Locus 5305

Sequence ID	X_DroMel_CAF1
Location	13,871,950 – 13,872,084
Length	134
Max. P	0.966666

overview

Window 3

Location	13,871,950 – 13,872,044
Length	94
Sequences	3
Columns	98
Reading direction	forward
Mean pairwise identity	86.90
Mean single sequence MFE	-33.13
Consensus MFE	-26.37
Energy contribution	-26.37
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.56
Structure conservation index	0.80
SVM decision value	1.60
SVM RNA-class probability	0.966666
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13871950 94 + 22224390
AAAAUGCCAAACUCGCAUUGUUGUUGC---UGCAGUUGUUGUUUCGUGUUGCGUUCG-GCAGCGAGACAAACAAAAGCAACAACAACGUCACCAACGG
..(((((.......)))))((((((((---(....((((((((((((..(((.....-)))))))))).))))).)))))))))..(((.....))). ( -32.60)
>DroSec_CAF1 17371 95 + 1
NNNNNNNNNNNNNNGCAUUGUUGUUGC---UGCAGUUGUUGUUUCGUGUUGCGUUCGCGCAGCGAGACAAACAAAAGCAACAACAACGUCACCAACGG
.................((((((((((---(....((((((((((((..((((....))))))))))).))))).)))))))))))(((.....))). ( -34.20)
>DroEre_CAF1 15154 97 + 1
AAAAUGCCAAACUCGCAUUGUUGUUGCUGCUGCUGUUGUUGUUUCGUGUUGCGUUCG-GCAGCGAGACAAACAAAAGCAACAACAACGUCACCAACGG
..(((((.......)))))(((((((.((((..((((..((((((((..(((.....-)))))))))))))))..)))).)))))))........... ( -32.60)
>consensus
AAAAUGCCAAACUCGCAUUGUUGUUGC___UGCAGUUGUUGUUUCGUGUUGCGUUCG_GCAGCGAGACAAACAAAAGCAACAACAACGUCACCAACGG
.................((((((((((........((((((((((((..(((......)))))))))).)))))..))))))))))(((.....))). (-26.37 = -26.37 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	13,871,950 – 13,872,044
Length	94
Sequences	3
Columns	98
Reading direction	reverse
Mean pairwise identity	86.90
Mean single sequence MFE	-32.50
Consensus MFE	-23.80
Energy contribution	-23.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.39
Structure conservation index	0.73
SVM decision value	1.27
SVM RNA-class probability	0.938757
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13871950 94 - 22224390
CCGUUGGUGACGUUGUUGUUGCUUUUGUUUGUCUCGCUGC-CGAACGCAACACGAAACAACAACUGCA---GCAACAACAAUGCGAGUUUGGCAUUUU
.....(....)(((((((((((..(((((.((.(((.(((-.....)))...))).)))))))..)))---))))))))(((((.......))))).. ( -31.80)
>DroSec_CAF1 17371 95 - 1
CCGUUGGUGACGUUGUUGUUGCUUUUGUUUGUCUCGCUGCGCGAACGCAACACGAAACAACAACUGCA---GCAACAACAAUGCNNNNNNNNNNNNNN
.(((((....)(((((((((((..(((((.((.(((.((((....))))...))).)))))))..)))---))))))))))))............... ( -31.60)
>DroEre_CAF1 15154 97 - 1
CCGUUGGUGACGUUGUUGUUGCUUUUGUUUGUCUCGCUGC-CGAACGCAACACGAAACAACAACAGCAGCAGCAACAACAAUGCGAGUUUGGCAUUUU
..((((....)((((((((((((.(((((.((.(((.(((-.....)))...))).))))))).)))))))))))))))(((((.......))))).. ( -34.10)
>consensus
CCGUUGGUGACGUUGUUGUUGCUUUUGUUUGUCUCGCUGC_CGAACGCAACACGAAACAACAACUGCA___GCAACAACAAUGCGAGUUUGGCAUUUU
.(((((....)(((((((((((..(((((.((.(((.(((......)))...))).)))))))..)))...))))))))))))............... (-23.80 = -23.80 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	13,871,977 – 13,872,084
