUGCAUGAUGCAUGCUGUCUAUGGCCACUGGUCAAUGGCCAAUGGCCAAGGGUCUGUUGCAAUUC
(((((....)))))...........................(((........(((..(((((...)))))..)))..((((..((((((........))))))..))))...)))..... (-24.23 = -24.47 +   0.25)

alignment

secondary structure

dotplot

Window 6

Location	4,752,757 – 4,752,864
Length	107
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.31
Mean single sequence MFE	-26.15
Consensus MFE	-23.10
Energy contribution	-24.10
Covariance contribution	1.00
Combinations/Pair	1.08
Mean z-score	-1.37
Structure conservation index	0.88
SVM decision value	0.07
SVM RNA-class probability	0.566676
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4752757 107 - 23771897
GAAUUGCAACAGACCCUUGGCCAUUGGCCAUUGACCAGUGGCCAUAGACAGCAUGCAUCAUGCACUCUUAUUAUUAUGCCAAAUAUUU-UGCU------------GAUGGAUUUUUCCAC
.....((((.......(((((...((((((((....)))))))).(((..(((((...)))))..))).........))))).....)-))).------------..((((....)))). ( -29.10)
>DroSec_CAF1 16133 118 - 1
GAAUUGCAACAGACCCUUGGCCAUUGGCCAUUGACCAAUGGCCAUAGACAGCAUGCAUCAUGCACUCCUAUUAUUAUGCCAAAUAUUU-AGCUA-GCCACCCAGUGAUGGAUUUUUCCAC
.....(((.......((((((((((((.......)))))))))).))...(((((...))))).............))).........-.....-.....(((....))).......... ( -28.40)
>DroSim_CAF1 13518 118 - 1
GAAUUGCAACAGACCCUUGGUCAUUGGCCAUUGACCAGUGGCCAUAGACAGCAUGCAUCAUGCACUCCUAUUAUUAUGCCAAAUAUUU-UGCUA-GCCACCCAGUGAUGGAUUUUUCCAC
.....((((..........(((..((((((((....))))))))..))).(((((...)))))........................)-)))..-.....(((....))).......... ( -28.10)
>DroEre_CAF1 5442 106 - 1
GAAUUGCAUCAGACCCUUGGC--------------CAGUGGCCAUAGACAGCAUGCAUCAUGCACUCUUAUUAUUAUGCCAAAUAUUUUUUCUAUAUCCCCCAGUGAUGGACUUGUCCAC
.................((((--------------(...)))))..(((((((((...))))).....................................(((....)))...))))... ( -19.00)
>consensus
GAAUUGCAACAGACCCUUGGCCAUUGGCCAUUGACCAGUGGCCAUAGACAGCAUGCAUCAUGCACUCCUAUUAUUAUGCCAAAUAUUU_UGCUA_GCCACCCAGUGAUGGAUUUUUCCAC
.....(((.......((((((((((((.......)))))))))).))...(((((...))))).............)))............................((((....)))). (-23.10 = -24.10 +   1.00)

alignment

secondary structure

dotplot

Window 7

Location	4,752,784 – 4,752,904
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.69
Mean single sequence MFE	-35.89
Consensus MFE	-30.20
Energy contribution	-31.41
Covariance contribution	1.21
Combinations/Pair	1.03
Mean z-score	-1.65
Structure conservation index	0.84
SVM decision value	0.65
SVM RNA-class probability	0.810428
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4752784 120 + 23771897
GGCAUAAUAAUAAGAGUGCAUGAUGCAUGCUGUCUAUGGCCACUGGUCAAUGGCCAAUGGCCAAGGGUCUGUUGCAAUUCUCCGAUUACCAAUGAUCCUUCCUCGGAUGGAUUGCUGAUU
(((.........(((..(((((...)))))..))).((((((.((((.....)))).))))))...)))....((((((((((((.................))))).)))))))..... ( -39.43)
>DroSec_CAF1 16171 120 + 1
GGCAUAAUAAUAGGAGUGCAUGAUGCAUGCUGUCUAUGGCCAUUGGUCAAUGGCCAAUGGCCAAGGGUCUGUUGCAAUUCUCCGAUUACCAAUUGUCCUUCCUCGGAUGGAUUGCUGAUU
(((......(((((...(((((...)))))..)))))((((((((((.....))))))))))....)))....((((((((((((.................))))).)))))))..... ( -43.93)
>DroSim_CAF1 13556 120 + 1
GGCAUAAUAAUAGGAGUGCAUGAUGCAUGCUGUCUAUGGCCACUGGUCAAUGGCCAAUGACCAAGGGUCUGUUGCAAUUCUCCGAUUACCAAUGGUCCUUCCUCGGAUGGAUUGCUGAUU
((((.....(((((...(((((...)))))..)))))((((..((((((........))))))..))))))))((((((((((((..(((...)))......))))).)))))))..... ( -38.00)
>DroEre_CAF1 5482 106 + 1
GGCAUAAUAAUAAGAGUGCAUGAUGCAUGCUGUCUAUGGCCACUG--------------GCCAAGGGUCUGAUGCAAUUCUCCGAUUACCAAUGGUCCUGCCUCGGAUGGAUUGCUGAUU
(((.........(((..(((((...)))))..))).(((((...)--------------))))...)))....((((((((((((........((.....))))))).)))))))..... ( -30.80)
>DroYak_CAF1 11881 99 + 1
GGCAUAAUAAUAAGAGUGCAUGAUGCAUGCUGUCUAUGG---------------------CCAAGGGUCUGAUGCAAUUCUCCGAUUACCAAUGGUCCGUCCUCGGAUGGAUUGCUGAUU
(((...(((...((.((((.....)))).))...))).)---------------------))...((((....((((((((((((..((.........))..))))).))))))).)))) ( -27.30)
>consensus
GGCAUAAUAAUAAGAGUGCAUGAUGCAUGCUGUCUAUGGCCACUGGUCAAUGGCCAAUGGCCAAGGGUCUGUUGCAAUUCUCCGAUUACCAAUGGUCCUUCCUCGGAUGGAUUGCUGAUU
(((.........(((..(((((...)))))..))).((((((.((((.....)))).))))))...)))....((((((((((((.................))))).)))))))..... (-30.20 = -31.41 +   1.21)

