Locus 420

Sequence ID	2L_DroMel_CAF1
Location	1,238,425 – 1,238,581
Length	156
Max. P	0.835609

overview

Window 0

Location	1,238,425 – 1,238,543
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.96
Mean single sequence MFE	-40.20
Consensus MFE	-36.59
Energy contribution	-37.15
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.53
Structure conservation index	0.91
SVM decision value	0.20
SVM RNA-class probability	0.632417
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1238425 118 + 22407834
UGCAUCUGGUCAAAGUUUGCGUGCUGCAAGAGUGUUGCACGCCUCUCGAGGCAAUCAGGCAUGGAUCC--GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUCCUUGGCCU
.......((((((.(((((.((((.(((....))).))))((((....))))...)))))..(((((.--...))))).(((((....)))))....................)))))). ( -38.10)
>DroSec_CAF1 15899 118 + 1
UGCAUCUGGCCAAAGUUUGCGUGCUGCAAGAGUGUUGCACGCCUUUCGAGACAAUCAGGCAGGGAUCC--GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCU
.......((((((.((((((((((.(((....))).)))))).....((.....)))))).((((((.--...))))))(((((....)))))....................)))))). ( -38.20)
>DroSim_CAF1 12062 118 + 1
UGCAUCUGGCCAAAGUUUGCGUGCUGCAAGAGUGUUGCACGCCUCUCGAGGCAAUCAGGCAGGGAUCC--GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCU
.......((((((.(((((.((((.(((....))).))))((((....))))...))))).((((((.--...))))))(((((....)))))....................)))))). ( -42.20)
>DroYak_CAF1 11944 120 + 1
UGCAUCUGGCCAAAGUUUGCGUGCUGCAGGAGUGUUGCACGCCUCUCGAGGCAAUCAGGCUGGGAUCCUGGAAGGUCCUACCGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCU
.......((((((.(....)(((.((.(((((((..((..((((....)))).....((.(((((((......)))))))))))...))))))))))))..............)))))). ( -42.30)
>consensus
UGCAUCUGGCCAAAGUUUGCGUGCUGCAAGAGUGUUGCACGCCUCUCGAGGCAAUCAGGCAGGGAUCC__GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCU
.......((((((.....((((((.(((....))).)))))).....((((......((((((((((......))))).....)))))...))))..................)))))). (-36.59 = -37.15 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	1,238,425 – 1,238,543
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.96
Mean single sequence MFE	-38.77
Consensus MFE	-34.94
Energy contribution	-35.50
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.44
Structure conservation index	0.90
SVM decision value	-0.02
SVM RNA-class probability	0.523492
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1238425 118 - 22407834
AGGCCAAGGAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC--GGAUCCAUGCCUGAUUGCCUCGAGAGGCGUGCAACACUCUUGCAGCACGCAAACUUUGACCAGAUGCA
.((.(((((..................(((((....))))).(((.(...--.).))).(((......((((....))))((((..((....))..)))))))..))))).))....... ( -36.50)
>DroSec_CAF1 15899 118 - 1
AGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC--GGAUCCCUGCCUGAUUGUCUCGAAAGGCGUGCAACACUCUUGCAGCACGCAAACUUUGGCCAGAUGCA
.(((((((((((((((...........(((((....))))).(((.(...--.).))).....))))))).)).....((((((..((....))..)))))).....))))))....... ( -39.80)
>DroSim_CAF1 12062 118 - 1
AGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC--GGAUCCCUGCCUGAUUGCCUCGAGAGGCGUGCAACACUCUUGCAGCACGCAAACUUUGGCCAGAUGCA
.(((((((................(((((..((((((.....(((.(...--.).)))))))).)....)))))....((((((..((....))..))))))....)))))))....... ( -40.40)
>DroYak_CAF1 11944 120 - 1
AGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCGGUAGGACCUUCCAGGAUCCCAGCCUGAUUGCCUCGAGAGGCGUGCAACACUCCUGCAGCACGCAAACUUUGGCCAGAUGCA
.(((((((................(((((.((....))(((.(((((.....)).)))..)))......)))))....((((((..((....))..))))))....)))))))....... ( -38.40)
>consensus
AGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC__GGAUCCCUGCCUGAUUGCCUCGAGAGGCGUGCAACACUCUUGCAGCACGCAAACUUUGGCCAGAUGCA
.(((((((................(((((..((((((.....(((((.....)).)))))))).)....)))))....((((((..((....))..))))))....)))))))....... (-34.94 = -35.50 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	1,238,465 – 1,238,581
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.98
Mean single sequence MFE	-42.30
Consensus MFE	-27.85
Energy contribution	-29.60
Covariance contribution	1.75
Combinations/Pair	1.00
Mean z-score	-2.56
Structure conservation index	0.66
SVM decision value	0.73
SVM RNA-class probability	0.835609
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1238465 116 + 22407834
GCCUCUCGAGGCAAUCAGGCAUGGAUCC--GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUCCUUGGCCUGGCCAAGGGCUCCUGUUCCUCCUUCGACCUCGCC--UGGC
((((....))))..((((((..((...(--(((((....(((((....))))).................((((((((...))))))))...........)))))).))..)))--))). ( -45.20)
>DroSec_CAF1 15939 113 + 1
GCCUUUCGAGACAAUCAGGCAGGGAUCC--GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCUGGCCAAGGCCUGU---UCCUCCUUCGACCUCGCC--UGGC
..............((((((..((...(--(((((....(((((....)))))......................(((((.....)))))...---....)))))).))..)))--))). ( -38.90)
>DroSim_CAF1 12102 113 + 1
GCCUCUCGAGGCAAUCAGGCAGGGAUCC--GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCUGGCCAAGGGCUCC---UGUUCCUUCGACCUCGCC--UGGC
((((....))))..((((((..((...(--(((((..(.((((((..............(((......))).((((((...))))))))))))---.)..)))))).))..)))--))). ( -46.70)
>DroYak_CAF1 11984 111 + 1
GCCUCUCGAGGCAAUCAGGCUGGGAUCCUGGAAGGUCCUACCGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCUGGG------CGGC---UGCUCCUUCGACCUCGUCCUCGGC
(((...((((((.....((.(((((((......)))))))))((.(((((((.(((...(((......)))...)))...)))------))))---.))......).))))).....))) ( -38.40)
>consensus
GCCUCUCGAGGCAAUCAGGCAGGGAUCC__GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCUGGCCAAGGGCUCC___UCCUCCUUCGACCUCGCC__UGGC
(((...((((((...(((((.((((((......))))))(((((....))))).......................)))))((.....))...............).))))).....))) (-27.85 = -29.60 +   1.75)