Length	107
Sequences	3
Columns	108
Reading direction	forward
Mean pairwise identity	97.52
Mean single sequence MFE	-29.34
Consensus MFE	-27.00
Energy contribution	-27.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.84
Structure conservation index	0.92
SVM decision value	0.27
SVM RNA-class probability	0.661063
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13871977 107 + 22224390
UGCAGUUGUUGUUUCGUGUUGCGUUCG-GCAGCGAGACAAACAAAAGCAACAACAACGUCACCAACGGAGCAAAAAUCGCCCCUUUUAGCAAAAAACGCAGGAAAGGA
(((.((((((((((..((((...((((-....))))...)))).))))))))))..(((.....)))..))).........((((((.((.......))..)))))). ( -29.00)
>DroSec_CAF1 17398 108 + 1
UGCAGUUGUUGUUUCGUGUUGCGUUCGCGCAGCGAGACAAACAAAAGCAACAACAACGUCACCAACGGAGCAAAAAUCGCCCCUUUUGGCAAAAAACGCAGCAAAGGA
(((.((((((((((..((((...(((((...)))))...)))).))))))))))..(((.....)))..))).........(((((..((.......))...))))). ( -30.10)
>DroEre_CAF1 15184 107 + 1
UGCUGUUGUUGUUUCGUGUUGCGUUCG-GCAGCGAGACAAACAAAAGCAACAACAACGUCACCAACGGAGCAAAAAUCGCCCCUUUUGGCAAAAAACGCAGCAAAGGA
((((((..((((((((((((((.....-)))))..(((...................)))....))))))))).....(((......))).......))))))..... ( -28.91)
>consensus
UGCAGUUGUUGUUUCGUGUUGCGUUCG_GCAGCGAGACAAACAAAAGCAACAACAACGUCACCAACGGAGCAAAAAUCGCCCCUUUUGGCAAAAAACGCAGCAAAGGA
(((.((((((((((..((((...((((.....))))...)))).))))))))))..(((.....)))..))).........(((((..((.......))...))))). (-27.00 = -27.00 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	13,871,977 – 13,872,084
Length	107
Sequences	3
Columns	108
Reading direction	reverse
Mean pairwise identity	97.52
Mean single sequence MFE	-34.30
Consensus MFE	-32.65
Energy contribution	-32.43
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.18
Structure conservation index	0.95
SVM decision value	1.01
SVM RNA-class probability	0.898881
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13871977 107 - 22224390
UCCUUUCCUGCGUUUUUUGCUAAAAGGGGCGAUUUUUGCUCCGUUGGUGACGUUGUUGUUGCUUUUGUUUGUCUCGCUGC-CGAACGCAACACGAAACAACAACUGCA
................(..((((..(((((((...))))))).))))..).((.(((((((.((((((((((.(((....-)))..)))).))))))))))))).)). ( -30.10)
>DroSec_CAF1 17398 108 - 1
UCCUUUGCUGCGUUUUUUGCCAAAAGGGGCGAUUUUUGCUCCGUUGGUGACGUUGUUGUUGCUUUUGUUUGUCUCGCUGCGCGAACGCAACACGAAACAACAACUGCA
.....(((.(((((....(((((..(((((((...))))))).)))))))))).(((((((.((((((((((.((((...))))..)))).))))))))))))).))) ( -36.60)
>DroEre_CAF1 15184 107 - 1
UCCUUUGCUGCGUUUUUUGCCAAAAGGGGCGAUUUUUGCUCCGUUGGUGACGUUGUUGUUGCUUUUGUUUGUCUCGCUGC-CGAACGCAACACGAAACAACAACAGCA
................(..((((..(((((((...))))))).))))..).((((((((((.((((((((((.(((....-)))..)))).)))))))))))))))). ( -36.20)
>consensus
UCCUUUGCUGCGUUUUUUGCCAAAAGGGGCGAUUUUUGCUCCGUUGGUGACGUUGUUGUUGCUUUUGUUUGUCUCGCUGC_CGAACGCAACACGAAACAACAACUGCA
.........((.....(..((((..(((((((...))))))).))))..)....(((((((.((((((((((.(((.....)))..)))).))))))))))))).)). (-32.65 = -32.43 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:26 2006