alignment

secondary structure

dotplot

Window 8

Location	4,752,784 – 4,752,904
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.69
Mean single sequence MFE	-32.82
Consensus MFE	-30.12
Energy contribution	-31.28
Covariance contribution	1.16
Combinations/Pair	1.08
Mean z-score	-2.08
Structure conservation index	0.92
SVM decision value	2.32
SVM RNA-class probability	0.992359
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4752784 120 - 23771897
AAUCAGCAAUCCAUCCGAGGAAGGAUCAUUGGUAAUCGGAGAAUUGCAACAGACCCUUGGCCAUUGGCCAUUGACCAGUGGCCAUAGACAGCAUGCAUCAUGCACUCUUAUUAUUAUGCC
.....(((((((.((....)).))))...(((((((.((((..............((((((((((((.......)))))))))).))...(((((...))))).)))).)))))))))). ( -38.50)
>DroSec_CAF1 16171 120 - 1
AAUCAGCAAUCCAUCCGAGGAAGGACAAUUGGUAAUCGGAGAAUUGCAACAGACCCUUGGCCAUUGGCCAUUGACCAAUGGCCAUAGACAGCAUGCAUCAUGCACUCCUAUUAUUAUGCC
.....(((.(((.((....)).)))....(((((((.((((..............((((((((((((.......)))))))))).))...(((((...))))).)))).)))))))))). ( -39.60)
>DroSim_CAF1 13556 120 - 1
AAUCAGCAAUCCAUCCGAGGAAGGACCAUUGGUAAUCGGAGAAUUGCAACAGACCCUUGGUCAUUGGCCAUUGACCAGUGGCCAUAGACAGCAUGCAUCAUGCACUCCUAUUAUUAUGCC
.....(((.(((.((....)).)))....(((((((.((((...(((....((((...))))..((((((((....))))))))......)))(((.....))))))).)))))))))). ( -38.60)
>DroEre_CAF1 5482 106 - 1
AAUCAGCAAUCCAUCCGAGGCAGGACCAUUGGUAAUCGGAGAAUUGCAUCAGACCCUUGGC--------------CAGUGGCCAUAGACAGCAUGCAUCAUGCACUCUUAUUAUUAUGCC
..................((((((.((((((((....((.((......))...))....))--------------))))))))..(((..(((((...)))))..)))........)))) ( -26.10)
>DroYak_CAF1 11881 99 - 1
AAUCAGCAAUCCAUCCGAGGACGGACCAUUGGUAAUCGGAGAAUUGCAUCAGACCCUUGG---------------------CCAUAGACAGCAUGCAUCAUGCACUCUUAUUAUUAUGCC
.....(((((...(((((..((.((...)).))..)))))..)))))...........((---------------------(...(((..(((((...)))))..))).........))) ( -21.30)
>consensus
AAUCAGCAAUCCAUCCGAGGAAGGACCAUUGGUAAUCGGAGAAUUGCAACAGACCCUUGGCCAUUGGCCAUUGACCAGUGGCCAUAGACAGCAUGCAUCAUGCACUCUUAUUAUUAUGCC
.....(((.(((.((....)).)))....(((((((.((((..............((((((((((((.......)))))))))).))...(((((...))))).)))).)))))))))). (-30.12 = -31.28 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:17 2006