Locus 522

Sequence ID	X_DroMel_CAF1
Location	1,512,260 – 1,512,491
Length	231
Max. P	0.832077

overview

Window 6

Location	1,512,260 – 1,512,373
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.99
Mean single sequence MFE	-17.02
Consensus MFE	-15.68
Energy contribution	-16.18
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.92
SVM decision value	0.58
SVM RNA-class probability	0.788569
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1512260 113 + 22224390
CUCUCUACUGAGGCCAGCCGUCCCUAUUCGGCUGAAUCUGCAUCUGUCUGUACAAGCAUUUCUUCUUCCUCUGUAUCUAU-------CCUUUAUCUCCUUGCCAAACACACUAACGAUCC
.....(((.((((.((((((........))))))....(((...(((....))).))).........)))).))).....-------................................. ( -18.60)
>DroSec_CAF1 1766 113 + 1
CUCUCUACUGAGGCCAGCCGUCCCUACUCGGCUGAAUCUGCAUCUGUCUGUACAAGCAUUUCUUCUUCCUCUGUAUCUAU-------CCUUUAUCUCCUUGCCAAACACACUAACGAUCC
.....(((.((((.((((((........))))))....(((...(((....))).))).........)))).))).....-------................................. ( -18.60)
>DroEre_CAF1 1761 113 + 1
CUCUCUACUGAGCCCAGCCGUCUCUACUCGGCUGUAUCUGCAUCUGUCUGUACAAGCAUUUCUUCUUCCUCUGUACCUAU-------CCUUUAUCUCCUUGCCAAUCACACUAACGAUCC
.....(((.(((..((((((........))))))....(((...(((....))).)))..........))).))).....-------................................. ( -14.90)
>DroYak_CAF1 3258 120 + 1
CUCUCUACUGAGCCCAGCCGUUUCUACUCGGCUGUAUCUGCAUCUGUCUGUACAAGCAUUUCUUCUUCCUCUGUAUCUAUAUCUGUACCUUUAUCUCCCUGCCAAUCACACUAACGAUCC
........((.((.((((((........))))))....((((..(((..(((((((.(........).)).)))))..)))..)))).............))))................ ( -16.00)
>consensus
CUCUCUACUGAGCCCAGCCGUCCCUACUCGGCUGAAUCUGCAUCUGUCUGUACAAGCAUUUCUUCUUCCUCUGUAUCUAU_______CCUUUAUCUCCUUGCCAAACACACUAACGAUCC
.....(((.((((.((((((........))))))....(((...(((....))).))).........)))).)))............................................. (-15.68 = -16.18 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	1,512,300 – 1,512,413
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.99
Mean single sequence MFE	-23.80
Consensus MFE	-22.56
Energy contribution	-23.38
Covariance contribution	0.81
Combinations/Pair	1.04
Mean z-score	-1.31
Structure conservation index	0.95
SVM decision value	-0.01
SVM RNA-class probability	0.528013
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1512300 113 - 22224390
AGAUUAGAGCGUUUCGCGAAGAAGGCGAAGCACGCUUAAUGGAUCGUUAGUGUGUUUGGCAAGGAGAUAAAGG-------AUAGAUACAGAGGAAGAAGAAAUGCUUGUACAGACAGAUG
......(((((((((.........((.(((((((((.((((...))))))))))))).))...........(.-------.......)..........)))))))))............. ( -26.20)
>DroSec_CAF1 1806 113 - 1
AGAUUAGAGCGUUUCGCGAAGAAGGCGAAGCACGCUUAAUGGAUCGUUAGUGUGUUUGGCAAGGAGAUAAAGG-------AUAGAUACAGAGGAAGAAGAAAUGCUUGUACAGACAGAUG
......(((((((((.........((.(((((((((.((((...))))))))))))).))...........(.-------.......)..........)))))))))............. ( -26.20)
>DroEre_CAF1 1801 113 - 1
AGAUUAGAGCGUAUCGCGAAGAAGGCGAAGCACGCUUAAUGGAUCGUUAGUGUGAUUGGCAAGGAGAUAAAGG-------AUAGGUACAGAGGAAGAAGAAAUGCUUGUACAGACAGAUG
.((((.((((((.((((.......))))...))))))....))))((((((...)))))).............-------....(((((.((.(........).)))))))......... ( -20.50)
>DroYak_CAF1 3298 120 - 1
AGAUUAGAGCGUGUCGCGAAGAAGGCGAAGCACGCUGGAUGGAUCGUUAGUGUGAUUGGCAGGGAGAUAAAGGUACAGAUAUAGAUACAGAGGAAGAAGAAAUGCUUGUACAGACAGAUG
.((((..((((((((((.......)))..))))))).....))))(((..((((...((((...........((((.......).)))..............))))..)))))))..... ( -22.31)
>consensus
AGAUUAGAGCGUUUCGCGAAGAAGGCGAAGCACGCUUAAUGGAUCGUUAGUGUGAUUGGCAAGGAGAUAAAGG_______AUAGAUACAGAGGAAGAAGAAAUGCUUGUACAGACAGAUG
......(((((((((.(......)((.(((((((((.((((...))))))))))))).))......................................)))))))))............. (-22.56 = -23.38 +   0.81)