alignment

secondary structure

dotplot

Window 3

Location	1,238,465 – 1,238,581
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.98
Mean single sequence MFE	-42.40
Consensus MFE	-31.67
Energy contribution	-31.80
Covariance contribution	0.13
Combinations/Pair	1.08
Mean z-score	-1.56
Structure conservation index	0.75
SVM decision value	0.19
SVM RNA-class probability	0.624883
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1238465 116 - 22407834
GCCA--GGCGAGGUCGAAGGAGGAACAGGAGCCCUUGGCCAGGCCAAGGAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC--GGAUCCAUGCCUGAUUGCCUCGAGAGGC
..((--((((.(((((((((............(((((((...)))))))..................(((((....)))))....)))))--))..)).))))))...((((....)))) ( -47.10)
>DroSec_CAF1 15939 113 - 1
GCCA--GGCGAGGUCGAAGGAGGA---ACAGGCCUUGGCCAGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC--GGAUCCCUGCCUGAUUGUCUCGAAAGGC
..((--((((.(((((((((....---...(((((.....)))))......................(((((....)))))....)))))--))..)).))))))......((....)). ( -41.60)
>DroSim_CAF1 12102 113 - 1
GCCA--GGCGAGGUCGAAGGAACA---GGAGCCCUUGGCCAGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC--GGAUCCCUGCCUGAUUGCCUCGAGAGGC
..((--((((.(((((((((..(.---......((((((...))))))...................(((((....))))).)..)))))--))..)).))))))...((((....)))) ( -44.60)
>DroYak_CAF1 11984 111 - 1
GCCGAGGACGAGGUCGAAGGAGCA---GCCG------CCCAGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCGGUAGGACCUUCCAGGAUCCCAGCCUGAUUGCCUCGAGAGGC
(((.....((((((.(((((..(.---((((------(....(((.....(..(((((....)))))..)..))).))))).)..)))))((((.......))))...))))))...))) ( -36.30)
>consensus
GCCA__GGCGAGGUCGAAGGAGCA___GCAGCCCUUGGCCAGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC__GGAUCCCUGCCUGAUUGCCUCGAGAGGC
(((.....(((((((....))..................(((((.......................(((((....))))).(((((.....)).)))..)))))....)))))...))) (-31.67 = -31.80 +   0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:47 2006