alignment

secondary structure

dotplot

Window 8

Location	1,512,373 – 1,512,491
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.72
Mean single sequence MFE	-29.23
Consensus MFE	-26.35
Energy contribution	-26.60
Covariance contribution	0.25
Combinations/Pair	1.12
Mean z-score	-1.69
Structure conservation index	0.90
SVM decision value	0.72
SVM RNA-class probability	0.832077
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1512373 118 + 22224390
AUUAAGCGUGCUUCGCCUUCUUCGCGAAACGCUCUAAUCUGUACAAAUUGUUUCUAGAUGAAAACAAUUAACCCGACCAACCACUGCGCAACAUC--AGUCAGUAUAUGGUCAGCUUGGC
.(((((((((.(((((.......))))).))).............(((((((((.....).)))))))).....(((((...((((.((......--.))))))...))))).)))))). ( -28.80)
>DroSec_CAF1 1879 118 + 1
AUUAAGCGUGCUUCGCCUUCUUCGCGAAACGCUCUAAUCUGUACACAUUGUUUCUAUACAAGAACAAUUAACCCGACCAACCACUGCGCAAAAUC--AGUCAGUAUAUGGUCAGCUUGGC
.(((((((((.(((((.......))))).)))..............(((((((........)))))))......(((((...((((.((......--.))))))...))))).)))))). ( -27.30)
>DroEre_CAF1 1874 118 + 1
AUUAAGCGUGCUUCGCCUUCUUCGCGAUACGCUCUAAUCUGUACAAAUUGUUUCUAGAUGAAAACAAUUAACCCGACCAGCCACUGUGCAAAAUC--AGUCAGUGUAUGGUUAGCUUGGC
.(((((((((..((((.......))))..))).............(((((((((.....).)))))))).....(((((..(((((.((......--.)))))))..))))).)))))). ( -30.40)
>DroYak_CAF1 3378 120 + 1
AUCCAGCGUGCUUCGCCUUCUUCGCGACACGCUCUAAUCUGUACAAAUUGUUUCUAGAUGAAAACAAUUAACCCGGCCAGCCACUGUGCAAAAUCACAGUCAGUAUAUGGUCAGCUUGGC
....((((((..((((.......))))))))))((((.((.....(((((((((.....).)))))))).....(((((((.((((((......))))))..))...))))))).)))). ( -30.40)
>consensus
AUUAAGCGUGCUUCGCCUUCUUCGCGAAACGCUCUAAUCUGUACAAAUUGUUUCUAGAUGAAAACAAUUAACCCGACCAACCACUGCGCAAAAUC__AGUCAGUAUAUGGUCAGCUUGGC
.(((((((((.(((((.......))))).))).............((((((((........)))))))).....(((((...((((.((.........))))))...))))).)))))). (-26.35 = -26.60 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:46 2006